BioGenomics2017 - Global Biodiversity Genomics Conference
February 21-23, 2017
Smithsonian National Museum of Natural History | Washington, D.C.

Program - Single Session


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P
Poster Session and Reception

Room: Salons 2-4, Marriott Hotel

18:30 - 20:00



P.1  Don't Cross the Streams: Population Structure Among Three Adjacent Steelhead Streams? Adams B*, US Fish & Wildlife Service; Holmes J, US Fish & Wildlife Service; Kennedy B, US Fish & Wildlife Service; Hanson K, US Fish & Wildlife Service; Smith C, US Fish & Wildlife Service; Warheit K, Washington Department of Fish and Wildlife

The use of genetic data can play a critical role in defining population components for management decisions. The lower Columbia River, WA is home to three adjacent watersheds; Mill, Abernathy and Germany creeks that together compromise an Intensively Monitored Watershed (IMW). The role of this IMW is to determine whether and how habitat restoration influences salmon and steelhead populations. The United States Fish and Wildlife Service operate a conservation supplementation hatchery on Abernathy Creek. This facility produces an integrated hatchery broodstock using a portion of returning natural-origin steelhead in order to investigate the impact of supplementation on steelhead populations in the context of the IMW study design. The goal of this project was twofold; 1) to determine if natural-origin steelhead produced in the three adjacent watersheds comprise a singular population or if there are independent populations; and 2) to determine how the hatchery-origin steelhead produced at AFTC fit into that population structure. Preliminary work based on 22 microsatellite markers indicated a lack of structure between the streams but was able to differentiate the hatchery-origin (HOR) components of the population. Using next-generation sequencing we generated and analyzed restriction associated DNA sequence data from out-migrating juveniles from each of the three watersheds in the lower Columbia River IMW and representatives of the HOR juveniles. The resulting dataset has allowed us to further assess the population structure between these three geographically adjacent watersheds in order to inform management decisions in this IMW.


P.2  Recent origin and semi-permeable species boundaries in the scleractinian coral Stylophora from the Red Sea. Arrigoni R*, King Abdullah University of Science and Technology; Berumen ML, King Abdullah University of Science and Technology

Reticulate evolution, introgressive hybridisation, and phenotypic plasticity have been documented in scleractinian corals and have challenged our ability to interpret speciation processes. Stylophora is a key model system in coral biology and physiology, but genetic analyses have revealed that cryptic lineages concealed by morphological stasis exist in the Stylophora pistillata species complex. The Red Sea represents a hotspot for Stylophora biodiversity with six morphospecies described, two of which are regionally endemic. We investigated Stylophora species boundaries from the Red Sea and the associated Symbiodinium by sequencing seven DNA loci. Stylophora morphospecies from the Red Sea were not resolved based on mitochondrial phylogenies and showed nuclear allele sharing. Low genetic differentiation, weak isolation, and strong gene flow were found among morphospecies although no signals of genetic recombination were evident among them. Stylophora mamillata harboured Symbiodinium clade C whereas the other two Stylophora morphospecies hosted either Symbiodinium clade A or C. These evolutionary patterns suggest that either gene exchange occurs through reticulate evolution or that multiple ecomorphs of a phenotypically plastic species occur in the Red Sea. The recent origin of the lineage leading to the Red Sea Stylophora may indicate an ongoing speciation driven by environmental changes and incomplete lineage sorting.


P.3  Molecular structure of some populations of Aedes aegypti in Lagos State, Nigeria. Ayorinde AF*, Redeemers University Ede OsunState; Oboh BO, University of Lagos Akoka Lagos; Oduola AO, University of Ilorin Kwara State; Otubanjo OA, University of Laos Akoka Lagos Nigeria

The humid and semi humid savannah areas of tropical Africa are prone to repeated emergence of arbovirus infections transmitted by Aedes aegypti (Diptera: Culicidae). There are recent reports on the emergence of some of these infections in Nigeria. This study was designed to provide information on the genetic structure of the vector in Lagos, Nigeria. Three sites were studied based on previous knowledge of insecticide susceptibility status of the mosquito species. These are Ikorodu (Lagos East), Badagry (Lagos West) and Ebute Metta (Lagos Central). The Mitochondrial DNA-ND4 gene was employed. Seven polymorphic strains (4 in Genbank :KC790371, KC 800689, KC 800690 and KC 800691) were detected; one common to the three populations. The polymorphic sites were at positions 1bp- A/T, 12bp-C/T; 16bp-T/A, 14bp -C/T, 105bp- T/G, 107bp-C/A and 142bp- C/T (Badagry), 17bp- G/T (Ikorodu) and 139bp- A/G, 190bp-A/G, 277bp-A/G and 322bp- C/T (Ebute Metta). Different strains of Ae aegypti, suggest differential activities on these vectors which will assist in Integrated Pest management .


P.4  Identification of differentially expressed genes as targets for functional studies of regeneration in Hydractinia echinata. Schnitzler C, Whitney Laboratory for Marine Bioscience; Barreira S, National Institutes of Health; Jones A*, National Institutes of Health; Bradshaw B, National University of Ireland Galway; Frank U, National University of Ireland Galway; Baxevanis A, National Institutes of Health

Hydractinia echinata is a colonial marine hydrozoan that is commonly found along the coast of the northwestern Atlantic Ocean. Hydractinia possesses multiple traits that make it a valuable model organism for studying key questions in regenerative medicine. It has a remarkable capacity to regenerate any part of its body, made possible by a population of self-renewing migratory stem cells that lie in the interstitial space between epithelial cells, known as interstitial cells (i-cells) that are capable of differentiating into any cell type. When the head of a Hydractinia polyp is cut off, the blastema, a mass of cells capable of growth and regeneration, begins to form at the wound site within 24 hours; by 72 hours post-decapitation, the head regeneration process is complete. Using stem cell markers, our collaborators were able to determine that i-cell proliferation is required for regeneration. In fully-grown, intact animals, i-cell expression is restricted to a band in the lower half of the polyp body column but, once decapitated, these cells migrate to the wound site within 24-48 hours. Currently, we are taking advantage of long reads produced through PacBio sequencing and long-range Dovetail scaffolding to sequence and assemble the genome of Hydractinia echinata. We have also generated a comprehensive reference transcriptome for this species. Using this reference transcriptome, we have started performing RNA-seq experiments to identify specific genes involved in regeneration. These experiments utilized feeding polyps, as they are most common and least specialized type of polyp and, therefore, the most representative. Heads were removed from two groups of 10 polyps from the same colony. The top 25% of tissue from the headless polyps was immediately removed in the first batch (the presumptive blastema sample). After 24 hours, the top 25% of the tissue was removed from the polyp (the blastema sample). Three replicates were generated for each sample type, and Illumina RNA-seq libraries were then prepared and sequenced for 2x125 paired-end Illumina HiSeq 2500 reads. Genes involved in regeneration were identified after performing quality control of the sequencing data, removing unwanted variation and normalization with RUVseq, and performing differential expression (DE) analysis using EdgeR, sSeq, and DESeq2. The results were highly concordant across all DE analyses, and the intersection of the results from all three DE analysis programs was used to identify differentially expressed transcripts during the regeneration process. In total, 2,438 transcripts were found to be differentially expressed, with 1,246 of these up-regulated and 1,192 down-regulated in the blastema samples. We have begun clustering and annotating these transcripts with the goal of identifying specific pathways and genes involved in the process of regeneration in this new model organism.


P.5  Exploring genomic and transcriptomic data for molecular determinates of host specificity in a parasitic nematode system. Bernot JP*, George Washington University; Rosa BA, Washington University in St. Louis; Makedonka M, Washington University in St. Louis; Hawdon JM, George Washington University

Little is known about the molecular mechanisms that regulate host recognition and host specificity in metazoan parasites. While some parasites develop in only a single host species others utilize a broad range of distantly related host species. Hookworms present a novel system for studying the mechanistic determinants of host specificity and host recognition due to the availability of genomic data for a number of closely related species that differ in their degree of host specificity. Using RNA-seq, we quantified gene expression for a variety of life cycle stages from 2 closely related hookworm species: a specialist parasite, Ancylostoma caninum, and a generalist, A. ceylanicum. Based on the prediction that the host recognition receptor is likely to be a chemosensory GPCR, we compared GPCR expression across a range of life stages in these 2 species and targeted GPCRs expressed more highly at the infective stage (iL3) relative to other stages. While hundreds of GPCRs were identified in the genomes of these 2 species, our filtering procedures lead to the identification of approximately 100 GPCRs in each species with expression profiles that match our predictions for a host recognition receptor. Of these candidate host recognition receptors, 19 were homologous in both species. The identification of a relatively small number of GPCRs with expression profiles that match putative host recognition receptors provides a strong foundation for future studies. If confirmed to be host recognition receptors, these GPCRs could be powerful tools for elucidating molecular determinants of host specificity, key developmental pathways in hookworms, and novel prophylactic drug targets for preventing hookworm infection.


P.6  Unraveling the Evolutionary History of Hyperiidea (Crustacea: Amphipoda). Biancani L*, Smithsonian National Museum of Natural History & University of Maryland, College Park; Osborn K, Smithsonian National Museum of Natural History; Cummings M, University of Maryland, College Park

Amphipoda, a highly speciose crustacean order, has traditionally been organized into four groups; Hyperiidea, Gammaridea, Caprellidea, and Ingolfiellidea. Hyperiidea is an abundant and diverse group consisting of about 350 described species. No single common morphological synapomorphy unites the group. Instead, hyperiid amphipods are defined only by an exclusively pelagic existence. Like many midwater animals, hyperiids possess a wide range of adaptations to this unique environment, including a vast array of visual strategies. Understanding these adaptations requires an accurate phylogenetic hypothesis onto which patterns of hyperiid ecology and functional morphology can be mapped. Previous morphological and molecular studies have led to uncertainty in the monophyly of hyperiids and the possibility of convergent evolution of a pelagic lifestyle in multiple amphipod lineages. Here we present preliminary results of a multi-gene phylogenetic analysis of all available amphipod sequences for 3 nuclear (18S, 28S, and H3) and 2 mitochondrial loci (COI and 16S). This is the largest analysis, to date, aimed at addressing the question of hyperiid monoplyly and is being used to inform taxon sampling for an ongoing transcriptome-based phylogenomic study.


P.7  The genome of the tardigrade Hypsibius dujardini and the phylogeny of Ecdysozoa. Blaxter M*, University of Edinburgh; Yoshida Y, Keio University; Koutsovoulos G, University of Edinburgh; Laetsch D, University of Edinburgh; Kumar S, University of Edinburgh; Stevens L, University of Edinburgh; Horikawa I, Keio University; Ishino K, Keio University; Komine S, Keio University; Arakawa K, Keio University

The superphylum Ecdysozoa was originally proposed based on analysis of ribosomal RNA genes, but has subsequently been validated by whole-genome and -transcriptome phylogenomics. Ecdysozoa encompasses the bulk of the planet's animal diversity as it includes the dominant phyla Arthropoda and Nematoda as well as six additional, less-speciose phyla. The internal structure of Ecdysozoa is generally accepted to include a monophylum of (Arthropoda, Onychophora, Tardigrada), named Panarthropoda. However, Panarthropoda has rarely been recovered in molecular phylogenetic analyses, as phylum Tardigrada (the waterbears or moss piglets) is usually found to be sister to Nematoda. We have reassembled the genome of the tardigrade Hypsibius dujardini, reannotated the genome of the tardigrade Ramazzottius varieornatus, and clarified the pattern and importance of horizontal gene transfer in these species. We collated a multigene dataset for phylogenetic analysis that included genomes from four, and transcriptomes from three additional, ecdysozoan phyla. Analysis of these data robustly recovers Tardigrada as sister to Nematoda (plus Nematomorpha). Investigation of rare genomic changes (gene birth and loss) yields equivocal data which tend to support Panarthropoda. The internal phylogenetic structure of Ecdysozoa must be considered an unresolved, and exciting, question, as molecular and morphological/developmental data continue to disagree.


P.8  Old school vs. new school: comparing inferences of population structure using RADseq and microsatellite datasets. Bohling J*, US Fish and Wildlife Service; DeHaan P, US Fish and Wildlife Service; Small M, Washington Department of Fish and Wildlife; Seamons T, Washington Department of Fish and Wildlife

For decades short-tandem repeats (aka microsatellite loci) have served as the primary marker of choice for population and conservation genetics. Highly variable microsatellites provide a cheap and computationally undemanding method to sample a subset of an organism's genome. However, the development of high-throughput sequencing technologies has provided the ability to obtain thousands of markers from across the genome. As conservation geneticists consider shifting to these types of datasets, there is a need to evaluate these new techniques compared to traditional approaches. Here we compared a 16 locus microsatellite dataset with a RADseq dataset for 24 bull trout (Salvelinus confluentus) populations from across the species' range. These microsatellites were previously used to help designate conservation units for this threatened species. Because the sequencing data had regions of low-coverage we used a probabilistic genotyping framework to process the data. All 24 populations were represented in the RADseq dataset, but some individuals within populations produced insufficient reads and were removed. Both datasets detected the primary phylogenetic signal distinguishing the coastal and inland bull trout populations west and east of the Cascade Mountain range. Further, the RADseq dataset resolved some population relationships that were ambiguous with the microsatellite data. Overall the two datasets were congruent, although the RADseq dataset provides opportunity to pursue research questions not feasible with the microsatellite dataset. We discuss the implications of this study for geneticists interested in the performance of RADseq data relative to traditional markers.


P.9  A phylogenomic approach for the evolution and biogeography of Ectatomma Smith (Hymenoptera: Formicidae). Camacho GP*, NMNH - Smithsonian Institution; Meza R, Universidad Nacional Aut�noma de Mexico; Branstetter Michael, University of Utah; River�n AZ, Universidad Nacional Aut�noma de Mexico; Feitosa RM, Universidade Federal do Paran�

Ectatomma can be considered the most commonly collected genus of Ectatomminae in the Neotropical Region. The genus is endemic to this region, with 15 species known to date, characterized by being big ants, abundant and conspicuous and with a clear preference for warm habitats. Recent phylogenetic research has focused on understanding the evolutionary and biogeographic relationships between the species of Ectatomma. However, the results don't provide adequate information for entirely resolving lineages relationships in the genus, since monophyly support for the clades varies across the genus and deep relationships are not clearly defined. Target-enrichment and next generation sequencing techniques have been suggested as a possibility of solving many vexing problems in phylogenetics, because it allows for the rapid generation of hundreds of loci for use as phylogenetic markers. One of those techniques, the capture of ultra-conserved elements (UCEs) regions in the genome, have been shown to be far superior than the multi-locus data sets for the estimation of genus and species relationships in ants, increasing the phylogenetic informativeness for the markers. The UCES are core, highly conserved regions of the genome that, when sequenced together with their more variable flanking regions, provide effective markers for phylogenetic reconstructions. The use of UCE for resolving phylogenetic relationships and obtaining divergence estimates for different ant genus can clarify and improve the understanding of the ancient divergence events within the genus, as well as unveil new and more robust hypothesis for the relationships between its species. This study is the first phylogenomic analysis of the genus Ectatomma and the UCE data presented here provide a robust and independent set of characters that clarify interspecific relationships, as well as provide a foundation for historical biogeographic analysis of this genus.


P.10  More than just a shot in the dark: assessing the bioinformatic compatibility of cross-platform de novo ddRAD sequencing in a non-model system. Campbell EO*, University of Alberta; Sperling FAH, University of Alberta

The reproducibility and cross-platform compatibility of de novo next-generation sequencing (NGS) methods has direct implications for biodiversity studies. Not only is biodiversity research necessarily focused on non-model systems with no genomic resources, common logistical sampling difficulties often make it necessary for researchers to augment their datasets with data from other studies. If de novo methods are not widely reproducible in non-model systems, this will likely impact the viability of NGS data in the long term. Despite this caveat, the reproducibility and compatibility of SNPs in non-model systems has not yet been directly tested. We sequenced 24 specimens from the butterfly genus Speyeria on two different NGS platforms, and incorporated differences in library preparation methods prior to sequencing. We then took a de novo approach to bioinformatic locus assembly and SNP discovery, and assessed the power for species delimitation in subsequent population genomic and phylogenomic analyses. Our results indicate a high re-sequencing rate of loci despite differences in initial library preparation and sequencing platforms, as well as overall high levels of data congruence after data processing and filtering. We also present the first application of NGS methods to species delimitation in Speyeria, and elucidate fine-scale patterns of genomic divergence between species.


P.11  The use of targeted gene enrichment to recover a fully supported phylogeny in a rapid and recent plant radiation: the genus Heliconia (Heliconiaceae, Zingiberales). Carlsen MM*, Smithsonian Institution; Fér T, Charles University in Prague; Kress WJ, Smithsonian Institution

In Heliconia, the only genus within the family Heliconiaceae (order Zingiberales), ca. 195 species are native to rainforests in the neotropics, Asia and the South Pacific. Previous studies suggest that species diversification in the genus occurred extremely fast in just over a few million years, thus phylogenetic reconstructions within Heliconia have been challenging so far. To unravel complex phylogenetic relationships characteristic of rapid tropical plant radiations, such as those present in the genus Heliconia, it is necessary to adopt a multigene approach that includes a large number of unlinked DNA regions. The overall goal of this study is to test the usefulness of HybSeq techniques (i.e. sequencing targeted nuclear genes and off-target chloroplast genomes), to reconstruct a fully supported molecular phylogeny for Heliconia. We explicitly focused on two aspects of the HybSeq process. First, we tested the hybridization efficiency of a set of target probes previously designed for the Zingiberaceae (also in the order Zingiberales) in a variety of Heliconia sample tissues that are representatives of the taxonomic, geographic, and morphological range of the genus. The original probe set contains sequences from up to 1,180 putatively orthologous nuclear loci (> 960 bp long). Second, we tested three different phylogenomic pipelines explicitly designed for analysis of HybSeq data, namely Phyluce, HybPiper and HybPhyloMaker. Our goal was to recover the highest possible number of exons and intron target sequences, as well as the most accurate alignments and supported phylogenetic reconstructions for the Heliconia species sampled. The amount of loci recovered per taxa varied greatly among Heliconia samples, with no apparent correlation with phylogenetic position within the genus. Of the three pipelines tested, Phyluce tends to be more conservative in the number of loci recovered, whereas HybPiper retrieved a higher number of target exons as well as their associated intronic spacers. These spacers were also very useful, in terms of percentage of phylogenetic informative characters, for phylogeny reconstruction. On average, for all samples studied, analyzed with all of the three pipelines, we were able to recover ca. 542 usable exons (ca. 46% of the original target loci) with their associated intron boundaries, for ca. 823,462 bps of genomic information (ca. 8% of phylogenetic informative characters). In addition, full chloroplast genomes were also recovered for all taxa, with a total of ca. 115,664 bps aligned (ca. 3% of phylogenetic informative characters).


P.13  Marine genomics: assembly and annotation of decapod genomes using hybrid short- and long-read technologies. Chung Y, The Chinese University of Hong Kong; Yu A, The Chinese University of Hong Kong; Leung A, The Chinese University of Hong Kong; Chan K, The Chinese University of Hong Kong; Kwan H, The Chinese University of Hong Kong; Hui J, The Chinese University of Hong Kong; Chu K, The Chinese University of Hong Kong; Chan T*, The Chinese University of Hong Kong

Decapods form the most speciose order under Crustacea. They have high economic values as global food source and are good pointers for evolutionary studies. Despite their importance, a reference-grade decapod genome is not yet available, obstructing progress in downstream genetics research. To address the need of high quality decapod genomic resources, we have chosen seven decapod species plus one outgroup (Stomatopoda) for whole genome assembly and annotation. We here present the sequencing and genome assembly analysis progress of Chinese mitten crab (Eriocheir sinensis), spiny lobster (Panulirus ornatus), cherry shrimp (Neocaridina denticulata), coconut crab (Birgus latro), redclaw crayfish (Cherax quadricarinatus), and red king crab (Paralithodes camtschaticus). Decapods have complex genome structures with high repetitive sequence content and high heterozygosity, which impede genome assembly. To overcome these challenges, we incorporated short- and long-reads during de novo genome assembly, with iterative correction to improve the assembly qualities. For genome annotation, both de novo gene prediction and homology-based methods were adopted to achieve higher comprehensiveness. We envision that the establishment of the seven decapod genomes would significantly advance the understanding of decapod evolution through comparative genomics.


P.14  Immune gene family characterization in long-read assembly of the koala genome. Cheng Y*, University of Sydney; Jones E, University of Sydney; O'Meally D, University of the Sunshine Coast; Belov K, University of Sydney

The vertebrate genome contains several key multigene families playing central roles in the immune system, such as the major histocompatibility complex (MHC), T cell receptor (TCR), and immunoglobulin (IG) genes. These gene families usually form gene clusters in the genome and, as a result of evolving in a birth-and-death manner, contain a large number of duplicate genes and pseudogenes. Due to the high degree of duplication and sometimes also high levels of genetic variability (e.g. MHC genes), these immune gene families are commonly among the most poorly assembled and annotated regions in genome assemblies, potentially hindering the study of their function and evolution. The recent sequencing of the koala genome using both short-read and long-read technologies have allowed us to examine the MHC, TCR, and IG genes in multiple assemblies and make comparisons between methodologies. Consistently more genes were identified on less scaffolds in the long-read de novo assembly compared to short-read or hybrid assemblies. The main MHC region containing class I, II, III, and framework genes is found on a single superscaffold in the long-read assembly, in which TCR alpha, beta, and gamma, and IG lambda clusters are also fully assembled. Our results show that long-read sequencing is advantageous in characterizing highly duplicated immune gene families.


P.15  A UCE perspective on the systematics of seabirds (Procellariiformes). Chesser RT*, USGS/NMNH; Welch AJ, Durham University; James HF, NMNH; Bretagnolle V, CNRS

The Procellariiformes (albatrosses, petrels, and shearwaters) are by far the largest group of oceanic birds, but no multi-locus phylogeny of the order is available. We are using genomic sequence capture of UCEs to study evolutionary relationships of all extant and recently extinct Procellariiformes, at and below the species level. Here we analyzed sequences of a representative sample of species to present a well supported backbone phylogeny showing relationships among families and other major groups of Procellariiformes. Our family-level results indicated that the albatrosses (Diomedeidae) were sister to the rest of the order, that the storm-petrels (Hydrobatidae) consisted of two groups that were not sister taxa, and that the shearwaters and petrels (Procellariidae) were paraphyletic with respect to the diving-petrels (Pelecanoididae). Other results of interest concerned the large family Procellariidae: (1) the fulmarine petrels were sister to the rest of the Procellariidae, (2) the Puffinus shearwaters were paraphyletic with respect to Calonectris, and (3) the Kerguelen Petrel Aphrodroma brevirostris was sister to but distantly related to the Pterodroma petrels. All nodes on the tree received 100% bootstrap support.


P.16  Comparing SNPs and microsatellites for sibship analysis in gray wolves (Canis lupus). Clendenin HR*, University of Idaho; Adams JR, University of Idaho; Hayden JA, Idaho Department of Fish and Game; Struthers JL, Idaho Department of Fish and Game; Hohenlohe PA, University of Idaho; Waits LP, University of Idaho

The successful reintroduction and recovery of gray wolves (Canis lupus) in the Northern Rocky Mountain distinct population segment resulted in their most recent delisting in 2011, shifting their subsequent management from federal to state agencies. Acting to prevent relisting within their jurisdiction, the Idaho Department of Fish and Game has conducted monitoring of gray wolves to maintain populations above recovery levels while permitting regulated harvest. As part of these monitoring efforts, managers would like to estimate a minimum count of the number of packs producing young. This metric can be obtained through use of genetic analyses to conduct sibship reconstruction of 'known fate' pups, i.e. individuals captured for collaring and of known mortality, including harvest, then aged by tooth analysis. DNA samples from these pups were collected from May 2014 - April 2015, and nuclear DNA microsatellite genotypes were generated at 18 loci for a subset of 98 pups. Sibship groups were identified using likelihood methods implemented in the program COLONY. Our analyses identified 23 sibgroups of 2-4 pups and 42 individuals that could not be placed into any sibgroup. These single individuals may represent samples from 42 additional packs or could be an artifact of low power to define sibgroups. Thus, we are currently generating RADseq data for these samples to identify thousands of single nucleotide polymorphism (SNP) loci that can be used to repeat the sibship analyses and compare results and statistical power between SNP and microsatellite loci. The shift to SNPs is expected to be desirable as it should increase statistical power, decrease uncertainty in likelihood analyses, and improve comparability among and within laboratories. Employing RADseq for SNP discovery can ultimately extend beyond kinship analysis to address questions related to pedigree, dispersal, adaptation to local environments, and variation over time and across landscapes.


P.17  Providing a Backbone of the Cnidaria Tree of Life through Phylogenomic Analysis. Kayal E, Station Biologique de Roscoff; Ryan J, Whitney Laboratory for Marine Bioscience; Plachetzki D, University of New Hampshire; Bentlage B, University of Guam; Collins A*, NOAA & NMNH

Cnidaria is a diverse group consisting of more than 13,000 known species, mostly marine, divided into three major groups: Anthozoa, Endocnidozoa and Medusozoa. Phylogenomic analyses of Cnidaria are still in their infancy, with just two published studies, each advancing knowledge of the cnidarian tree of life, but also with limited taxon sampling. The positions of several key groups have been equivocal, specifically the tube anemones of Ceriantharia and stalked jellyfishes of Staurozoa, and we place a special focus on these groups by providing new data for them. We created several datasets using publicly released as well as newly-generated DNA and RNA-seq data for representatives of all cnidarian classes to test all previously-proposed phylogenetic hypotheses.After stringently removing potential contamination from bacteria and bilaterian animals, we explore two popular orthology assessment methods, AGALMA and OrthoFinder, to build gene alignments for phylogenetic purposes, and compare their outcomes regarding both gene representation and phylogenetic signal (aka species trees). Our Cnidaria dataset is the most extensive to date, including sequence-rich datasets for staurozoans and a ceriantharian, whose phylogenetic positions appear robust and stable in all of our analyses.


P.18  Phylogenetic relationship among strains of Dictyostelium discoideum inferred from whole genome sequencing. Castillo A, University of Bath; Reznik G, Universidade Federal de Sao Carlos; Gruenheit N, University of Manchester; Thompson CR, University of Manchester; Wolf JB, University of Bath; de Brito RA*, Universidade Federal de Sao Carlos

The social amoeba Dictyostelium discoideum has been studied as a resourceful experimental system to investigate the evolution of cooperation and competitive conflict. This species has a complex life cycle in which amoebae live as single-celled organisms in terrestrial habitat, but when food gets scarce they aggregate into multi-cellular slugs that differentiate into a fruiting body with viable spores held by a stalk. This process requires cooperation since stalk cells sacrifice themselves to benefit the spores. Studies on the cooperation among different strains have revealed that some aggregations produce a mixture of different genotypes in the fruiting body in some cases, coupled with a remarkable variation in cooperative behavior, which appears to be quantitative. An investigation of the levels of genetic variation and diversity in this system is essential to understand the evolution of cooperation and conflict in this species. Here we sequenced the genome of several strains of D. discoideum across the globe to better understand the distribution of variation. With the help of the genome sequence of a strain from North Carolina, we sequenced another 132 strains available on Dicty Stock Center, mostly from United States, but from several places across the globe as well, such as Costa Rica, Mexico, Trinidad, Germany and Japan, aiming to investigate levels of variation in US, contrasted with more distant localities. We generated Illumina paired-end reads for all the strains, and mate-paired reads of a few to help in scaffolding. The average coverage, after removing potentially contaminant DNA from the bacteria Klebsiella aerogenes which is used as food source for D. discoideum was 30x, varying from 10-60x coverage, which was sufficient to allow the reliable identification of thousands of SNPs. The assembly was performed using SPAdes and A5, using Medusa as a reference guided scaffolder to increase the average scaffold N50. The identification of SNPs performed with PLINK allowed us to produce phylogenetic trees that identified at least 4 different lineages in D. discoideum. We identified a main branch encompassing most strains from US, as well as from several other places, such as German and Japan. This lineage is separated in two closely related lineages, which must be confirmed by other strategies that are more adequate to identify differentiation with gene flow. We also identified two lineages, still composed of continental US strains, which are not as closely related to this main branch (between 4-5% genetic distance) and two more divergent strains from Costa Rica and Mexico which showed between 10 and 20% genetic distance from the main lineage. These data suggest a much more diverse genetic background for D. discoideum which brings relevant information to the evolution of conflict in this species, but this need to be investigated further, since the proper identification of homologous genes across lineages is paramount for an adequate analysis.


P.19  Parasites, Microbes, Parasites and Microbes. Dheilly N M*, Stony Brook University

Over the past decade we have witnessed an explosion in the number projects characterizing the bacteriome and virome of environmental samples and free living organisms, even though most species on earth have a parasitic life style. Despite the limited amount of data, evidences suggest that parasites also interact with microbes: parasites spanning all major phyla, including worms, viruses, bacteria and fungi have been documented to disrupt their host microbiome, and others have been found associated with bacteria, viruses or both. But what is the role of parasite-microbe interactions in the diseases and their epidemiology? There is now a critical need to characterize the role of parasite alterations of their host microbes, to test parasites from various phyla for the presence of associated microbes, and to investigate the role of host- and parasite-associated microbes in parasite fitness and in the symptoms associated with infection. If we do not know if a parasite interaction with microbes is stochastic, dependent on the composition of the host microbiome, or specifically controlled by the parasite, it is impossible to determine in which circumstances, and how it should be taken into consideration in epidemiological models and to develop new therapeutic strategies. Here we identify key biological questions, specific challenges, technical approaches and experimental designs that have proven useful to advance the Parasite Microbiome Project.


P.20  Investigating population genetics and gene expression of scleractinian coral in a highly variable environment along the northern Florida Reef Tract. Dodge DL*, FAU Harbor Branch Oceanographic Institute; Voss JD, FAU Harbor Branch Oceanographic Institute

Coral reef populations on Florida's central east coast are susceptible to many anthropogenic influences including controlled freshwater discharges and agricultural runoff. Natural environmental variability is relatively high as a result of seasonal rainfall and upwelling patterns. Neither coral spawning nor gamete development have been observed at the northern end of the Florida Coral Reef Tract. Therefore we hypothesize that this region may represent a population sink for multiple coral species. To better understand coral population structure and responses to sublethal stressors, populations of the scleractinian coral Montastraea cavernosa were examined using a combination of genomic and transcriptomic techniques. The expansive geographic distribution of M. cavernosa throughout the Tropical Western Atlantic and broad depth range (3 -100 m) warrant investigations of both horizontal and vertical connectivity. However, few population connectivity studies for this species have focused on southeast Florida. The study region is strongly influenced by the Florida Current and represent the upper latitudinal limits for many scleractinian coral species along the Florida Coral Reef Tract, including M. cavernosa. Microsatellite genetic markers were used to assess population structure and connectivity along Florida's east coast. RNA Seq analysis were completed on an Illumina NextSeq platform to characterize transcriptomic responses of corals in this highly variable environment. The goals of this project are to quantify and predict coral responses to freshwater discharge, to provide insight into the fundamental metabolic processes that may enhance stress tolerance and coral resilience, and to promote data-driven management decisions that enhance conservation of these coral ecosystems.


P.21  Integrating diverse genomic resources for cost-effective phylogenomics. Dupuis JR*, University of Hawaii; Bremer FT, University of Hawaii; Geib SM, USDA-ARS

An advantage of high-throughput sequencing methodologies is that the sheer amount of data returned by such technologies can be mined and re-used for a multitude of projects. Methodologically, however, this task is often far from easy, given variable output formats and data characteristics that might be specific to each library. Phylogenetics and systematics are well-posed to take advantage of this accumulation of genomic resources, as their data inputs are conceptually simple (orthologous genes) and relatively easily reconciled from diverse data types. Here we present an approach for phylogenomic locus selection in tephritid fruit flies (Diptera: Tephritidae) that takes advantage of a variety of genomic and transcriptomic data sources: well-annotated genomes assembled from multiple sequencing library strategies (e.g. fragment, mate pair), more basic genome assemblies from single sequencing libraries, and transcriptomes of varying quality from multiple approaches. We utilized well-annotated genomes to predict annotations for poorer quality assemblies, which allowed us to predict single copy orthologs as well as infer intron/exon boundaries for assemblies lacking such information. Focusing on conserved exonic regions in orthologs facilitated downstream gene sequencing for additional species without pre-existing genomic data. To this end, we developed a cost-effective, multiplexed high throughput sequencing approach, and generated gene sequence data for several hundred species in the Tephritidae. Our sampling focused on two evolutionary time scales, one more broad to construct a backbone phylogeny, primarily for the genus Bactrocera, and the other finer to explore the relationships and taxonomy of several contentious species complexes. These phylogenies not only provide insight into the evolution and systematics of a morphologically-challenging group of insects, but also provide diagnostic tools for many serious, but difficult to identify, agricultural pests. Our approach provides a novel way to combine diverse genomic and transcriptomic data sources, particularly when at least one well-annotated data source is available, and will undoubtedly prove useful as genomic data continues to accumulate at unparalleled rates.


P.22  Mekong Fish Biodiversity: from barcodes to genomics. Elliott VL*, Moore Centre for Science; Chheng P, Inland Fisheries Research and Development institute; Uy S, Inland Fisheries Research and Development institute

The Mekong is an understudied highly biodiverse freshwater system. We developed an inventory for the Lower Mekong basin against which we are testing the opportunity for environmental DNA applications to track and maintain the biodiversity of the region. With climate change and hydropower development threatening this biodiversity, we are using RADs to generate the first understanding of important migratory pathways for much of the diversity. Using our results we will be able to understand the variety of movement patterns and identify ways to mitigate the impacts of development in the Mekong


P.23  The Methylome of the Marbled Crayfish Procambarus virginalis. Falckenhayn C*, DKFZ; Gutekunst J, DKFZ; Gatzmann F, DKFZ; Lyko F, DKFZ

Vertebrates and invertebrates share key features of DNA methylation, but they differ in their methylation patterns, indicating that DNA methylation may have different functions. Crustaceans are keystone species with ecological and environmental relevance for their habitats, however, little is known about the methylome of crustaceans. The parthenogenetically reproducing marbled crayfish (Procambarus virginalis) is a triploid descendant of the sexually reproducing freshwater crayfish Procambarus fallax [1]. Despite its genetic uniformity, the marbled crayfish shows a substantial degree of phenotypic variation and environmental adaptation, which establishes this species as a unique model system for the field of epigenetics. We have recently completed a draft genome assembly for the marbled crayfish which encodes Dnmt1, Dnmt3 and Tet homologues and thus, contains a full complement of enzymes that mediate de novo and maintenance methylation as well as hydroxymethylation. We used whole-genome bisulfite sequencing (WGBS) to comprehensively analyze the methylation patterns at single-base resolution. The methylation was found to be CpG-specific, bimodally distributed and symmetric on both strands, which are key features of animal methylomes. Furthermore, methylation was enriched in gene bodies displaying the typical pattern of a mosaically methylated invertebrate genome with a bimodal distribution. Interestingly, DNA methylation preferentially targeted gene bodies of housekeeping genes. Repetitive elements were generally hypomethylated and the methylation of repeats depended on their position to gene bodies. We then performed RNA-Seq to analyze the relationship of gene body methylation and expression. Moderate expressed genes were highly methylated, while lowly and highly expressed genes displayed the lowest methylation level. A similar relationship was observed for housekeeping genes suggesting that DNA methylation of housekeeping genes might fine-tuning their expression. Finally, inter-individual and inter-tissue comparison of gene body methylation revealed a substantial degree of reproducibility of the methylation patterns distinguishing them from the dynamic tissue-specific methylation of mammalian methylomes. Our results thus identify several novel features in the marbled crayfish methylome that might be evolutionary conserved among invertebrates. Future studies will focus on the integrative analysis of the DNA methylation, gene expression and chromatin structure which will provide new insights into the P. virginalis epigenome and should elucidate the epigenetic regulatory function of DNA methylation in the marbled crayfish. [1] Vogt G et al.; (2015). The marbled crayfish as a paradigm for saltational speciation by autopolyploidy and parthenogenesis in animals. Biol Open. 4(11):1583-94.


P.24  Hybridization-based target enrichment as a tool for phylogenetic analyses at different evolutionary levels. Fer T*, Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic; Schmickl R; Kress WJ, Botany Department, National Museum of Natural History, Smithsonian Institution, Washington, D.C., USA; Carlsen M, Botany Department, National Museum of Natural History, Smithsonian Institution, Washington, D.C., USA; Pospisilova M, Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic; Flaskova L, Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic; Leong-Skornickova J, Research & Conservation Branch, Singapore Botanic Gardens, Singapore

Using a high number of independent and putatively orthologous low-copy loci is a large benefit for phylogenetics. Species trees reconstructed from big phylogenomic datasets are often completely resolved and well supported. Hybridization-based target enrichment (Hyb-Seq) is one of the methods for effective sampling of thousands of exons from hundreds of genes. Because hybridization enrichment is not 100% efficient nearly complete chloroplast genomes can be obtained from off-target reads. Huge amount of data generated by the Hyb-Seq NGS method need an appropriate bioinformatic pipeline for processing raw reads up to the reconstruction of species tree. We developed HybPhyloMaker, a modular set of BASH scripts for UNIX-like environment that is designed for compact and easy-to-use processing of raw Illumina paired-end reads, selecting suitable loci and constructing gene and species trees using different methods. Probe set covering 1,180 genes was designed for the genus Curcuma (Zingiberaceae) comparing C. longa transcriptome and C. ecomata genome-skimming data. The probes were successfully applied to enrich sequencing libraries not only within the genus Curcuma but also at the level of the whole family Zingiberaceae and the order Zingiberales. More than 1,000 loci were usable for the genus Curcuma and around 700 loci were used to establish the phylogeny of Zingiberaceae and Zingiberales. With our work we demonstrated really broad evolutionary applicability of the set of orthologous genes initially designed for generic level phylogeny.


P.27  Assembling large heterozygous/polymorphic genomes. Limasset A., INRIA, France; Marchet C., INRIA, France; Peterlongo P., INRIA, France; Flot J.-F.*, ULB, Belgium

One of the main challenges hindering the assembly of non-model organisms is heterozygosity: as most assemblers were designed with the human genome in mind (the heterozygosity of which is a mere 0.1 percent), they often fail when applied to the genomes of species with larger effective population sizes (in which heterozygosity commonly reaches 1 to 6 percent). Solving this problem requires first redefining the assembly problem: should we aim to reconstruct a single haploid sequence or should we rather aim to reconstruct the various haplotypes? The second option is clearly more appealing, as it does not assume that the genome is organized in pairs of colinear homologous chromosomes; besides, comparing the haplotypes among themselves makes it possible to perform "1-genome population genomics" and gain unique insights into the genome dynamics of the organism under scrutiny. However, the few assemblers currently able to perform diploid genome assembly (MIRA, DiscovarDeNovo) require huge amounts of RAM, disk space and computing power when applied to genomes larger than a few hundred Mbp. Here we present a novel short-read assembler that assemble the haplotypes of heterozygous/polymorphic genomes in a fast and resource-efficient fashion. This assembler is particularly useful when dealing with asexual organisms, the heterozygosity of which cannot be reduced using inbreeding.


P.28  Phylogenetic placement and internal relationships of ceriantharia. Forero A*, University of Genova; Molodtsova T, Shirshov Institute of Oceanology RAS; Arrigoni R, Kaust; Astman C, Uppsala; Bavestrello G, University of Genova; Berumen M, Kaust; Rouse G, Scripps; Ravasi T, Kaust

The lack of genetic data for Ceriantharia it is the main reason why this group often is excluded from phylogenetic analyses. Based on our combined analysis Ceriantharia is considered as a separate clade within Anthozoa and is the sister group of Octocorallia with relatively good support in the ML and BI analyses (81% bootstrap and 0.95 pp respectively). A combined molecular phylogeny reconstruction supported by morphological features for the tree families of Ceriantharia are also presented here. Our results clearly support Arachnactidae as a monophyletic group whilst the last two families: Cerianthidae and Botrucnidiferidae were grouped in different clades, suggesting that the division in suborders reported by den Hartog (1977) is apparently not right. Based on genetic and morphological evidence the type species of the genus Cerianthus (C. membranaceus) is closely positioned to Ceriantheomorphe brasiliensis, both genera has the second protomesentery reaching the aboral pore. All the Pachycerianthus species were clustered in the same clade as a consistent group, which are genetically closer to Arachnactidae's clade, same was previously proposed in 1910 by McMurrich. We present here four putative new species among which there is one deep-sea cerianthid that belong to Botrucnidiferidae (Botrucnidifer sp1) that seems to be the basal clade compare with the rest of cerianthids studied here.


P.29  Comparative genomics of Asilidae, Mydidae, and Tabanidae (Diptera): adding to our evolutionary understanding of the center of the fly radiation. Frandsen* PB*, Smithsonian Institution; Dikow RB, Smithsonian Institution; Turcatel M, Smithsonian Institution; Dikow T, Smithsonian Institution

Genomes are presented for Asilidae (Proctacanthus coquilletti), Mydidae (Mydas clavatus) and Tabanidae (Tabanus discus), three families in the center of the 160,000 species fly radiation. The larvae of each species are known to be predators of other immature insects or arthropods and potentially use a venom to kill their prey. In contrast, the adult flies have dramatically different life history traits: Asilidae (assassin flies) are predators of other insects, Tabanidae (horse flies) are primarily blood feeders of large mammals, and Mydidae are flower feeders. Venom is only used by assassin flies in the adult stage. Although no information is available concerning the location of the production of venom in the larvae, it is known that venom is produced in the salivary glands of adult assassin flies. It is possible that the same genomic loci are responsible for venom production in both the adult assassin flies and the larval stages of all three species. While many Diptera genomes have previously been sequenced, most of this work has focused on mosquitoes and fruit flies, which are more than 200 million years diverged from our taxa of interest. We used two different sequencing strategies: the Illumina 2X250bp/DISCOVAR de novo method for P. coquilletti and 10X Genomics/Supernova for M. clavatus and T. discus. In light of the differences in life history traits, we compare the resulting genome assemblies in terms of size, heterozygosity and gene content. Whole genome alignments across these species are also presented, which provide orthologous loci necessary for future large-scale phylogenomics studies in this area of the fly tree of life.


P.31  Saltational speciation in the marbled crayfish P. virginalis. Gatzmann FB*, German Cancer Research Centre; Falckenhayn C, German Cancer Research Centre; Gutekunst J, German Cancer Research Centre; Raddatz G, German Cancer Research Centre; Lyko F, German Cancer Research Centre

The marbled crayfish Procambarus virginalis is a triploid organism which is the only known obligatory parthenogen among the decapod crustaceans. It is of particular interest due to its suitability as a research model organism and potential as an invasive species. The marbled crayfish has recently evolved by autopolyploidy from its diploid, sexually reproducing parent species Procambarus fallax. Therefore, the species pair is an excellent model system to study the genetic and epigenetic changes necessary for saltational evolution. To estimate genome sizes, we combined flow cytometry intensities with k-mer analyses from whole-genome sequencing data. Our results indicate genome sizes of 3.5 GB for P. virginalis and 4.1 GB for P. fallax. Using the draft genome assembly completed in our group, we therefore compared P. fallax and P. virginalis whole-genome sequencing data, and identified 770 MB of genomic information that is specific to P. fallax. Using RNA-seq, we performed a differential gene expression analysis for abdominal muscle tissue and found 61 differentially expressed genes. Finally, we compared the methylation patterns between the two species using whole-genome bisulfite sequencing data. The global methylation ratio difference is 0.02, mainly resulting from a hypomethylation of genes and repeats in the P. virginalis genome. We identified several genes for which differential methylation correlates with corresponding gene expression changes. These results constitute a first step in defining the genomic and epigenomic changes that underpin the instant speciation of the marbled crayfish. Future studies will focus on the experimental validation of enriched genes that are unique to P. fallax, and of genes that are differentially regulated between the two species. Such comparative analyses of the P. virginalis and P. fallax genomes and methylomes provide a unique opportunity to study the genetic and epigenetic changes that are necessary for parthenogenetic reproduction and saltational evolution in animals.


P.32  The draft genome of Ruditapes philippinarum (the Manila clam). Ghiselli F*, University of Bologna; Komissarov A, St. Petersburg State University; Milani L, University of Bologna; Dunham JP, University of Southern California; Breton S, University of Montreal; Nuzhdin SV, University of Southern California; Passamonti M, University of Bologna

Bivalve molluscs are a highly successful and ancient Class, including over 20,000 known species, and they are an interesting group for evolutionary and biodiversity studies. Bivalves represent a good model for studying adaptation to anoxia/hypoxia, salinity, and temperature, and they are useful bioindicators for monitoring the concentration of pollutants and heavy metals in the water. They also make up an important source of food all over the world, with a production corresponding to ~20% of the global aquaculture yield; clams are first in production, followed by oysters, mussels, and scallops. A striking feature of bivalves (and the main reason behind this project) is the presence of an unusual mitochondrial inheritance system: the Doubly Uniparental Inheritance (DUI), so far detected in ~50 bivalve species, belonging to seven families. In DUI species, two mitochondrial genomes (mtDNAs) are present: one is transmitted through eggs (F-type, for female-inherited), the other through sperm (M-type, for male-inherited), and the amino acid p-distance between conspecific M and F genomes ranges from 10% to over 50%. DUI provides a unique and privileged point of view for studying several fundamental aspects of eukaryote biology. In DUI systems: i) males are naturally heteroplasmic, with two very divergent mtDNAs; ii) it is possible to follow germ line mitochondria during development (to study mitochondrial inheritance and bottleneck); iii) mitochondria are under selection for male functions (e.g.: spermatogenesis, sperm swimming); iv) there are two coexisting mitochondrial genomes in the same nuclear background (coevolution, conflicts). All these interesting biological features are in sharp contrast with the lack of genomic resources about bivalve molluscs. Here we present the draft genome of the DUI species Ruditapes philippinarum (the Manila clam). DNA from a male individual was sequenced with x40 Illumina HiSeq and with x30 PacBio RSII. We have tried to assembly this dataset with all available hybrid or PacBio only assembly pipelines. The best results were obtained with PacBio reads assembled by Canu assembler with contig N50 76 kb, and 39.92% completed and 74.60% partial genes according to CEGMA. We annotated families of tandem and dispersed repeats, we found a new highly repeated dispersed element, and characterised the major families of satellite DNA. We report the results of the first analyses as well as the technical challenges we faced, especially during the phase of de novo assembly.


P.33  Building a reference genome for Centrapalus pauciflorus (Compositae), an African oilseed crop . Gonzalez* VL*, Smithsonian Institution; Dikow RB, Smithsonian Institution; Frandsen PB, Smithsonian Institution; Kweskin MP, Smithsonian Institution; Johnson G, Smithsonian Institution; Gostel MR, Smithsonian Institution; Muruvanda T, US Food and Drug Administration; Allard M, US Food and Drug Administration; Keeley/Funk S/VA, University of Hawaii/Smithsonian Institution; Mandel JR, University of Memphis

Plant genomes pose significant bioinformatics challenges because they are often very large, highly repetitive, and polyploid. Existing reference-quality plant genomes are over-represented by domesticated species, which have undergone significant artificial selection. The family Compositae is the largest of the flowering plant families and yet is only represented by a handful of genomes. Here we present a high-quality genome for an undomesticated oilseed crop with economic importance, Centrapalus pauciflorus (Compositae), generated with single-molecule, long-read sequencing. Centrapalus is from an early diverging lineage, has a diploid chromosome number, and is found in a part of the phylogeny that is crucial for understanding evolution in the family. Different genome assembly strategies, including FALCON, Canu, and MaSuRCA are compared. The C. pauciflorus genome is compared to others from Compositae (sunflower, lettuce, artichoke, and horseweed) in terms of size, repeat, and gene content. Expanding the number of available plant genomes is essential to our ability to understand the evolutionary history of gene duplication and polyploidy, which in turn informs our hypotheses of orthology and phylogenetic relationships. For Centrapalus in particular, it could also lead to strategies for domestication.


P.34  Phylogeography and Species Delimitation of Zebra-tailed Lizards (Callisaurus) in Western North America. Gottscho A*, Smithsonian Institution; de Queiroz K, Smithsonian Institution

What is a species? How do species form? These basic questions are not only of theoretical interest, but are fundamental to understanding and sustaining a biodiverse planet, one of the four grand challenges of the Smithsonian Institution. Recent advances have renewed interest in speciation and species delimitation. The general lineage species concept (GLSC) challenged researchers to distinguish between the theoretical concept of species and the operational criteria that are used to put the concept into practice, setting the stage for new coalescent model-based approaches to test alternative taxonomic hypotheses regarding the numbers and boundaries of species. Furthermore, novel NGS technologies such as restriction-associated DNA sequencing (RADseq) now allow researchers to obtain genomic single-nucleotide-polymorphism (SNP) data for non-model organisms. Here, we use genome-wide SNP data to investigate the phylogeography and species delimitation of Zebra-tailed Lizards (Callisaurus draconoides complex), which have an enormous distribution in the deserts of North America. Eleven (sub)species have been described between 1835 and 1942, but the genus is currently considered to be monotypic despite extensive geographic variation. We also test biogeographic hypotheses of dispersal and vicariance across the North American aridlands, including seven islands in the Gulf of California.


P.35  Microbiome of the corallivorous amphinomid Hermodice carunculata (Annelida: Amphinomidae). Grimes C*, Texas A&M at Galveston; Schulze A, Texas A&M at Galveston; Fofanov Y, University of Texas Medical Branch; Golovko G, University of Texas Medical Branch; Khanipov K, University of Texas Medical Branch

Microbial communities, also known as 'microbiomes', associated with hermatypic corals and other invertebrates have recently come into focus as they contribute their specific functions and molecular machineries to the functioning of the 'holobiont'. Microbiomes are dynamic and may contain an assortment of commensal, symbiotic, and pathogenic microorganisms. Here we explore the potential impact of the mobile corallivore Hermodice carunculata to harbor and transfer microbes between hosts. H. carunculata is an amphinomid annelid and has been suggested as a vector for the coral bleaching pathogen Vibrio shiloi in the Mediterranean. Preliminary microbiome studies based on 16S bacterial ribosomal sequences from collected surface swabs and tissues samples of H. carunculata from the coastal region of the Gulf of Mexico in Florida show the presence of a diverse microbiome on the external surfaces including Vibrio spp. The anterior chaetal region was dominated by an Arcobacter sp., while the posterior chaetal region by an uncultured member of the SAR324 clade. Endozoicomonas euniceicola, a possible symbiotic bacterium for the octocoral, Antillogorgia elisabethae, was found in high abundance in tissue samples from the chaetal regions. Dissected tissue from the anal rectal area was dominated by Spiroplasma sp., pathogen for arthropod disease. Further studies will determine the relevance of the microbial communities associated with different body regions in H. carunculata in the transference of beneficial and pathogenic microbes among coral colonies.


P.36  Landscape genomics of California valley oak (Quercus lobata). Gugger PF*, University of Maryland Center for Environmental Science; Fitz-Gibbon ST, University of California, Los Angeles; Wright JW, USDA Forest Service, Pacific Southwest Research Station; Sork VL, University of California, Los Angeles

Understanding the role of the environment in shaping genetic variation is a major goal of population genetics, and also provides important background for species management under global change. New genomic tools available for oaks (Quercus spp.) enable unprecedented insight into the genes that may be involved in local adaptation to changing environments along the landscape. To identify specific loci under the influence of natural selection for local adaptation and the particular climate factors shaping genome-wide variation, we analyzed thousands of SNPs from genotyping-by-sequencing of over 400 trees across the distribution of Q. lobata, a California endemic oak. We employed multivariate non-linear models and latent factor mixed models that account for underlying spatial genetic structure to identify SNPs with significant environmental associations and map their distributions on the landscape. We then utilized our recently generated annotated valley oak reference genome sequence to characterize the genomic context of SNPs with significant associations and attribute potential functions to them. We found that climate variables were associated with genomic variation but they varied along different gradients and spatial scales. However, a number of specific SNPs and genes were repeatedly identified as candidates for local adaptation. These results provide insight into selective forces along the natural landscape and generate a list of candidate genes associate with response to climate that warrant additional study with experimental approaches.


P.37  Assembly and annotation of the marbled crayfish genome. Gutekunst J*, German Cancer Research Center; Falckenhayn C, German Cancer Research Center; Gatzmann F, German Cancer Research Center; Raddatz G, German Cancer Research Center; Lyko F, German Cancer Research Center

Marbled crayfish (Procambarus virginalis) are the only freshwater crayfish known to reproduce by cloning (apomictic parthenogenesis). Notably, among genetically identical offspring raised in the same environment, distinct phenotypic differences can be observed. These characteristics establish the marbled crayfish as a particularly interesting laboratory model. A prerequisite for introducing this triploid arthropod as a new model organism is the identification of its complete genome sequence. We experimentally determined the genome size at approximately 3.5 Gbp by k-mer analysis and flow cytometry. Multiple shotgun and long jumping distance libraries, with a total coverage of ~70X were generated from one individual female. Sequencing data was then used for a first de novo draft assembly with a length weighted median scaffold size (N50) of 40 kb. High fragmentation of genome assembly is often a result from high heterozygosity levels. Indeed, we estimated the heterozygosity of P. virginalis at 0.53% which is significantly higher compared to other genomes. We further refined the assembly using transcriptome data to improve gene representation. Eventually, we identified 56% complete and 21% fragmented conserved single-copy arthropod orthologs using the bechmarking software BUSCO. Single nucleotide variations (SNP) analyses of four additionally sequenced individuals from different strains confirmed the clonal reproduction of marbled crayfish and enabled us to describe additional genomic characteristics such as triploidity and common genotypes. Furthermore, we are able to support a theory of origination by autopolyploidization and provide evidences for genetic separation from P. fallax. Automatic annotation of roughly 21,000 genes using the annotation pipeline MAKER provides a detailed overview of genetic features and identified several interesting genes, such as a cellulase gene, with a potentially important role in omnivorousness in P. virginalis. The genome of marbled crayfish thus provides first genetic insights into the unknown but very versatile order of decapod crustaceans as economically and ecologically relevant keystone species. Genomic data and several online services are, after registration, publicly accessible at our Marmorkrebs web server (http://marmorkrebs.dkfz.de).


P.38  Traditional ecological knowledge in Mexico: Applying new genetic technologies to understanding Indigenous traditional ecological knowledge. Amith J.D., Gettysburg College; Hasenstab-Lehman K.E.*, Smithsonian Institution; Kress W.J., Smithsonian Institution

New genomics tools, which cross the spectrum from targeted loci to entire genomes, are opening up exciting new avenues of research. Ethnobotanical investigations focus on the identification of plant species that are named, categorized, or used by Indigenous people. In such studies, species identification is especially difficult, particularly in study areas where the flora is poorly documented and highly diverse, such as the high elevation forests of the Sierra Nororiental in Puebla, Mexico. In this region about one-third of the area's half-million inhabitants speak an endangered language: Nahuat or Totonac. Through a unique collaboration between botanical researchers, social scientists, and Indigenous communities we are evaluating the utility of DNA barcodes for both broad interdisciplinary research on culture and biodiversity, as well as for species identification. This project provides a highly synergistic partnership between botanists, linguists, anthropologists, and Indigenous communities in the Department of Botany at the Smithsonian's National Museum of Natural History (NMNH), the NMNH Department of Anthropology, the Instituto de Biología at the National Autonomous University of Mexico (UNAM), and local communities in Puebla. To construct a cultural and botanical reference library for the Sierra, we are generating DNA barcodes (rbcL, matK, trnH-psbA, and ITS) for all specimens collected during three years of comprehensive botanical and ethnobotanical field collection. The fertile specimens are each identified by expert taxonomists, creating a rich set of floristic material that is then linked to molecular sequences in a DNA barcode reference library. Additional (fertile and sterile) specimens are being collected through community-specific ethnobotanical research and sequenced to compare the resulting DNA barcodes against those of the reference library with the aim of streamlining species identification of both field specimens and plant products used in various forms by traditional communities. Here we present preliminary results of the regional DNA barcode library and a phylogenetic analysis of the local plant communities. These results will lead to a genomics tool that will facilitate collaborative participation of Indigenous communities with scientific research by simplifying the collection and identification process by which ethnographic knowledge can be linked to scientifically identified species.


P.39  Identifying genomic differences underlying phenotypic changes using Forward Genomics. Hecker N*, Max Planck Institute of Molecular Cell Biology and Genetics, and Max Planck Institute for the Physics of Complex Systems, Dresden, Germany; Hiller M, Max Planck Institute of Molecular Cell Biology and Genetics, and Max Planck Institute for the Physics of Complex Systems, Dresden, Germany

Numerous sequenced genomes allow us now to systematically search for the genomic basis underlying phenotypic differences between mammals. To this end, we have previously developed the "Forward Genomics" approach that focuses on phenotypic traits that are independently lost in different species. Forward Genomics relies on two main principles. First, species in which a given phenotypic trait is under selection should also preserve the genetic information for this phenotypic trait. In contrast, if this phenotypic trait is lost, the genetic information underlying this phenotypic trait will evolve neutrally in these species. Consequently, genomic regions that only contain information for this phenotypic trait will diverge faster in the lineages that lost the trait. This "use it or lose it" principle is exemplified by the loss of olfactory receptors in cetaceans or the loss of enamel-related genes in toothless mammals. Second, the repeated loss of a phenotypic trait in independent lineages should result in a specific genomic signature where genomic regions that only contain the information for this phenotypic trait are conserved in the trait-preserving lineages while being diverged or lost in the lineages which lost the trait. Forward Genomics uses this specific independent divergence signature to conduct a genome-wide search for genomic regions involved in the independent loss of a given phenotypic trait. We previously extended this Forward Genomics framework to control for phylogenetic relatedness and evolutionary rate differences. This approach successfully detected genomic loci involved in the repeated loss of physiological traits such as the ability to synthesize vitamin C as well as morphological traits such as the loss of vision. We present and discuss results from applying Forward Genomics to new phenotypic differences between sequenced mammals. Detecting associations between genomic and phenotypic changes will deepen our understanding of the evolution of nature's phenotypic diversity.


P.40  Applying genomics to conservation: a tale of two cancers. Hendricks S*, University of Idaho; Hohenlohe P, University of Idaho

Genomic tools have enormous potential to inform conservation and management of rare species. Here we apply genomic tools to two taxa that are each threatened by a unique type of cancer, with the goal of better understanding the genetic basis of cancer susceptibility and providing genetic tools for population monitoring, prediction of disease dynamics, and management of natural and captive populations. In the first case, Tasmanian devils suffer from devil facial tumor disease (DFTD), one of only a handful of transmissible cancers known in the animal kingdom. DFTD first appeared two decades ago and has decimated wild devil populations, yet recently some populations have shown evidence of tumor regression and population recovery. In the second case, Santa Catalina island foxes have a remarkably high incidence of ear tumors, associated with chronic inflammation from ear mites, although island fox populations on other islands exhibit high mite burdens but no incidence of cancer. In both cases, we have used RAD sequencing to characterize overall levels of genetic diversity and population structure. In devils, we have used an extension of RAD to assay thousands of individuals over multiple time points in several populations and identified a set of candidate genes showing signatures of selection in response to the disease. In island foxes, a preliminary case-control study with RAD data has led to a single candidate gene associated with cancer incidence. In both cases, we are further using targeted sequencing and RNA sequencing to identify causal variants linked to susceptibility. Our results will help predict whether these taxa have sufficient genetic variation to evolve resistance to these unique diseases, and provide a set of functionally important genetic markers for population monitoring and management.


P.41  Single Cell RNA-Seq of abnormal and normal sperm in the domestic cat. Huffmeyer A*, University of California Los Angeles; Pukazhenthi B, Smithsonian Institute; Koeplfi KP, Smithsonian Institute; Wayne B, University of California Los Angeles

Carnivore species are at high risk for extinction. This is the result of human expansion, reduction of suitable habitat and dwindling population sizes. As population sizes decrease, species are at risk for increased levels of inbreeding. Increased homozygosity places carnivores at further risk for accumulation of deleterious alleles that are associated reduced fertility. Currently, goals for managing carnivores focus on maintaining suitable habitat and large population sizes. Going forward, maintaining large populations sizes may not be possible. Rather understanding the molecular mechanisms that contribute to abnormal sperm production in carnivores, may contribute to mitigating or reversing abnormal sperm production. Using the domestic cat, as a model, this study identified genes associated with abnormal sperm production as a result of low heterozygosity. We separated abnormal and normal sperm cells from 2 inbred cats and 2 outbred cats. We created two cDNA libraries, one comprised of abnormal sperm cells and the other normal cells, per cat, with the QIAseq FX Single Cell RNA kit. The libraries were then sequenced on an Illumina HiSeq 2500. The sequences were analyzed using RNA-seq, we found genes were differentially expressed between abnormal and normal sperm cells.


P.42  The Genomic Consequences of Asexuality. Jalinsky J*, University of Iowa; Bankers L, University of Iowa; Fields P, University of Basel; Larkin K, University of Iowa; McElroy K, University of Iowa; Sharbrough J, Colorado State University; Wilton P, University of California, Berkeley; Boore J, Institute for Systems Biology; Logsdon J, University of Iowa; Neiman M, University of Iowa

Why sex is so common despite its many costs remains a hotly debated topic, even termed 'the queen of problems' in evolutionary biology. A newly formed asexual lineage is expected to have an immediate advantage over sexual counterparts because only sexual females invest in the production of males, which are costly because only females can directly produce offspring. Sexual females thus pay a cost of replacing daughters with sons that should culminate in the rapid elimination of sex. Counter to these expectations, asexual reproduction is nearly always limited to a spotty and 'twiggy' distribution across the tree of life. Direct study of the advantages and disadvantages of sex requires direct comparison between otherwise similar sexual and asexual forms. Potamopyrgus antipodarum, a New Zealand snail, thus represents a model system to apply to the sex question because ecologically and phenotypically indistinguishable sexual and asexual individuals coexist in nature. Asexual P. antipodarum lineages are the product of multiple separate transitions from sexual ancestors, allowing us to treat asexual lineages as naturally replicated experiments into asexuality. Comparing the genomes of sexual and asexual P. antipodarum lineages will provide important new insights into the adaptive value of sex. Here, we discuss our ongoing genome project and its application to the sex question. How the genomes of sexual vs. asexual lineages manage the accumulation of deleterious mutations is one of our many ongoing projects using P. antipodarum. First, genes whose functions are limited to sex are predicted to evolve in a manner that reflects an absence of purifying selection. If sex-specific genes are evolving under relaxed selection, the transition away from purifying selection should be associated with pseudogenization via unchecked mutation accumulation. A second project focuses on the evolution of transposable elements (TE's) in sexual vs. asexual lineages. TEs contribute to genome size variation, are often deleterious, and are expected to be affected by sex leading to the question of whether sex acts to increase or eliminate TE expansion. P. antipodarum is also notable for extensive variation in ploidy level. We integrate ecological and genomic approaches to address how recent polyploidy affects adaptive molecular evolution. We are assessing whether there are positive genomic consequences of polyploidy by comparing signatures of adaptation across the genomes of P. antipodarum lineages that vary in ploidy. Finally, we are finalizing our efforts to complete and analyze the first complete genome sequence of P. antipodarum. Preliminary results show repetitive elements are enriched in this species, perhaps linked to a recent genome duplication that is in the process of diploidization. Together, our genome assembly and its application to these projects will provide new and exciting insights into the genomic consequences of sexual reproduction.


P.43  Phylogenomics and taxonomy: Species delimitation in the fungus-farming ant genus Sericomyrmex. Jesovnik A*, Smithsonian Institution; Schultz T, Smithsonian Institution

Ants in the Neotropical genus Sericomyrmex cultivate fungi for food, and both ants and fungi are obligate, coevolved symbionts. The taxonomy of Sericomyrmex is problematic because the morphology of the worker caste is generally homogeneous across all of the species within the genus, species limits are vague, and the relationships between them are unknown. Ultraconserved Elements (UCEs) are phylogenomic markers that have proven useful in resolving both deep and shallow phylogenetic relationships. We used UCEs as to reconstruct evolutionary history and to infer species boundaries in Sericomyrmex. We recovered an average of ~990 UCE loci for 88 Sericomyrmex samples from across the geographical range of the genus as well as for 5 outgroup taxa. Using maximum-likelihood and species-tree approaches, we recovered nearly identical topologies across data sets with 50% to 95% matrix completeness. We integrated the results of the UCE analyses with the results of morphological studies, which consist of morphological characters and measurements of workers, queens, males, and larvae. Both molecular and morphological data show that Sericomyrmex consists of a lesser number of species than previously described. We identify 9 species-level lineages in Sericomyrmex, including 2 new species. This is less than the previously described 19 species, even accounting for 2 species for which we had no UCE samples, which brings the total number of Sericomyrmex species to 11. Divergence-dating analyses recovered 4.3 million years as the crown-group age estimates for Sericomyrmex, indicating a recent, rapid radiation.


P.44  Genome size, metabolism, and powered flight in birds: perspectives from orthologous retrotransposons. Ji Y.*, The Field Museum of Natural History; DeWoody J. A., Purdue University

Avian genomes are of interest because the rapid metabolic rate associated with powered flight requires small cells which constrain genome size. Consequently, flying birds tend to have small genomes relative to other vertebrates such as mammals. It thus stands to reason that flying birds should have smaller genomes than ground-dwelling birds with lower metabolic rates. Small genomes could be condensed but uncompromised in a number of ways, including smaller intergenic intervals, shorter introns, and/or a reduced transposable element (TE) complement. We evaluated genome size in light of the orthologous TE complement among 41 flying (FY) and 7 ground-dwelling (GD) bird species to determine if a preponderance of deletions in orthologous TEs might explain the compact genomes of flying birds with high metabolic rates. We measured, across multiple loci in all 48 species, the lengths of 50 contemporary orthologous chicken repeat 1 (CR1, a non-LTR retrotransposon) copies relative to inferred ancestral CR1 sequences. We found genome sizes in GD birds were not different than those in FY birds, but the mean lengths of orthologous CR1 loci were significantly shorter in FY birds than in GD birds. Moreover, we observed a negative correlation between basal metabolic rate and length of orthologous CR1 loci. Finally, we observed positive correlations between body mass and both genome sizes as well as length of orthologous CR1 loci, which we expected given that body mass correlates negatively with metabolic rates. Our results support the contention that metabolism helps shape the avian TE complement and thus indirectly contributes to the compact genomes of birds.


P.45  The European Variation Archive At EMBL-EBI. Keane T*, EMBL-EBI; EVA Archive EVA, EMBL-EBI

EMBL-EBI has launched a brand new genetic variation resource: The European Variation Archive (EVA; www.ebi.ac.uk/eva). EVA archives all types of variation data from all species and currently, more than 40% of all data in EVA is from non-human species. We aim to provide a resource to the community that can accession, archive and provide views of genetic variation data more quickly and in a more granular manner than any other resource of this nature, worldwide. EVA predominantly archives genetic variation data in Variant Call Format (VCF) files, which is the community standard for describing and sharing variants. Importantly, EVA works with data submitters during the submission process, to ensure that archived data is truly valid and associated with rich metadata to ensure that these data are of most benefit to the community. Variants stored at EVA are annotated using a variety of standardized methods, including Ensembl's Variant Effect Predictor. We shall present the ways in which users can mine these data using filters on the website to construct both study-centric and global queries, filtering on any combination of species, methodology, variant type, phenotype, consequence and/or allele frequency and how results from these queries can be downloaded in a variety of formats including VCF and CSV. Additionally, EVA provides a comprehensive REST API web-service, to allow programmatic access, and hence the integration of these data with other resources such as Ensembl Variation and Uniprot, and this shall also be presented.


P.46  Multiple mouse reference genomes defines subspecies specific haplotypes and novel coding sequences. Keane TM*, EMBL-EBI; Mouse Genomes Project consortium MGP, many

Until the end of the 20th century the molecular basis for morphological, physiological, biochemical and behavioural variation in laboratory mice remained largely obscure. At the beginning of the 21st century, decoding the complete genome of one strain, C57BL/6J, the mouse reference genome, revolutionized our ability to relate sequence to function. The Mouse Genomes Project has recently completed the first draft assembled genome sequences and strain specific gene annotation for 16 laboratory and wild-derived mouse strains, spanning approximately 1.5M years of divergence. For genome annotation, we used a hybrid approach that combines evidence from the C57BL/6J Gencode annotation and strain specific transcript evidence (RNA-Seq and Pacbio cDNA) to identify and refine strain specific gene structures and alleles. We can now determine the underlying sequence and coding alleles in subspecies specific regions of the genome. We have identified over a hundred of these loci to date, finding enrichment in genes related to immunity, olfaction, and sensory function. We have completed detailed analysis of several highly divergent regions with known associations to pathogen infection and host defence, finding new protein coding alleles and haplotypes shared amongst subsets of the strains. These new strain gene sets have provided many updates to the C57BL/6J mouse reference genome, including genes that were previously completely missing or mis-annotated. Finally, by employing a transcript aware method for detecting truncating mutations, we revise downwards previous estimates of the number of null alleles in these strains relative to the C57BL/6J reference genome. Following on from this, we are now building genome sequences for other rodents species groups such as Onychomys and Acomys.


P.47  Speciation reversal in ravens: genomic evidence of mosaic genomes in western North America. Kearns AM*, Smithsonian Conservation Biology Institute; Restani M, St. Cloud State University; Szabo I, Cowan Tetrapod Collection, Beaty Biodiversity Museum, University of British Columbia; Marzluff JM, University of Washington; Fleischer RC, Smithsonian Conservation Biology Institute; Johnsen A, Natural History Museum, University of Oslo; Omland KE, University of Maryland Baltimore County

Reticulate speciation histories are emerging all across the tree of life. Here we explore a case of speciation reversal in the Common Raven (Corvus corax) wherein introgressive hybridization has caused two highly diverged lineages (Holarctic and California) to collapse into a single lineage with an admixed/mosaic genome across a broad contact zone in western North America. MtDNA estimates suggest the Holarctic and California lineages diverged ~2 million years ago. Using geographically extensive sampling from both zones of allopatry and sympatry we show that mtDNA, genome-wide SNPs, Z chromosome and autosomal introns all reconstruct strikingly concordant geographic signatures of speciation reversal in Common Ravens. Namely, we find (1) a region with pure Holarctic ancestry in Eurasia, Canada and eastern USA, (2) a region with almost pure California ancestry in southwestern US and Mexico, and (3) a broad region of admixed California/Holarctic ancestry across the western US. All datasets show clinal variation in the proportion of California/Holarctic ancestry along a north-south axis within the western US contact zone with higher frequencies of Holarctic ancestry in the north and California ancestry in the south. However, genomic SNPs, Z-linked and autosomal introns show more extensive northward introgression of California alleles compared to mtDNA. We also found that mtDNA and nuclear backgrounds were uncoupled at the individual-level within the western US. Suggesting that there is a lack of reproductive isolation and long-term interbreeding between the two Common Raven lineages throughout western North America. In contrast, our data suggest that Common Ravens maintain strong reproductive isolation with sympatric Chihuahuan Ravens (C. cryptoleucus), despite the fact that Chihuahuan Ravens are sister to the California lineage of Common Ravens in mtDNA.


P.48  Non-integrating Reprogramming of Mammalian Cells for Genome Resource Banking. Kehler J*, MTI-GlobalStem; Driscoll C, NIAAA, NIH; Roelke-Parker ME, Leidos, NIH; Reinbold R, Institute for Biomedical Technologies-CNR (Italy); Zucchi I, Institute for Biomedical Technologies-CNR (Italy); Barr C, NIAAA, NIH

The derivation of induced pluripotential cell (iPSC) lines from somatic cells undergoing Whole Genome Sequencing (WGS) provides a complementary resource for conservation and comparative genomic studies. Routine reprogramming of human patient cells is being used to capture the genetic diversity of individuals included in Genome Wide Association Studies (GWAS) to generate new cell models that can recapitulate developmental and disease processes in a dish. This strategy can be extended across genera to generate unlimited amounts of pluripotent cells from individual animals included in WGS projects. The conservation of identity of key transcription factors is sufficient that transduction with pseudotyped retroviral vectors expressing the human Oct4, Sox2, Klf4 and c-Myc cDNAs can reprogram somatic cells from a wide range of mammals without the need to clone species specific genes. One concern of this retroviral approach is that the putative iPSC lines can become transformed, due to incomplete silencing of the integrated transgenic proto-oncogenes preventing differentiation, as well as promoting the accumulation of aneuploidies. To overcome these technical hurdles, non-integrating reprogramming methods including transduction with mRNA viral vectors and daily transfection with synthetic mRNAs were compared and have proven effective in reprogramming fibroblasts from a range of canine, feline and Non Human Primate species. Of practical utility, these putative iPSC lines grow rapidly and can be cultured for over 15 passages, well beyond the point at which the parental fibroblast lines undergo senescence. The majority of putative iPSC lines derived by these non-integrating methods maintain a normal diploid karyotype by Giemsa banding. Standard in vitro and in vivo assays are underway to test the pluripotency of these cell lines. In addition, WGS is being performed on select samples to compare the genomes before and after reprogramming to make sure that no significant genetic drift has occurred in culture. RNA-based reprogramming provides a reproducible approach to generating viable cell models free of DNA-artifacts and can add value to current genome resource banking efforts.


P.49  Developing high-quality genomic resources for understudied classes of Mollusca. Kocot KM*, The University of Alabama; Varney R, The University of Alabama; Speiser D, University of South Carolina

Mollusca is the second most species-rich animal phylum and includes many economically, ecologically, and biomedically important species. Molluscs have evolved to produce a phenomenal range of biomineralized structures with a diversity of shapes, functions, and properties. The ability of molluscs to fabricate these intricate and robust structures from sea water, which is at least in part responsible for their great success, is well beyond human engineering capabilities. There has been progress in identifying and characterizing genes involved in biomineralization, but there remain fundamental gaps in our understanding of this process. Presently, fewer than ten molluscan genomes have been sequenced to date and, with the exception of Octopus, all are from gastropods or bivalves. In order to conduct comparative and evolutionary genomic analyses aimed at improving understanding of the evolution of molluscan genomes, particularly with respect to biomineralization, we are sequencing high-quality draft genomes from representatives of all remaining major lineages of Mollusca without available genomic resources. This includes Solenogastres (=Neomeniomorpha; Neomenia carinata and Wirenia argentea), Caudofoveata (=Chaetodermomorpha; Chaetoderma nitidulum), Polyplacophora (Chiton tuberculatus), Monoplacophora (Vema ewingi), and Scaphopoda (Antalis entails). Notably, some of these taxa (Solenogastres, Caudofoveata, and Polyplacophora) possess mineralized sclerites whose homology to the shells of gastropods and bivalves has not been firmly established. We are generating initial draft assemblies by sequencing 2 X 150 bp paired-end libraries on one-half to one lane of an Illumina HiSeq X and 2 X 125 bp ~3 kb and ~10 kb mate-pair libraries pooled on one lane of an Illumina HiSeq 2500 in high output mode. Because genome size varies greatly for these taxa (~0.3 Gbp for Neomenia versus ~3.5 Gbp for Antalis), further steps toward completing these genomes will be determined on a case by case basis. For taxa with particularly large genomes, optical mapping is planned. Once high-quality assemblies have been produced, gene model annotation will be performed using a total evidence approach (including transcriptome data) with the MAKER pipeline. The high-quality genomic resources produced by this work will be leveraged in our studies of the evolution of molluscan biomineralization. Further, these resources will be useful to numerous fields, especially neurobiology (where molluscs have long been used as models for the study of learning and memory) and evolutionary biology (as very few lophotrochozoan genomes are currently available for comparative studies).


P.50  Comparative population genomics of mimetic butterflies in the Neotropics. Kozak KM*, STRI; McMillan WO, STRI

Population genomics of rapidly evolving species offers a powerful lens to explain the rise of the astounding and endangered biodiversity in the Neotropics. Two such species are Heliconius erato and H. melpomene, which diverged 12 MYA and spread across the American tropics, where each displays a dazzling array of aposematic wing pattern variants. The two species are Muellerian mimics across their range, thus displaying both interspecific convergence and rapid intraspecific diversification. We use comparative population genomics to understand how the geographic mosaics of races arose. We hypothesise that the two radiations have not proceeded in parallel and we start to test this prediction by examining the demography and biogeography of H. erato. Through a series of expeditions we densely sampled the majority of races across the valleys and river catchments of the Neotropics, including critical material from the Amazon basin. Whole genome re-sequencing data for H. erato were aligned to the recently assembled reference and simulations were used to establish the optimal re-sequencing depth for accurate and cost-effective parameter estimation from further hundreds of individuals. A Bayesian phylogeographic analysis suggests that H. erato arose in allopatry three to four MYA, when it was isolated from its rare Amazonian sister species during the final phase of Andean orogeny in Colombia. Divergence was followed by spread into Central America over the recently established Isthmus of Panama and an invasion back into the Amazon basin. Demographic analyses of several populations reveal that eventually the most complex and recently developed rayed pattern races swept across the catchment, replacing several presently restricted phenotypes. Our study exploits an exceptional biogeographic sampling to lay the groundwork for a comparative analysis of rapid radiation and parallel evolution. More broadly, our research program will address several hypotheses about the drivers of evolution in the most biodiverse region of the planet.


P.51  Evolutionary genomics of the crustacean Triops cancriformis (Branchiopoda, Notostraca). Luchetti A*, University of Bologna; Mantovani B, University of Bologna

WHO? Triops cancriformis is a crustacean of the class Branchiopoda, order Notostraca. The order comprises only two genera (Triops and Lepidurus) world-wide distributed owing to their ancient origin. T. cancriformis lives in freshwater ponds that may be subjected to dry period during which the tadpole shrimps survive as encysted egg resistant stages. It is also well known for its high morphological stasis, compared with fossil forms; hence the debated status of "living fossil". WHY? Aside from the peculiar morphological stasis, T. cancriformis represents an interesting framework to address evolutionary studies: i) across its European range it is present with bisexual, parthenogenetic, hermaphroditic and androdioecious populations: it would be, thus, interesting to check whether different reproductive strategies leave genomic signatures such as differential evolutionary rates and/or transposable element accumulation; ii) Branchiopod crustaceans are phylogenetically close to Hexapoda, in most analyses resulting their sister clade. The study of T. cancriformis genomic features in comparison with those of early-branching Hexapoda could tell about the origin of hexapods and their most represented taxon, Insecta. HOW? Genomic resources on T. cancriformis and related species are slowly accumulating (transcriptomes, RAD-sequencing and one genome draft), although a comprehensive and co-ordinated project of a genomic evolutionary study is still lacking. We therefore, undertaken Illumina sequencing of T. cancriformis genomes, starting from Italian parthenogenetic samples and Spanish bisexual ones. Moreover, we included two species from the related genus Lepidurus (L. apus lubbocki and L. arcticus) in order to have a clearer picture of Notostraca genomes. Further sequencing will be performed on transcriptome and already published data will be also included in the analyses. TO GET WHAT? A total evidence picture on the hardwares (genomes) and softwares (transcriptomes) evolution, with a special focus on repetitive DNA (transposable elements and satellite DNA), in the same species presenting genomes subject to different reproductive milieau. We have already some results indicating that transposable elements (R2 lineages) are differently evolving in different T. cancriformis genomes. The full genome sequencing of further population/species will help drawing a more complete picture, including the possibility to study all transposable element lineages as well as satellite DNAs. Moreover, the strengthening of the genomic dataset with new branchiopod species will likely result in a more stable phylogenetic relationship of Branchiopoda with closer taxa. Finally, we will get knowledge on the genome structure and composition that will be compared with the close relatives, the Hexapoda.


P.52  Plans for scaling vertebrate genome sequencing and assembly at the Sanger Institute. McCarthy SA*, Wellcome Trust Sanger Institute; Dolle D, Wellcome Trust Sanger Institute; Malinsky M, Wellcome Trust Sanger Institute; Svardal H, Wellcome Trust Sanger Institute; Klarqvist M, Wellcome Trust Sanger Institute; Quail M, Wellcome Trust Sanger Institute; Howe K, Wellcome Trust Sanger Institute; Chow W, Wellcome Trust Sanger Institute; Keane T, Wellcome Trust Sanger Institute; Durbin R, Wellcome Trust Sanger Institute

During 2017 the Wellcome Trust Sanger Institute plans to ramp up efforts to produce high quality assemblies for hundreds of vertebrate genomes in association with the Genome 10K Project. We are selecting species so as both to extend phylogenetic breadth, and to enable strong comparative genomics research by concentrating some effort on a few clusters of related species and samples. Our initial focus will be on fish, mouse and caecilian species. We will present preliminary results from the cichlid fish Astatotilapia calliptera, several strains of zebrafish Danio rerio and the grasshopper mouse Onychomys torridus. Sequencing and assembly technologies are advancing rapidly, so we are actively evaluating a range of sequencing technologies from PacBio, Oxford Nanopore, 10X Genomics, BioNano and Illumina with the aim to consistently achieve reference quality genomes with greater than 1Mb contig N50, 10Mb scaffold N50 and 90% DNA assignment to chromosomes. We are exploring a novel approach to contig scaffolding using linkage disequilibrium from population variation data to order and orient contigs. Finally, we are collaborating with the European Bioinformatics Institute to streamline data deposition into the relevant archives, and ensure efficient gene annotation and presentation in Ensembl.


P.53  The fungal half of the mycorrhizal equation: comparing the fungal genes related to orchid and other plant mycorrhizal associations. McCormick M.K.*, Smithsonian Environmental Research Center; Whigham D.F., Smithsonian Environmental Research Center

Understanding the plant symbiotic toolkit, those genes responsible for successful establishment of symbiotic associations, has made great strides in recent years, with the successful identification of a suite of genes that are important for the formation of mycorrhizal associations leading the way. However, the effort to identify the fungal genes that are needed to interact with the plant symbiotic toolkit is only just beginning. Mycorrhizal associations are present in >80% of land plants and are critical for plant acquisition of nutrients and water and defense against pathogens. They also play an important role in carbon cycling and soil carbon storage. Orchid mycorrhizal associations differ from other dominant types of mycorrhizae in that they are generally obligate for the plants, but not for the fungi, and orchids are generally thought to parasitize their fungi. We sequenced the genomes of two fungi in the most common orchid mycorrhizal genera, Tulasnella and Ceratobasidium, and combined these with transcriptomes of the fungi growing axenically and as part of orchid mycorrhizae. The genomes of both fungi are distinguished from ectomycorrhizal, endophytic, and saprotrophic fungi by the types and copy numbers of copper oxidase and glycosyl hydrolase genes. Unlike ectomycorrhizal fungi and arbuscular mycorrhizal fungi, which are strongly dependent on their plant hosts, orchid mycorrhizal fungi do not show a loss of plant cell wall degrading enzymes, with gene abundance patterns that appear more similar to endophytes and ericoid mycorrhizal fungi than to ectomycorrhizal or arbuscular mycorrhizal fungi. In orchid mycorrhizal fungi, genes that were down-regulated in mycorrhizal associations, compared to in axenic hyphae, were especially distinct from genes identified as down-regulated in other types of mycorrhizal associations, but the functions of those genes are currently poorly characterized. Because orchid mycorrhizae are so different from other types of mycorrhizae, identifying the fungal genes that support orchid mycorrhizae will allow a better understanding of the different ways symbiotic associations can form. Both fungal genera include a wide range of ecological groups, including plant endophytes, pathogens, and ectomycorrhizal fungi, in addition to saprotrophs and orchid mycorrhizal fungi, providing excellent opportunities to compare gene expression among related, but functionally distinct, fungi in the future.


P.54  Genome-scale data sets yield new insights into the evolution and genomic basis of beetle diversity. McKenna D.*, University of Memphis

The order Coleoptera (beetles) contains more than 400,000 described extant species. The causes of this apparent 'inordinate fondness' (Hutchinson 1959) are widely debated, but the evolution of specialized trophic interactions with plants is thought to have played an important role. I will begin my talk by introducing higher-level phylogenies for the order Coleoptera and some of its largest and most species rich lineages, based on analyses of phylogenomic data obtained via whole genome sequencing, RNA-Seq, and anchored hybrid enrichment. I will then briefly discuss timing and patterns of ecological and taxonomic diversification in beetles, with special reference to the evolution of phytophagy (plant-feeding) and the apparent role of plants in beetle diversification. Finally, I will discuss the genomic basis and evolution of phytophagy in the Phytophaga (leaf beetles, longhorned beetles, and weevils) ' arguably the most species rich lineage of beetles. Using results from the Asian longhorned beetle genome project (a collaboration with the insect 5,000 genomes project), I will highlight how new discoveries revealed by genome sequencing, annotation, and comparative genomic study are refining and changing our views of beetle evolution. For example, I will discuss how amplification and functional divergence of genes associated with specialized phytophagy, including genes originally obtained via horizontal gene transfer from fungi and bacteria, have contributed to the addition, expansion and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Taken together, these studies illustrate how systematics, genomics and other subdisciplines of biodiversity science are converging around new data, methods and broadly collaborative research efforts to reveal the evolutionary history and genomic basis of insect diversity.


P.55  Global change rapidly alters foundation species intraspecific diversity and identity. Mozdzer TJ*, Smithsonian Environmental Research Center & Bryn Mawr College; McCormick MK, Smithsonian Environmental Research Center; Bauer CE, Villanova University; Bowen J, Northeastern University; Deegan LA, Woods Hole Research Center; Megonigal JP, Smithsonian Environmental Research Center

Global change factors such as nutrient pollution and elevated CO2 concentrations are known to have strong effects on organisms, altering community dynamics and leading to changes in biodiversity. While the influences of global change on species diversity are well-studied, the influences of global change factors on intraspecific genetic variation are generally understudied. This lack of information at the species-level, especially within clonal foundation species, hampers our ability to understand the response of ecosystems to interacting global change factors, given that intraspecific genetic diversity can be even more important than interspecific diversity with respect to ecosystem function. To evaluate the influences of current and near-future global change on ecosystem function, we examined the effect of nutrient pollution and elevated CO2 concentrations, on genetic composition and genetic diversity in two clonal foundation species, Spartina alterniflora and Phragmites australis, in two long-term global change experiments. S. alterniflora was exposed to nitrogen pollution at the landscape level for up to nine years in a salt marsh in Massachusetts, and P. australis was exposed to both elevated nitrogen and elevated carbon dioxide concentrations for three years in an open top chamber experiment at the Smithsonian Global Change Research Wetland. We found that both nitrogen and CO2 acted as a strong environmental filter decreasing intraspecific genetic diversity and genetic identity in both experiments as little as three years, and this decrease in genetic diversity was magnified over time. Reference treatments in both experiments maintained starting levels of intraspecific genetic diversity and genetic identity. Furthermore, in the P.australis experiment we found there may be inherent genetic tradeoffs in the ability of individual genotypes to respond to multiple global change factors, such that any genotype can only respond positively to only one global change factor, but not both. Over this same time period, we observed changes in S. alterniflora functional traits (e.g. flowering phenology) that may be genetically inherited. It is still unclear whether these changes in plant traits are a result of phenotypic plasticity or whether environmental filtering has favored particular genotypes. Our data suggest that global change will serve as an environmental filter that, in the short-term, will likely result in less diverse plant populations and may inadvertently select for individuals that are less resilient to interacting global change factors, potentially jeopardizing ecosystem services.


P.56  Lost and Found: Tuatara ND5 Gene Identified . Buring ES*, Smithsonian Institution; Gonzalez VL, Smithsonian Institution; Mulcahy DG, Smithsonian Institution

Tuatara (Sphenodon punctatus) are relict reptiles that possess uniquely configured mitochondrial genomes, with several gene rearrangements, lacking the ND5 gene, and two tRNAs. Because the presence of a functional ND5 gene is essential for cellular respiration, it is conceivable it transferred to the nuclear genome in the evolutionary history of Sphenodon, or there is a free-floating ND5 gene in the cytosol. Here, we report the identification of a putative ND5 gene from a previously published SRA transcriptome of tuatara. However, this ND5 gene does not appear to be located inside the mitochondrial genome, which suggests a nuclear or cytosolic location of ND5 in Sphenodon. This ND5 gene translates to amino acids only under the vertebrate mitochondrial genetic code; stop codons are present under the standard code. Our assembly coverage of the putative tuatara ND5 gene from the transcriptome library contains a partial tRNA-Leu at the 5' end and abruptly terminates at the 3' end. We were unable to find any flanking regions that would identify the location of the sequence within the tuatara genome. We conducted several phylogenetic analyses among Chordates using protein-encoding mitochondrial genes, including ND5, and a concatenated mitochondrial gene tree to verify the authenticity of the putative tuatara ND5 gene. Mitochondrial DNA deterioration and mutations are known to be associated with aging and certain diseases in humans, respectively. Transfer of the ND5 gene to the nucleus, or simply its removal from the mitochondrial genome, may be partly responsible for the unusual longevity of tuatara. We discuss the implications of the removal of ND5 from the tuatara mitochondrial genome, and conjecture on the evolutionary origin of this event.


P.57  Identification and characterization of SNP markers for the Columbia Basin pygmy rabbit (Brachylagus idahoensis). Nerkowski SN*, University of Idaho; Hohenlohe PA, University of Idaho; Waits LP, University of Idaho

Brachylagus idahoensis, the pygmy rabbit, is the smallest rabbit in North American and is unique among rabbits due to its ability to consume sagebrush, which is toxic to most mammals. Loss and fragmentation of habitat due to agricultural conversion has led to the near extirpation of the disjunct pygmy rabbit population in the Columbia Basin. In 2001, the Columbia Basin pygmy rabbit, in the state of Washington (WA), was listed as an endangered distinct population segment under the Endangered Species Act. Sixteen Columbia Basin pygmy rabbits were taken from the last remaining population in Sagebrush Flats, WA to start a captive breeding program. To achieve the recovery goal of re-establishing a free-ranging population, 111 rabbits from other states were added to the captive breeding population and moved to semi-wild breeding enclosures at Sage Brush Flats, WA in 2012. Since then, nearly 1900 mixed ancestry rabbits have been released into the wild. Currently, nuclear DNA microsatellite analyses are being used to examine the genetic diversity and estimate Columbia Basin ancestry in the captive and wild populations. To provide further insight into genomic diversity, genetic structure, individual ancestry and local adaptations within each founding group, we have used RAD sequencing to generate the first genome-wide set of single nucleotide polymorphism (SNP) markers for this species. We applied a single-digest RADseq protocol, designed to interrogate roughly 80,000 loci, to 114 pygmy rabbit samples from the source populations in Columbia Basin, Utah, Nevada, Oregon, Wyoming, and Idaho. We aligned RADseq data to the European Rabbit (Oryctolagus cuniculus) genome and identified genotypes at SNP loci associated with each source population. These markers will allow us to assess ancestry, test for adaptive variation, and genetically monitor captive and wild populations of Columbia Basin pygmy rabbits to guide strategies for conservation and management.


P.58  Comparative genomics of procyonids: testing alternative de novo assembly methods and their impact on genome annotation. Tsuchiya MTN*, Smithsonian Institution and George Mason University; Dikow RB, Smithsonian Institution; Koepfli K-P, Smithsonian Institution; Frandsen PB, Smithsonian Institution; Rockwood LL, George Mason University; Kays RW, North Carolina State University and NC Museum of Natural Sciences; Helgen KM, Smithsonian Institution; Maldonado JE, Smithsonian Institution

Here we present the whole genome sequences for the raccoon (Procyon lotor) and the kinkajou (Potos flavus). Kinkajous are the most divergent lineage within the Procyonidae (Mammalia, Carnivora), with the separation from the remaining genera estimated to have occurred around 20 million years ago. Raccoons and kinkajous differ in their social behavior (female philopatry in raccoons vs. male philopatry in kinkajous), food habits (generalist vs. frugivorous specialist) and habitat (temperate vs. tropical). These two species are the first procyonids to have their genomes sequenced, filling a gap of about 30 million years to the next closest relative for which a genome has been generated. In this study, we compared different de novo assembly strategies and their effect on genome annotation. Our initial de novo assembly results using ALLPATHS-LG indicated a very fragmented assembly, with a large number of very small contigs (kinkajou N50 contig size = 10,507; raccoon contig N50 = 5,969). Since both species have large population sizes, and to the extent of our knowledge were not inbred, we decided to test de novo assemblers better suited to deal with high levels of heterozygosity. We compared the results of the initial ALLPATHS-LG assembly with those implemented in Platanus and MaSuRCA. Summary statistics such as the number of contigs, contig size, N50 and other metrics were evaluated using QUAST (Quality Assessment Tool for Genome Assemblies). Genome completeness and contiguity were assessed using BUSCO (Benchmarking Universal Single-Copy Orthologs). We annotated all three assemblies for each species in order to assess how different assemblies impact the annotation quality. Genome annotation was performed using the MAKER pipeline, which includes a number of tools such as BLAST, Exonerate, SNAP, and Augustus. Our overarching goal is to understand the effect of different assembly de novo strategies in genome contiguity and completeness in non-model organisms so that we have the most robust data on which to base biological hypotheses and to propose an approach to improve the quality of existing draft genome assemblies and annotation even without additional sequence data.


P.59  National Center for Biotechnology Information's (NCBI) Eukaryotic Genome Resources. O'Leary N. A.*, National Center for Biotechnology Information, U.S. National Library of Medicin; Murphy T. D., National Center for Biotechnology Information, U.S. National Library of Medicin; Pruitt K. D., National Center for Biotechnology Information, U.S. National Library of Medicin

The availability of high quality annotated reference genomes from a broad range of taxa is an increasingly essential tool for comparative genomic research. NCBI's Eukaryotic Genome Annotation Pipeline (www.ncbi.nlm.nih.gov/genome/annotation_euk/) integrates genomic, transcript, and protein sequence records, including RNA-seq data available in SRA, to comprehensively annotate public genome assemblies submitted to NCBI's Assembly resource (www.ncbi.nlm.nih.gov/assembly). These genome annotations are maintained and periodically updated through NCBI's Reference Sequence (RefSeq) Project. For some taxa, RefSeq curators augment genome annotations using input from expert communities, published functional data and, when available, other sources of functional genomic information. RefSeq curation takes advantage of the rich datasets available from relevant well-studied organisms (human, mouse, fruit flies, zebrafish) to inform the annotation of less studied genomes. To date, the genomes of more than 300 taxa ranging from invertebrates and plants to mammals have been annotated through this pipeline. This poster will describe some of the computational and manual curation procedures used in NCBI's genome annotation process, as well as the criteria that new genome assemblies must meet to benefit from NCBI's annotation efforts. We will also provide guidance on how to access and utilize these resources.


P.60  Genomics of symbiosis driven developmental transition in the scyphozoan jellyfish Cassiopea . Ohdera A*, Pennsylvania State University; Fitt W, University of Georgia; Diaz-Almeyda E, Emory University; Steinworth B, University of Florida; Martindale M, University of Florida; Medina M, Pennsylvania State University

The upside-down jellyfish Cassiopea xamachana forms a mutualistic association with the dinoflagellate Symbiodinium, requiring the symbiosis for its nutritional benefits. The jellyfish also undergoes a metamorphic transition known as strobilation that is triggered upon successful infection by Symbiodinium. Unlike non-symbiotic scyphozoans, the jellyfish will remain in the polyp stage until infection occurs, providing a unique opportunity to study symbiosis driven development. In order to understand the genetics driving strobilation, we sequenced the transcriptome during infection and strobilation to determine the differentially expressed genes that may shed light on the molecular interaction occurring between host and symbiont. In addition to the transcriptome, we have also begun assembly of the Cassiopea xamachana genome. The retinoic acid pathway appears to be involved in the metamorphosis of non-symbiotic scyphozoans, with the retinoic X receptor (RxR) and retinol dehydrogenase being differentially expressed during the transition, in addition to scyphozoan specific hormones. The involvement of the homologs of the RxR gene in insects and amphibians suggests a conserved role for the pathway. Our transcriptome data does not show genes of the retinoic acid pathway in Cassiopea to be differentially expressed, suggesting an alternative mechanism driving strobilation. Instead, other genes of unknown function were differentially expressed, in addition to several canonical developmental genes. Thus, we have begun testing candidate genes through whole-mount in situ hybridization to confirm the non-involvement of the retinoic acid pathway in Cassiopea strobilation and determine alternative pathways that may have been co-opted to regulate the transition. Thus, the data suggests symbiosis may have a role in driving changes to the developmental regulation in scyphozoans.


P.61   Investigating cooperativity between the ZBTB18 transcriptional repressor and pRb tumor suppressor in neural development and brain tumor pathogenesis. Ortega-Gomez V*, Iowa State University; Schultz L, Iowa State University; Solin S, Iowa State University; Haltom J, Iowa State University; Torrie M, Iowa State University; McGrail M, Iowa State University

The decision to adopt a specific fate is a fundamental property of cells during animal development that involves the coordinated suppression of genetic programs to limit division and activation of genetic programs to promote differentiation. Both processes of proliferation and differentiation are disrupted in malignant human cancer. The ZBTB18 gene encodes a transcriptional repressor that is known to regulate neural progenitor proliferation, neural differentiation and neuronal migration in the developing mouse brain (Baubet et al., 2013; Hirai et al., 2012). The goal of this project is to test the hypothesis that ZBTB18 cooperates with the pRB tumor suppressor to regulate genetic programs that ensure proper neural progenitor proliferation and differentiation and suppress brain tumor oncogenesis. Our lab has recently shown that somatic inactivation of the pRB tumor suppressor leads to highly proliferative brain tumors in adult fish with features of primitive neuroectodermal tumors (Solin et al., 2015). The tumors appear to originate from proliferative zones where ZBTB18 is expressed in normal brain. Transcriptome analysis of pRB-defective tumors shows the level of ZBTB18 gene expression is down >10 fold. Together these data support the hypothesis that ZBTB18 cooperates with pRB to regulate neural progenitor proliferation and suppress tumor formation. Our hypothesis predicts that mutations that disrupt ZBTB18 function will enhance the pRB mutant phenotype, leading to increased numbers of proliferating cells in the brain of pRB rb1/rb1 homozygous mutants. To test our hypothesis we will target mutations to ZBTB18 gene zbtb18 in rb1/rb1 mutant zebrafish embryos using CRISPR/Cas9 genome editing. The number of proliferating cells will be measured in larval brain tissue sections of targeted animals and compared to the number in non-targeted pRB rb1/rb1 homozygous mutants. These studies will provide insight into the mechanism by which pRB suppresses tumorigenesis through control of gene expression programs that limit proliferation and promote neural differentiation.


P.62  The Barcode of Wildlife Project: Enforcing Endangered Species Laws with DNA Barcodes. Trizna M, CBOL/SI; Redmond NE*, CBOL/SI

The Barcode of Wildlife project (BWP) was funded by a Google Global Impact Award to the Consortium for the Barcode of Life (CBOL) at the Smithsonian Institution in 2012. The main aims of this project were to demonstrate the value of DNA barcoding in the fight against wildlife crime, and to help up to six international partner countries implement DNA barcoding as a sustainable tool for species protection. To date, Kenya, Mexico and South Africa have reached Phase 3 of the project, and Nepal and Ecuador are in earlier phases. DNA barcoding as a forensic tool involves the sequencing of one or more short marker genes in order to compare against a high quality reference library of taxonomically identified species. Endangered and protected species are, by their nature, more difficult to obtain and sequence, so the BWP aimed to construct a reference BARCODE library to support the priority endangered species that are most often targeted for poaching. CBOL worked with scientific experts and law enforcement officials from each partner country to build their custom list of priority species to barcode. The lists contained 200 priority species of endangered plants and animals that are most commonly being poached and trafficked in each country. In addition, close relatives and look alikes of each species were also added, to ensure that the reference library contained the most comprehensive representation as possible. CBOL also coordinated meetings with scientific experts and law enforcement officials to develop expanded specimen metadata standards and SOPs that deal with collecting, chain-of-custody, and lab procedures. To ensure that the expanded specimen metadata standards were met, CBOL built a custom informatics pipeline that was comprised of a Field Information Management System (FIMS), a Lab Information Management System (LIMS), and a tracking system that connected the two. CBOL then trained the scientists in each country on the DNA barcoding workflow, and how to use the informatics pipeline at each step of the process. Through the first 2 phases of the project, the countries have generated and published over 3,000 high quality sequence records to GenBank, and DNA barcoding has been utilized in investigations and prosecutions of wildlife crimes.


P.63  Kickstarting the Beaver Genome: a Community-Based Genome Project. Rhodes A*, Oregon State University; Kronmiller B, Oregon State University; Tyler B, Oregon State University; Jaiswal P, Oregon State University; Ramsey S, Oregon State University; Epps C, Oregon State University; Hendrix D, Oregon State University; Loehr C, Oregon State University; Elser J, Oregon State University; Beaver Genome Science Consortium , Oregon State University

The North American beaver (Castor canadensis) is a keystone species of Northwest riparian ecosystems. Beavers thrive in a wide range of wetlands habitats due to their variety of unique behavioral, musculoskeletal, metabolic, and dietary adaptations. With their dam-building behavior beavers contribute to species and habitat diversity. The beaver is a symbol of the industrious and pioneering spirit of Pacific Northwesterners and is the Oregon state animal and as the mascot of Oregon State University (OSU). Genetic studies of wild beaver populations and efforts to understand its biological adaptations are hampered by the lack of a beaver genome. The OSU Center for Genome Research and Biocomputing (CGRB) has crowd-funded $30,000 to sequence and annotate the beaver genome, to obtain a tissue transcriptome atlas, and to profile the gut micro biome. Using Illumina sequencing we have assembled a 4 Gb beaver genome (N50 300Kb). We have completed a 17 tissue composite transcriptome assembly. We will present results of repeat element identification, gene prediction, gene annotation, non-coding RNAs, and orthology. Phylogenetic analysis of an alignment of whole-genome orthologous proteins from 19 species shows that beaver is found in the rodent group alongside kangaroo rat. Shotgun metagenomes from beaver stool samples were functionally annotated to profile the metabolic capacity of the gut micro biome. Sequencing the Beaver Genome has brought the diverse Oregon State University community together, providing an opportunity for collaborative science between 8 colleges, 27 departments, and students from undergraduate through Ph.D. This presentation will also talk about this community effort.


P.64  Phylum-level comparison of nuclear genome size diversity among understudied marine invertebrate groups. Roebuck KS*, Nova Southeastern University; Lopez JV, Nova Southeastern University; Messing CG, Nova Southeastern University; Grant SG, Nova Southeastern University

Invertebrates represent the vast majority of faunal diversity on the planet and to a greater extent, the marine environment, but most remain inaccessible and understudied. The burgeoning field of genomics can provide a substantial amount of information on the biology of understudied invertebrate taxa. Genome size analysis can help reevaluate evolutionary relationships, provide basic information on genomes, and resolve phylogenetic discrepancies that may be controversial. Moreover, genome size estimates will soon be a necessary co-requisite for high-throughput DNA sequencing projects, such as those affiliated with the Global Invertebrate Genomics Alliance (GIGA-cos.org). Genome sequences illuminate adaptations, such as how marine organisms transitioned to new environments. Technically, genome size estimates can help avoid unnecessary, expensive sequencing of genomes too large for current methods (>3 Gb). Metazoan genome size data is easily accessible through the Animal Genome Size Database (genomesize.com), which serves a hub for data on multiple animal groups. However, the current rapid progress in genome sequencing technology and its capabilities is quickly outpacing the rate at which new data can be entered and publicly accessed in the database, an exciting dilemma nonetheless. Genome projects focusing more intensely on marine invertebrates will help to shift the attention to more accurately reflect the vastness of invertebrate diversity, specifically within our oceans. Flow cytometry (FCM) is a widely used, reliable, and accurate means of estimating genome sizes, which yields valid measurements in this recent studies focusing on marine invertebrates. FCM quantifies genome size by measuring fluorescence from nuclei that have been saturated with DNA-binding dyes, such as propidium iodide (PI). Genome sizes of unknown species are quantified by comparison to known genome sizes of standard species (e.g., chicken, rainbow trout).


P.65  Increased taxon sampling reveals thousands of hidden orthologs in flatworms. Martín-Durán JM, Sars International Centre for Marine Molecular Biology; Ryan JF*, Whitney Laboratory for Marine Bioscience; Vellutini BC, Sars International Centre for Marine Molecular Biology; Pang K, Sars International Centre for Marine Molecular Biology; Hejnol A, Sars International Centre for Marine Molecular Biology

Gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the complement of an organism consists of hidden orthologs, those with no apparent homology with commonly sequenced animal lineages, mistakenly considered new genes but actually representing rapidly evolving orthologs or undetected paralogs. Here, we describe Leapfrog, a simple automated BLAST pipeline that leverages increased taxon sampling to overcome long evolutionary distances and identify hidden orthologs in large transcriptomic databases. As a case study, we used 35 transcriptomes of 29 flatworm lineages to recover 3,427 hidden orthologs. Unexpectedly, we do not observe a correlation between the number of hidden orthologs in a lineage and its 'average' evolutionary rate. Hidden orthologs do not show unusual sequence composition biases (e.g. GC content, average length, domain composition) that might account for systematic errors in sequence similarity searches. Instead, gene duplication with divergence of one paralog and weak positive selection appear to underlie hidden orthology in Platyhelminthes. By using Leapfrog, we identify key centrosome-related genes and homeodomain classes previously reported as absent in free-living flatworms, e.g. planarians. Altogether, our findings demonstrate that hidden orthologs comprise a significant proportion of the gene repertoire in flatworms, qualifying the impact of gene losses and gains in gene complement evolution.


P.66  A complete de novo genome and population genomics study of the mountain lion. Saremi NF*, UC Santa Cruz; Schaefer NK, UC Santa Cruz; Shapiro B, UC Santa Cruz; Green RE, UC Santa Cruz; Wilmers CC, UC Santa Cruz; Eizirik E, PUCRS; Marqui P, University Sao Paolo; Coutinho L, University Sao Paolo; Stahler D, National Parks Service; Dalen L, Swedish Museum of Natural History

The mountain lion (Puma concolor), commonly called puma or catamount, is a large felid species that once occupied much of North and South America. Their movements and habits have been studied extensively through geo-tagging. Genomic analysis for mountain lions has been limited to mitochondrial DNA and feline-specific microsatellite loci. We present a complete genome assembly of a wild mountain lion from Santa Cruz, California and resequencing data from a panel of mountain lions from North and South America. The data show that genetic variation within geographic regions can vary widely. We confirm that North American mountain lions harbor less genetic variation than seen in South American mountain lions.


P.67   The Genomes of Luminous Organisms (GLO) Initiative. Schultz D*, University of California Santa Cruz, Monterey Bay Aquarium Research Institute; Shapiro B, University of California Santa Cruz; Green R, University of California Santa Cruz; Haddock S, Monterey Bay Aquarium Research Institute (MBARI)

We have begun a whole-genome sequencing initiative of luminous species distributed across the tree of life. Until recent years, molecular research of bioluminescent organisms was largely confined to single-gene and transcriptome-level studies. These techniques have yielded a large body of knowledge of photoproteins and luciferases in many taxa, yet the molecular biology of bioluminescence in many clades remains a mystery. Currently, very few genomes of bioluminescent organisms have been published, limited to the ctenophore Mnemiopsis leidyi [1], the larvacean Oikopleura dioica [2], the acorn worm Ptychodera flava [3], and several bioluminescent bacteria [4]. These genomes have contributed to our understanding of the developmental biology and evolutionary history of each respective lineage. In the case of ctenophores, this information has contributed to the search for luciferin biosynthesis genes. We selected a list of 100 species that represent the diversity of bioluminescent organisms in the tree of life. In selection, we prioritized animals that are common, easy to collect with available technologies, and have a precedent for scientific study. To facilitate comparative studies, several of these species we selected are closely-related non-luminous species. This session aims to illustrate our progress in sequencing these genomes, as well as to solicit further collaboration in sample collection, sequencing, annotation, and analysis. [1] Ryan JF, Pang K, Schnitzler CE, et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science. 2013;342(6164):1242592. [2] Denoeud F, Henriet S, Mungpakdee S, et al. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science. 2010;330(6009):1381-5. [3] Simakov O, Kawashima T, Marlétaz F, et al. Hemichordate genomes and deuterostome origins. Nature. 2015;527(7579):459-65. [4] Ruby EG, Urbanowski M, Campbell J, et al. Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with pathogenic congeners. Proc Natl Acad Sci USA. 2005;102(8):3004-9.


P.68  Conserved oxygen sensing mechanism in the marine fireworm, Hermodice carunculata (Annelida: Amphinomidae) inferred from RNA-Seq data. Schulze Anja*, Texas A&M University at Galveston

Survival and growth of most eukaryotic organisms depend on oxygen, although tolerance thresholds for oxygen depletion vary greatly among species. To sense environmental oxygen levels, all animals studied to date utilize a conserved molecular cascade in which transcription factors known as Hypoxia Inducible Factors (HIFs) play a key role. HIFs and other components of the oxygen sensing cascade have been extensively studied in humans and other vertebrates as well as in some invertebrate model organisms. However, with the exception of some molluscs, these studies have largely overlooked the lophotrochozoan/spiralian clade. Lophotrochozoans/spiralians are significant contributors to biomass and diversity in shallow water benthic communities. Considering the increasing number, extent and severity of hypoxic zones in our changing oceans, understanding the responses of lophotrochozoan species to hypoxia is an essential step to predicting ecosystem responses. This is the first study to demonstrate the expression of several key genes involved in oxygen sensing in an annelid, the amphinomid polychaete Hermodice carunculata, a common corallivorous species with a distribution throughout the tropical and temperate Atlantic, Caribbean, Gulf of Mexico, Mediterranean and Red Seas and a wide range of environmental tolerances. First, RNA-Seq data for H. carunculata, generated on an Illumina HiSeq platform, were assembled. The assembly was then used as a database to search for the relevant genes using mollusc, crustacean and vertebrate sequences as bait. The Open Reading Frames of the hit sequences were extracted and analyzed for their domain structure. Using this procedure, genes for the alpha and beta subunits of HIF and the enzymes HIF Prolyl Hydroxylase and Factor Inhibiting HIF were identified in the H. carunculata transcriptome and exhibit a conserved domain structure. Future studies will determine the thresholds at which the HIF cascade is activated as well as identify downstream genes in the hypoxia response of H. carunculata.


P.69  Deep-sea, deep sequencing: challenges in de novo sequencing of the demosponge Geodia barretti. Steffen K*, Uppsala University, Department of Medicinal Chemistry, Division of Pharmacognosy; Cárdenas P, Uppsala University, Department of Medicinal Chemistry, Division of Pharmacognosy

In theory, that is from an economical and technological point of view, whole genome de novo sequencing projects are feasible for an ever-increasing number of organisms. However, one of the key difficulties when not working with non-model organisms is obtaining high-quality DNA. Long-read sequencing technology requires large amounts of contaminant-free high molecular weight DNA as library input. The use of readymade kits to extract this DNA presents a static solution amenable for many standard tissues and model organisms but allows for little to no adaptation for systems containing degrading enzymes, inhibitory chemical compounds or particularly fragile DNA. Revisiting the early extraction protocols and techniques allows for individual assessment, adaptation and optimization of DNA extraction and storage. Here, we use a pre-treatment of frozen tissue with EDTA to inactivate DNA degrading enzymes, centrifugation to roughly separate host and bacterial cells followed by a traditional Phenol:Chloroform fractionation to obtain high quality genomic host DNA. Thereby, we present a strategy for isolating selected, chemically pure, high-molecular weight DNA from the deep-sea north Atlantic sponge Geodia barretti. The procedure yields DNA confirming to high-quality standards required for long-read sequencing (library input >20 ng; purity, measured by absorbance 260/280: 1,8'2,0; 260/230: 2,0'2,2; DNA fragment size > 40 kb) enabling de novo whole genome sequencing in the marine animal. Individual adaptation of classical DNA extraction protocols thus yields high-quality DNA for organisms posing challenges in the molecular genetics workflow.


P.70  Gene flow in the twilight zone: assessing genetic connectivity of a depth generalist coral species across shallow and mesophotic reef ecosystems in the Gulf of Mexico and Caribbean . Studivan MS*, FAU Harbor Branch; Voss JD, FAU Harbor Branch

Successful management of spatially extensive marine environments is contingent on an understanding of the ecological connections across populations. Mesophotic coral ecosystems (MCEs) have been identified and characterized as reef environments between 30-150m with coral communities similar to those found on shallow reefs. Despite an increasing area of identified mesophotic habitat, population dynamics of coral species across depths are relatively unknown. Early research into the ecological role of MCEs proposed that deeper reefs may act as a coral refuge by providing larvae to nearby shallow reefs. A key question underlying this theory remains unanswered, specifically how well are MCEs connected to shallow reefs? In conjunction with benthic community characterization across mesophotic habitats in the Gulf of Mexico, microsatellite genotyping was employed to investigate genetic connectivity of Montastraea cavernosa, a ubiquitous depth-generalist species. A series of upstream and downstream reef sampling sites were chosen in the Gulf of Mexico and Caribbean that correspond to dominant oceanographic current patterns, including Carrie Bow Caye, Belize, the Flower Garden Banks National Marine Sanctuary (FGBNMS) and outlying Coral Habitat Areas of Particular Concern (CHAPCs), Pulley Ridge CHAPC, and the Dry Tortugas Ecological Reserve. Additionally, coral sampling was conducted across shallow (15-25m) and mesophotic (30-45m) habitats within sites where applicable. Microsatellite genotyping suggests relatively high levels of gene flow between FGBNMS banks and relatively open coral populations across the Caribbean and SW Florida, consistent with strong current patterns and availability of reef habitats in the Gulf of Mexico. Genetic differentiation in the Pulley Ridge population indicates relative isolation of M. cavernosa from other sites in the Gulf. This research is designed to provide data for improved regional management of deeper coral reef ecosystems and collaborative marine research with NOAA partners through the Cooperative Institute for Ocean Exploration, Research, and Technology (CIOERT). Specifically, these data contribute to a proposed expansion of the Flower Garden Banks NMS boundaries from 90 to over 600 square kilometers of protected habitat, the majority of which includes mesophotic reef environments. Detailed benthic surveys combined with targeted molecular methods for characterizing mesophotic coral communities can contribute to the development of effective management strategies for these ecologically important, but threatened, coral reef ecosystems throughout the Tropical Western Atlantic.


P.71  Effects of taxon sampling on phylogenetic stability and speciation rates. Superson A.*, Oakland University, Department of Biological Sciences; Culver M., Oakland University, Department of Mathematics and Statistics; Phelan D., Oakland University, Department of Biological Sciences; Spagnuolo A., Oakland University, Department of Mathematics and Statistics; Battistuzzi F. U., Oakland University, Department of Biological Sciences

The Tree of Life (TOL) is a graphic reconstruction of the evolutionary history of the vast diversity of extant species providing a value tool to understanding how speciation events shaped our Earth. The expansion in genomic data from enhanced sequencing technologies carried an expectation that evolutionary reconstruction models would converge towards a stable TOL. Unfortunately, this expectation has not been realized, especially within microbes that, because of complex evolutionary processes and skewed taxon sampling diversity among phyla, still present unstable deep phylogenetic relationships. Prokaryotic speciation events are associated with critical evolutionary innovations and influence evolutionary changes in environmental conditions. We utilized a dataset of 766 fully-sequenced proteomes from six phyla that compose the Terrabacteria superphylum. Current TOL reconstruction studies have exposed conflicting phylogenies for this superphylum, particularly in the placement of the Deinococcus-Thermus (DT) phylum, possibly caused by the DT species representation that is much lower compared to that of other phyla. To investigate this, we created a pipeline that allowed us to perform various permutations on this dataset to determine how altered sampling scenarios affect the accuracy of phylogenetic reconstruction and speciation rates. Each sampling scenario provided a simple framework for analyzing diversification patterns and rates in prokaryotes. For patterns, we used a discrete Robinson-Foulds metric to quantify the level of discord among permutated maximum-likelihood trees while for rates we utilized ordinary differential equations to model speciation events. The model assumes evolution as a continuous process and at each node the current number of species is proportional to the speciation rate thus the time elapsed between nodes drives the signal for speciation rate changes. Our empirical data shows that different taxon samplings affect phylogenetic reconstruction suggesting that to obtain a stable and accurate TOL sequencing efforts should be more evenly distributed across taxonomic categories.


P.72  Species Delimitation in the Coral Genus Goniopora. Terraneo TI*, King Abdullah University of Science and Technology; Berumen ML, King Abdullah University of Science and Technology

We investigated the species boundaries of the scleractinian coral genus Goniopora from several localities in the Indian and Pacific Ocean and from the Saudi Arabian Red Sea. We used an integrated morpho-molecular approach to better clarify the complex scenario derived from traditional classification efforts based on skeletal morphology. Molecular analyses of evolutionary relationships between different traditional morphospecies of Goniopora were performed to re-evaluate the informativeness of macromorphological and micromorphological features. Several lineages were molecularly resolved within Goniopora samples on the basis of four molecular markers: the mitochondrial intergenic spacer between Cytochrome b and the NADH dehydrogenase subunit 2, the entire nuclear ribosomal internal transcribed spacer region, the ATP synthase subunit &beta gene, and a portion of the Calmodulin gene. DNA sequence data were analyzed under a variety of methods and exploratory species-delimitation tools. Subsequent analyses of micromorphological and microstructural skeletal features identified the presence of distinctive characters in each of the molecular clades. Unique in vivo morphologies were associated with the genetic-delimited lineages, further supporting the molecular findings. Some colonies show a peculiar genetic pattern that could indicate hybridization. The proposed re-organization of Goniopora will resolve several taxonomic problems in this genus while reconciling molecular and morphological evidence.


P.73  Genomic identification of queen conch seafood products from commercial markets . Truelove NK*, Smithsonian; Palumbi SR, Stanford University; Box SJ, Rare; Cox CE, Smithsonian

In recognition of extensive overfishing and limited international management, the Convention on International Trade of Endangered Species of Flora and Fauna (CITES) voted in 1990 to list Caribbean queen conch (Lobatus gigas) on Appendix II in an effort to regulate international commercial trade. Are the queen conch products available in the market today exclusively from countries in compliance with international treaties? We tested the potential of using genomic methods to identify the source country of queen conch seafood products. In 2015 we collected samples from six queen conch fisheries in the greater Caribbean. Three were CITES approved Fisheries (Bahamas, Belize, and Jamaica) and three were Fisheries where export is currently prohibited (Aruba, Florida, and St. Eustatius). In 2016 we deeply sequenced the coding region of 96 queen conch (n=16/site) using RNA-Seq. This allowed us to identify 21,123 single nucleotide polymorphisms (SNPs). We then focused on identifying the smallest number of SNPs required to accurately distinguish the fishery. The outlier SNP analysis using the population genomics software Bayescan identified 311 outlier SNPs with high levels of population divergence. Population assignment testing using the 311 outlier SNPs unambiguously (>99%) assigned individual queen conch to their correct population of origin. Our results demonstrate that a panel of 311 outlier SNPs can accurately distinguish between CITES approved and CITES prohibited queen conch fisheries.


P.74  Leaf Cutter Ant fungal garden microbiome and associated plants. Vargas Timchenko M*, Smithsonian Tropical Research Institute; Saltonstall K, Smithsonian Tropical Research Institute; Fernandez-Marin H, Instituto de Investigaciones Cientificas y Servicios de Alta Tecnologia; Wcislo W, Smithsonian Tropical Research Institute

Leaf cutter ants are one of the most important herbivores in neotropical rainforests, and thus are considered to be important drivers of the evolution of plant life history traits. They also play an important role in ecosystem functioning by redistributing carbon, fertilizing the soil and acting as seed dispersal agents. In this study we characterize the microbiome and the plant communities harvested by leaf cutting ants using a Metagenomics approach. Fungal gardens were collected from 11 Atta colombica nests in and around Gamboa, central Panama. Total DNA was extracted from 5 surface subsamples per nest, and amplicon libraries were constructed for 16S rRNA for bacteria, and TrnH-psbA and rbcl for plants, and sequenced on an Illumina MiSeq. The most abundant group of bacteria in the nests was Proteobacteria, consistent with previous studies that suggest high carbohydrate processing capacity of ant fungal garden microbiota. Despite relative uniformity of microbiota across nests, the harvested plant communities tended to be different between nests, with taxa distributed across various plant families and habits. For the plant families that were shared between nests, the relative abundance of each taxa varied greatly, even between geographically close nests. To our knowledge, this is the first study to asses the relative abundance of different plant taxa harvested by leaf cutting ants using molecular methods.


P.75  Phylogenomics of the phaseoloid and millettioid legumes using a target enrichment approach. Vatanparast M*, Smithsonian Institution; Powell A, Cornell University; Sherman-Broyles S, Cornell University; Doyle JJ, Cornell University; Egan AN, Smithsonian Institution

The legume family (Leguminosae) is the third largest family of flowering plants and is the second most important family in economic value. The phaseoloid (ca. 2,070 species in 112 genera) and millettioid (ca. 1,100 species in 56 genera) legumes form a single large clade of the papilionoid subfamily and include various important crops such as soybean, common bean, cowpea, pigeon pea and winged bean. The majority of taxa in this clade correspond to the Phaseoleae sens. lat. and Millettioid sens. stric. subclades; however, in spite of multiple molecular phylogenetic studies, relationships within this clade remain unresolved or with low statistical support, particularly along the backbone. To understand the evolutionary history of these legumes, we used transcriptomes of 24 taxa from this group as well as six outgroup legume genera to develop thousands of hybridization probes. Our probes include representatives of all subtribes and major, delineated clades determined in previous studies within the millettioid clade. We obtained sequences for hundreds of genes to build a robust phylogenetic tree encompassing phaseoloid and millettioid legumes. Our results reveal robust phylogenetic relationships of multiple clades and subclades within the millettioid clade and provide well-supported phylogenetic evidence useful for the classification within this important legume clade.


P.77  Development of a reference standard library of chloroplast genome sequences, genometrakrcp. Zhang N*, Food and Drug Adminstration; Ramachandran P, Food and Drug Adminstration; Wen J, National Museum of Natural History; Ottesen AR, Food and Drug Adminstration; Timme RE, Food and Drug Adminstration; Handy SM, Food and Drug Adminstration

An increasing number of people have turned to herbal dietary supplements for preventing diseases, staying healthy, and as an alternative to medicines after getting sick. In 2015, the total sales of herbal dietary supplements in the United Stated reached $6.92 billion, a 7.5% increase from the year before, and demand for botanicals have increased for 12 consecutive years. Many different chemical techniques have been used to monitor authenticity of supplements and more recently DNA based tools have been included. While DNA barcoding has been found to be a powerful identification tool for many species, questions remain about its utility in plants, especially for processed products and closely related species. Therefore, developing methods targeting smaller diagnostic regions and reference libraries for rapid species identification of plants in foods and dietary supplements would be useful and complementary to chemical methods. In the past, the United States Food and Drug Administration (FDA) has been able to develop species specific assays targeting plant species of interest by utilizing chloroplast genome sequences. Presented here are the details for FDA's whole chloroplast genome sequencing effort and database, known as GenomeTrakrCP. Targeted species include plants found in foods and dietary supplements as well as plants known as toxin producers. Additionally, contaminants or adulterants and closely related species to these targeted species were sequenced. All data will be publically available through a bioproject in GenBank, e.g., PRJNA325670 derived from authenticated specimens and fully annotated. Currently there are 40 complete chloroplast genomes in the database from authenticated specimens. These data can be used by FDA and other government agencies, industry and any other researcher as complete chloroplast genomes or to design species specific assays to target plant species of interest.


P.78  Assessing genomic diversity via whole genome resequencing in bean cultivars (Phaseolus L. spp.) from Brazil, a putative secondary center of diversity. Egan AN*; Lim HC; Miller T

Pulse crops, such as the lima bean (Phaseolus lunatus) and the common bean (Phaseolus vulgaris), are critical components of human health and the global economy. With the designation of 2016 by the United Nations as the International Year of Pulses, much research has centered on understanding the evolutionary, nutritional, and agronomic impacts of beans. Both the common bean and lima bean were domesticated by indigenous peoples of the New World and are said to each have two centers of domestication: a Mesoamerican origin and an Andean origin. However, genetic studies have suggested Brazil as another center of diversity. This is supported by anthropological studies of the Canela indigenous culture of northeast Brazil who cultivate an astonishing diversity of beans, with over 60 vernacular-named varieties. To assess the genetic diversity within Brazilian cultivars, we re-sequenced the complete genomes of 29 P. lunatus and 17 P. vulgaris accessions as well as the wild species P. filiformis collected from Mexico and P. polystachios collected from Virginia. All lunatus and vulgaris accessions were from small garden plots or local markets, with the exception of one proximately collected wild accession of P. vulgaris. Single nucleotide polymorphisms were called against the P. vulgaris complete nuclear genome. Genetic diversity of Brazilian accessions was compared against SNPs from each species’ two gene pools that represent centers of domestication and population structure as examined for each species. Brazilian germplasm presents a high level of genetic diversity and should be considered for preservation and conservation to help mitigate loss of genetic diversity.




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