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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Society, Health, Disease & Genomics

Room: Salon 4, Marriott Hotel

14:00 - 15:30

Moderator: Eric Green, NIH/NHGRI

13.1  14:10  Rapid evolution and the genetics of disease resistance in Tasmanian devils. Epstein B, Washington State University; Jones M, University of Tasmania; Hamede R, University of Tasmania; Hendricks S, University of Idaho; McCallum H, Griffith University; Storfer A, Washington State University; Hohenlohe P*, University of Idaho

Although cancer rarely acts as an infectious disease, a recently emerged transmissible cancer threatens the persistence of Tasmanian devils (Sarcophilus harrisii). Devil facial tumor disease (DFTD) has swept across nearly the entire species range, causing a population decline of 80 percent in just 20 years. Using high-throughput genomic sequencing approaches, we have detected evidence for rapid evolution in response to DFTD as well as a genetic basis for variation in disease-related traits. First, we applied a genome scan approach in three populations for which we have devil samples from both before and after DFTD outbreak, and we identified two genomic regions showing strong signatures of rapid parallel response to selection. Both regions contain candidate genes with immune and cancer-related functions. We have expanded this list of candidate loci under selection by targeting regions of the genome across several more independent populations. Further, we have conducted genome-wide association mapping of disease-related phenotypic traits across several populations. Key traits, including time of survival with disease and tumor growth rate, show a significant genetic basis and association with a relatively small number of major-effect loci. Our results suggest the presence of standing genetic variation that could facilitate the evolution of resistance and/or tolerance to DFTD in devil populations, providing hope for the persistence of devil populations in the face of this devastating disease.

13.2  14:30  Constricted T cell repertoire diversity in Tasmanian devils with contagious cancer. Cheng Y*, University of Sydney; Makara M, University of Sydney; Peel E, University of Sydney; Fox S, Department of Primary Industries, Parks, Water and Environment, Tasmania; Papenfuss AT, The Walter and Eliza Hall Institute of Medical Research; Belov K, University of Sydney

The Tasmanian devil (Sarcophilus harrisii), the world's largest living carnivorous marsupial, is threatened by an unusual contagious cancer, known as Devil Facial Tumor Disease (DFTD). The tumor is transmitted between unrelated devils as an allograft without triggering immune rejection. To understand how DFTD infection impacts on the host immune system, we characterized T cell receptor (TCR) genes in the devil genome, and examined T cell repertoire diversity in healthy and DFTD-affected devils via Illumina Miseq sequencing of TCR beta (TCRB) chain transcripts. A total of 6,281,698 sequences were obtained for 40 individuals, from which 982,581 distinct TCRB transcripts were identified. Compared to the control group, DFTD-affected animals have a considerably less diverse TCRB repertoire with smaller number of distinct transcripts and lower degree of uniformity, which is indicative of pronounced TCR repertoire constriction associated with DFTD infection. We also found lowered expression levels of cytokines centrally involved in T cell differentiation, homeostasis, and activation in the peripheral blood of devils with the cancer. These results indicate that DFTD can induce suppression of the immune system in affected devils, which not only further explains why devils are incapable of fighting off DFTD, but also suggests that devils with DFTD may also be susceptible to other secondary infections and cancers.

13.3  14:50  Complex immune systems encoded in invertebrate genome sequences. Buckley KM*, The George Washington University; Rast JP, University of Toronto

Invertebrates are characterized by extraordinary diversity in terms of body plan, life history and life span. Recent analyses of emerging genomic sequences from these phyla indicate that the immune systems of these organisms harbor similarly complex immune responses. In contrast to the predictions of relatively simple systems (based on sparse sample), immune systems in invertebrate organisms exhibit significant evolutionary novelty and complexity. One accessible measure of this complexity is the multiplicity of genes that encode homologs of pattern recognition receptors. These multigene families vary significantly in size, and their sequence character suggests functional variation. Coincident with this rapid evolution, certain aspects of downstream signaling appear to be conserved. I present here an analysis of five major classes of immune recognition receptors from newly available animal genome sequences. These include the Toll-like receptors (TLR), Nod-like receptors (NLR), SRCR domain scavenger receptors, peptidoglycan recognition proteins (PGRP), and Gram negative binding proteins (GNBP). Analyses indicate that innate immune complexity in the invertebrate deuterostomes, which was first recognized in sea urchins, reflects the wider context of emerging genomic information across animal phyla.

13.4  15:10  Understanding the complex and controversial phylogenetic relationships among closely related and potentially harmful dinophysiacean genera (Dinophyceae, Dinophysiales). Handy SM*, US Food and Drug Administration; Wolny J, Maryland Department of Natural Resources; Deeds JR, US Food and Drug Administration; Egerton T, Virginia Department of Health; Smith J, Virginia Institute of Marine Science; Bachvaroff TR, University of Maryland Center for Environmental Science and Institute of Marine and Environmental Technology

Dinoï¬'agellates are a highly diverse and environmentally important group of protists with relatively poor resolution of phylogenetic relationships, particularly among heterotrophic species. Select members of the dinoflagellate family Dinophysiaceae including the genus Dinophysis, produce okadaic acid (OA), and dinophysistoxins (DTXs), the causative toxins of diarrheic shellfish poisoning (DSP). At present, the taxonomy of this group is in flux. The ability to reliably distinguish the various members of the genus Dinophysis is the first step towards understanding more complex topics such as the determination of the causative organism during toxicity events, bloom development, food-web dynamics, etc. Until recently, most of the dinophysiaceans were unculturable which made this topic particularly challenging, and there are many questions remaining about what gene targets should be used to identify these species. Previously, we examined the phylogeny of several dinophysiacean dinoflagellates using individual cells isolated from Atlantic sites and targeted a 3.5 kb sequence that included the nuclear ribosomal genes SSU, 5.8S, LSU, in addition to the ITS spacers (Handy and Bachvaroff et al. 2009). Dinophysis continues to be in the news as a result of substantial blooms and toxin production in the Gulf of Mexico, Puget Sound, and most recently Maine that resulted in the prohibition of shellfish harvesting. In recent years, Dinophysis species have also occurred more frequently on the east coast of the United States, including in the Maryland and Delaware coastal bays. Here, we examined genetic sequence data from both ribosomal DNA and mitochondrial Cox1, as well as the secondary structures formed by the ribosomal DNA. This data was compared to data collected with traditional morphologic analyses using light and scanning electron microscopy to understand more about the particular species of Dinophysis occurring in the mid-Atlantic area. This information will hopefully provide further insight into the species of Dinophysis occurring both here and in other coastal regions of the US and support the development of management strategies to prevent the occurrence of DSP events.

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