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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Invertebrate Genomics

Room: Salon 3, Marriott Hotel

11:00 - 12:50

Moderator: Joe Lopez, Nova Southeastern University

20.1  11:00  The Global Genome Initiative and the Global Genome Biodiversity Network. Coddington JA*, Smithsonian Instittution; Seberg O, Univ. Copenhagen; Droege G, Botanic Garden and Botanical Museum Berlin-Dahlem; Barker KB, Smithsonian Institution

The Global Genome Initiative (GGI) is a six year, funded program to collect, organize, share, and study genomic samples of non-human species. Our mission is 'to preserve and understand the genomic diversity of life.' With national and international partners, it seeks to create a systematic understanding of Earth's biodiversity. The approach is phylogenetic and tree-based, seeking to sample and study all major branches life--operationally all families and perhaps half of described genera. In 2011

20.1  11:10  Censusing the sea in the 21st century. Knowlton N*, Smithsonian; Leray M, Smithsonian; Plaisance L, Smithsonian

We still lack a well-constrained estimate for the diversity of marine life. The challenge stems from the fact that most marine species are small, rare, and undescribed by science. However, high-throughput DNA sequencing used on standardized environmental samples provides a cost-effective way to estimate the number of species in a specific location and compare such estimates with those made elsewhere. Studies of the diversity of eukaryotic organisms on oyster reefs in the US and coral reefs in Jordan are examples of the power of this approach. Autonomous Reef Monitoring Structures (ARMS) mimic the reef matrix by providing spaces in which small invertebrates and fish can shelter and surfaces onto which sessile organisms can attach. Genetic analyses reveal hundreds of species associated with each unit, with the smallest organisms being the most diverse, and rarefaction curves suggest that many more remain to be detected. Remarkably, fewer than 10% of these sequences can be matched to named species, reflecting the fact that most marine life remains unrepresented in genetic databases. Ongoing analyses include samples from shallow water reefs of Panama and Belize, mesophotic reefs of Curaçao, and acidified reefs of Papua New Guinea. Marine ecosystems are rapidly changing due to overfishing, pollution, transport of non-native species, habitat destruction, warming, and acidification. With the ability to obtain environmental metabarcodes at relatively low cost, comprehensive analyses of human impacts on biodiversity are now possible.

20.2  11:30  DEEPC and GLO: Integrating physiological and genomic data to understand evolution in the deep ocean. Haddock SHD*, MBARI / UCSC; Francis WR, LMI; Schultz DT, MBARI / UCSC; Ryan JF, Whitney Labs, U Florida; Thuesen EV, The Evergreen State College

Comparative transcriptomics and genomics can address fundamental questions of evolution and molecular biology, but these methods may also be used to gain insight into specific questions of adaptation and diversification. We are applying comparative genomics in two initiatives: The first is DEEPC (Diversity, Ecology, and EcoPhysiology of Ctenophores), an NSF-supported program to find the specific genetic signatures involved in adaptation to life in the deep sea. This collaboration includes physiologists who measure metabolic activity in organisms collected as deep as 4000 meters, computational biologists who look for signatures of convergence in physiological genes from dozens of transcriptomes and targeted genomes, and "synthesizers" who take the predicted genes from the transcriptomes and express them for physiological characterization. The second initiative is GLO (Genomes of Luminous Organisms), which aims to foster the study of the genetic aspects of light-producing organisms through "open sourcing" sequences from some iconic bioluminescent species and their closest non-luminous relatives. Through this program, we hope to reveal the genetic pathways for producing luminous substrates and enzymes. These two efforts can show the power of integrated approaches (physiologists, chemists, informaticians, and biologists working together) on diverse datasets taken from non-model organisms for answering specific but broadly interesting questions. Among these are "How did bioluminescence arise so many times through evolutionary history?" and "What is special about the proteins of deep-sea organisms that allow them to operate at 400 atmospheres of pressure?'

20.3  11:50  The evolution of bioluminescence and light detection in deep-sea shrimp. Bracken-Grissom H*, Florida International University

Many organisms rely on bioluminescence for communication, feeding, and defense, especially in the deep sea where downwelling light is limited. This research combines phylogenetic/omic and transcriptomic studies to test several hypotheses addressing the evolution of bioluminescence and light detection in a remarkable family of deep-sea shrimp. All shrimp within the family Oplophoridae use a luminescent secretion discharged from the mouth to deter predators, while only some possess a second mechanism of bioluminescence in the form of cuticular photophores. Photophores are light-emitting organs found across the body that are thought to function in counterillumination. These different mechanisms of bioluminescence emit light at slightly different wavelengths and spectral bandwidths. Past studies have shown shrimp with both the secretion and photophores possess unique visual systems to possibly distinguish between different types of emitted bioluminescence, however genomic approaches have never been applied to investigate this system. In addition, new preliminary evidence suggests that the photophores contain photopigment proteins (opsins) that allow for light detection. This is the first indication that autogenic light organs (those in which the animal itself makes the luciferases and/or luciferins for luminescence) may also have light detection capabilities. Here, a phylogenetic approach is used to investigate the evolutionary origins of the two bioluminescence modes (secretion and photophore) within oplophorid shrimp. Secondly, this project will characterize the visual sensitivity system in the eyes of deep-sea shrimp to better understand how shrimp distinguish between different wavelengths of emitted bioluminescence. Lastly, findings will be presented that investigate the photosensitivity in a non-bacterial (autogenic) light organ ' the photophore.

20.4  12:10  The genomics of Hydractinia: understanding regeneration, allorecognition, and stem cell biology. Baxevanis AD*, National Human Genome Research Institute, National Institutes of Health

The cnidarians - organisms unified in a single phylum based on their use of cnidocytes to capture prey and defense from predators - occupy a key phylogenetic position as the sister group to the bilaterians. Members of this phylum, which include the corals, sea anemones, jellyfish, and hydroids, are quite attractive for study by researchers with an interest in fundamental biological processes such as regeneration, allorecognition, and stem cell biology, particularly due to their experimental tractability. Given their great potential as new animal models for human disease, we are actively sequencing and annotating the genomes of two cnidarian species: Hydractinia echinata, which is used in the context of studying regeneration and stem cell biology, and Hydractinia symbiolongicarpus, which is used in the context of allorecognition studies. What makes Hydractinia particularly well-suited as an emerging model organism lies in the fact that they possess a specific type of interstitial cell (or 'i-cell') that is pluripotent and provides the basis for tissue regeneration, expressing genes whose bilaterian homologs are known to be involved in stem cell biology. Hydractinia is also colonial, possessing an allorecognition system that may provide insights into important questions related to host-graft rejection. Using PacBio, Illumina, and Dovetail-based strategies, preliminary sequencing data indicate an estimated genome size of 774 Mb for H. echinata (84x coverage) and 514 Mb for H. symbiolongicarpus (94x coverage), with these genomes being both AT-rich (65%) and highly repetitive (at least 47%). The vast majority of a set of evolutionarily conserved single-copy orthologs can be easily identified in these preliminary assemblies, and these large-scale whole-genome sequencing data are already providing a strong foundation for current genomic and functional studies that have the potential to identify new targets for therapies in regenerative medicine.

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