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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21
Genomic Projects

Room: Salon 4, Marriott Hotel

11:00 - 12:50

Moderator: Jon Coddington, Smithsonian Institution



21.1  11:10  Progress and perspectives on the i5K pilot sequencing of 30 arthropod species. Richards S*, Baylor College of Medicine Human Genome Sequencing Center; Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center; i5K-pilot-consortium

The i5K is an initiative to generate reference genome sequences for 5,000 arthropods of 'all species known to be important to worldwide agriculture and food safety, medicine, and energy production; all species used as models in biology; the most abundant insects in world ecosystems; and, to achieve a deep understanding of arthropod evolution, representatives of insect relatives in every major branch of arthropod phylogeny.' As a pilot for this audacious goal we at the Baylor College of Medicine Human Genome Sequencing Center sequenced the genomes of 30 arthropod species from a range of arthropod orders, with agricultural, ecological, scientific and phylogenic importance. Whilst the sequencing and assembly could be performed within the genome center over 1000 researchers from around the world have played a part in analyzing their favorite species. The project is now nearing the end with one third of the individual species genome papers published or in the publishing process, and a larger analysis of gene content evolution across the phylum Arthropoda ongoing. We present here progress of the pilot project as a whole, initial results of gene content change across the Arthropoda, improved genome assemblies, and a discussion of the practical successful consequences, lessons learned from this endeavor to be taken forward as we reach towards a full genomic survey of the arthropods.


21.2  11:30  1KITE: phylogeny and beyond. Zhou Xin*, Beijing Advanced Innovation Center for Food Nutrition and Human Health & College of Food Science and Nutritional Engineering, China Agricultural University

The 1000 Insect Transcriptome Evolution (1KITE) project aims to understand the phylogenetic relationship and evolutionary history of insects, using orthologous genes obtained from transcriptome sequences. Initiated in early 2011, the project has made major breakthrough in reconstructing the backbone of insect phylogeny using less than 10% of the taxa sequenced. A series of phylogenies are expected for sub-lineages of insects based on the remaining data. In addition to the improved understanding of phylogenetic relationships, the 1KITE also make a significant contribution to gene repositories of major insect groups. These gene sets provide a unique opportunity to examine many interesting questions, e.g., gene family evolution, co-occurring microbial diversity, gene interactions, etc. This talk will give a brief peak at what can be learned from a large -omics survey based on systematic taxon sampling. At last, experiences assuring a successful global project and aspects that can be improved in project design, sampling, and organization will be discussed.


21.3  11:50  The Global Ant Genomics Alliance (GAGA). Boomsma JJ, University of Copenhagen; Brady SG*, Smithsonian Institution; Dunn R, North Carolina State University; Gadau J, University of Münster; Heinze J, University of Regensburg; Keller L, University of Lausanne; Moreau CS, Field Museum; Sanders NJ, University of Copenhagen; Schrader L, University of Copenhagen; Schultz TR, Smithsonian Institution; Sundstr÷m L, University of Helsinki; Ward PS, University of California; Wcislo WT, Smithsonian Institution ; Zhang G, University of Copenhagen and China's National Gene Bank, BGI-Shenzhen

Researchers from the University of Copenhagen, the Smithsonian Institution, the Kunming Institute of Zoology and China's National Gene Bank at BGI-Shenzhen have initiated the Global Ant Genomics Alliance (GAGA), an activity subsequently joined by the other authors of this abstract (listed in alphabetical order). Our objective is to study ant genomics in a joint comprehensive framework during the coming five years, which will involve obtaining high-quality genome sequences of at least a single representative of each ant genus in the world that can be feasibly collected. Funding for the first 200 genomes has been secured and a draft list of candidate species currently is being finalized. We are also reaching out to the social insect research communities and beyond to participate - with collecting efforts, with (joint) grant applications to fund sequencing of the remaining taxa, or by spearheading further research topics under GAGA's umbrella. The official launch of the project occurred at the end of 2016 and we aim to publish the results as a coordinated set of papers in a handful of specific journal issues no later than 2021. Core research questions will focus on phylogenomics, caste evolution, life-history variation, macroecology, and additional topics as suggested by the social insect research community. Our presentation for the BioGenomics2017 Conference will first summarize how ant genomes previously published by ourselves and our colleagues have already begun to address these research questions. These studies include comparative genomic analyses of coevolution in fungus-growers, caste evolution in social parasites, ant-plant mutualisms, genomic signatures of invasive species, and social organization within ant colonies. We will then outline the impact that high-quality, comprehensively sampled ant genomes at the genus scale promises to provide. Additional background and contact information for GAGA can be found at the project website http://antgenomics.dk.


21.4  12:10  Animals transcribe at least half of the genome. Francis WR*, LMU M├╝nchen; Wörheide G, LMU M├╝nchen

One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here we analyze the genomes of 68 species across all animal groups and some single-cell eukaryotes for general trends in genome usage and composition, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of non-model organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought.


21.5  12:30  China National GeneBank: from single biobank to international networks. Coddington J*, Smithsonian Institution

Aiming to "Store, Read, Understand, Write, and Use" genetic resources, China National GeneBank (CNGB) is designed to integrate both genetic information database and biospecimen repository. CNGB has built an integrated infrastructure of "Three banks and Two platforms". "Three Banks" represents the Biorepository, Bio-informatics Data Center and Living Biobank, while "Two Platforms" includes Digitalization Platform and Synthesis and Editing Platform. CNGB Biorepository has achieved storage capability of 10 million traceable bio-samples, and established international standards on bio-sample and sequencing data collection, storage and management. We collect and store bio-samples with its genetic information from both human and non-human resources, with samples ranging from animals and plants, living cells, microorganisms, human blood, urine, tissue, cells, DNA, RNA, protein and small molecules. CNGB Bio-informatics Data Center owns 60pb storage capacity and has opened 46 databases to public while the page views have reached 118 million from the inception to date. Up till now, CNGB has already established two living biobanks, The Tibetan Plateau Living Biobank and Yunnan Living Biobank. Moreover, the Synthesis and Editing Platform possesses 400,000 Pb/year synthesis capacity while the Digitalization Platform has 5 Pb/year high quality data output. CNGB has also formed a global collaboration network, leveraged the low cost of sequencing platform, published massive digital data for science institutions and scientists all over the world. More than 140 papers have been published in peer-reviewed journals, including more than 30 papers in the world's most influential journals, covering major international projects such as G10K (Genome 10K Project), B10K (Phylogenomics analysis of Birds), 1TP (The 1000 plants initiative), and 1KITE (1K Insect Transcriptome Evolution). To fulfill the long-term strategy of CNGB as a global genebank, we look forward to collaborating with global premier bio-repositories, jointly developing and promoting genomic sample preservation and international data standards.


12:30 - 14:00 Lunch


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