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Evolution of Gene Regulation Among Drosophila Species

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8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS) ABSTRACTS | INVITED SPEAKERS EVOLUTION OF GENE REGULATION AMONG DROSOPHILA SPECIES Patricia Wittkopp, University of Michigan Genetic dissection of phenotypic differences within and between species has shown that genetic changes affecting the regulation of gene expression are an important source of phenotypic diversity. We have seen this in our own work investigating the genetic basis of pigmentation differences between closely related Drosophila species. To better understand the genetic mechanisms responsible for the evolution of gene expression, we have been investigating the evolution of a specific gene yellow( ) as well as the evolution of gene expression on a genomic scale. Work on both of these topics, with an emphasis on methods adaptable to non-model systems, will be presented. METAMORPHOSIS AND EVOLUTION OF ARTHROPOD GENOMICS Judith H. Willis, University of Georgia I began work on arthropod genomics 50 years ago. At first, I was only interested in the genetic underpinnings of metamorphic transitions, but I have ended up with an increasing orientation toward arthropod evolution. During those 50 years the field itself has evolved (gaining a name in the process) and metamorphosed (witness this meeting). My talk will address both the biology and the history. I began by testing whether each metamorphic stage was underwritten by a unique set of genes by using cuticular proteins (CPs) as molecular markers. Results, starting with tube gels and progressing to the isolation and characterization of two CP genes and their promoters, demolished that hypothesis. A shift from a giant silkworm to Anopheles gambiae that devotes ~2% of its protein coding genes to structural CPs was accompanied by a larger scale analysis of their activity, including mRNA expression and recovery of authentic CPs from cuticle determined by LC-MS/MS analyses. Collaboration with Stavros Hamodrakas’s group in Athens, Greece has provided homology models that combine structure and function and sequence prediction programs that facilitate cross-species comparisons. CPs have shed light on several aspects of insect evolution: the benefit of gene duplication, importance of concerted evolution, the phylogenetic position of basal arthropods. I have found that fundamental problems can be resolved, and the metamorphosis of models and the evolution of techniques can be followed and summarized by focusing on just one group of proteins of particular importance to arthropods. 11 ABSTRACTS | INVITED SPEAKERS PHYLOGENY-DRIVEN INITIATIVE ON GENOMIC SEQUENCING Guojie Zhang 1,2 1. Chinese National Genebank, BGI-Shenzhen, 518083, Shenzhen, China, 2. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark. Comparative genomics has been a powerful and routine tool in revealing the complex evolutionary history and species adaptation. The dramatic development of sequencing technologies has boosted the fast development of genomic studies, from targeting on model organisms to non-model organisms, from single individual genomes to large-scale population genomics, and from single species genome studies to phylogenomic scale studies. In the past few years, we have decoded the genomes of hundreds of animal species, including ~50 arthropod species from 20 different families. However, decoding the genomes with high repetitive contents and high heterozygosity has not been fully resolved with current technologies. Therefore, my group has given the top priority to organisms with simple genome structure, and developed several projects within the phylogenetic framework for eusocial insects and birds. The avian phylogenomic project is one of projects we recently accomplished. In this project, we have collected genomes of 48 bird species, representing nearly all of the major groups of living birds, and applied information from the entire genome to resolve the deep avian phylogenetic relationships, which has been a challenge to biologists for centuries. With the newly reconstructed phylogenetic tree, our analyses also revealed that the genomic biodiversity across birds covaries with diverse adaptations to different lifestyles. We have learned a lot of lessons from this large-scale international coordinating project that could be useful for the i5k group. AUTOMATED ANNOTATION OF I5K GENOMES Dan Hughes, Genome Sequencing Center at Baylor College of Medicine We are using a combination of MAKER and an extended version of the Cegma pipeline to perform automated annotation of the various i5k genomes. Heuristics are used to post-process tophat/cufflinks RNASeq predicted transcripts to systematically limit the presence of fusion transcripts. MAKER is then used to run alignments of ~1M non-redundant Metazoan peptide sequences and synthesize the results of RNASeq analysis and ab initio predictions. Further heuristics are used to choose between MAKER and Cegma derived models and each locus and tweak models where necessary to generate the final gene set. Gene names are assigned via a synthesis of OrthoMCL and reciprocal BLAST analysis and InterProScan5 is run on the resulting proteome prior to public release. 12 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS) THE I5K WORKSPACE@NAL – ENABLING GENOMIC DATA ACCESS, VISUALIZATION AND CURATION FOR THE I5K COMMUNITY Monica Poelchau, USDA Maryland Genomic data access and visualization – in particular, the establishment of ‘genome portals’ - is a critical, yet often overlooked component of genome sequencing projects. Genomic data should be visualized to assess and improve the quality of genome assemblies and annotations, both at the pre- and post-release steps of a genome’s life cycle. In addition, gene model curation, during which a community manually inspects and improves computationally predicted gene models, is a critical step in the maturation of a genome project. Existing or preconfigured genome portals facilitate data access and community building, but not all research groups have the means or connections to host a dedicated portal for their sequenced organism. The National Agricultural Library (NAL), as part of our broader mission to enable access to genomic information for arthropod genomes and the agricultural community, has implemented a genome portal for such ‘orphaned’ i5k genomes (http://i5k.nal.usda.gov/). We provide access to genomic information via organism and gene pages, data downloads, a Blast interface, and the JBrowse genome browser. We also provide the Web Apollo manual annotation editor for these species. In this talk, I will describe the post-gene prediction life cycle of a typical i5k genome, and the NAL’s plan/vision to support i5k genomes at this stage via the i5k Workspace@NAL and other services. 13 ABSTRACTS | INVITED SPEAKERS CHROMOSOME ORGANIZATION AND EVOLUTION OF THE YELLOW FEVER MOSQUITO GENOME Maria V. Sharakhova, Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA The yellow fever mosquito Aedes aegypti has a large 1.37 Gb genome with a high density of repetitive elements. Physical genome mapping in Ae. aegypti is difficult due to the poor quality of polytene chromosomes. As a result, chromosome organization and evolution of the yellow fever mosquito genome remain largely unexplored. We developed an approach for physical mapping of genomic supercontigs based on the banding pattern of mitotic chromosomes of Ae. aegypti. Using fluorescentin situ hybridization, we assigned 624 Mb of the genome assembly (45%) to specific bands of chromosome idiograms. Chromosome and genome maps were integrated with the linkage genetic map by direct placement of 100 BAC clones carrying major genetic markers. As a result, 12 QTLs related to the pathogen transmission were also anchored to the chromosome positions. These QTLs were combined into five major clusters on the chromosome map. In addition, we analyzed the distribution of genes, tandem repeats and transposable elements along the chromosomes and explored the patterns of chromosome homology and rearrangements between Ae. aegypti and An. gambiae. The study demonstrated that the q arm of the sex-determining chromosome 1 has the lowest gene content and the highest density of minisatellites. A comparative genomic analysis with An. gambiae determined that the previously proposed whole-arm synteny is not fully preserved; a number of pericentric inversions have occurred between the two species. The sex-determining chromosome 1 had a higher rate of genome rearrangements than observed in autosomes 2 and 3 of Ae. aegypti. The research tools and information generated by this study contribute to a more complete understanding of the genome organization and evolution in mosquitoes. 14 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS) GENOME STUDIES OF THE LYME DISEASE TICK, IXODES SCAPULARIS: FACILITATING RESEARCH ON TICK AND MITE VECTORS OF DISEASE Catherine A. Hill 1, Monika Gulia-Nuss 1, Jyothi Thimmapuram 2, Jason M. Meyer 1, the Ixodes scapularis Genome Consortium and VectorBase 3 1. Purdue University, Department of Entomology, 901 West State Street, West Lafayette, IN, 47907, USA. 2. 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