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Tyler poster v2

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Tyler poster v2

  1. 1. Improving our Knowledge of Transposable Element Content and the Future of TE Research Tyler A. Elliott and T. Ryan Gregory @TransposableMan @TRyanGregory References Elliott, T.A., Gregory, T.R. 2015. Do larger genomes contain more diverse transposable elements? BMC Evol Biol. 15:69 Hoen, D.R. et al. 2015. A call for benchmarking transposable element annotation methods. Mob DNA. 6:13 Piégu B. et al. 2015. A survey of transposable element classification systems – a call for a fundamental update to meet the challenge of their diversity and complexity. Mol Phy Evol. 86: 90-109 Dotto, B.R. et al. 2015. HTT-DB – Horizontally transferred transposable element database. Bioinf. 31:2915-2917 Jurka, J. et al. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cyt Gen Res. 110:462-467 Vassetzky, N.S., Kramerov, D.A. 2013. SINEBase: A database and tool for SINE analysis Nucl Acid Res. 41:D83-D89 Wicker, T. et al. 2007. A unified classification system for eukaryotic transposable elements Nat Rev Genet. 8:973-982 Dai, L. et al. 2003. Database for mobile group II introns. Nucl Acid Res. 31:424-426 Siguier, P. et al. 2006. ISFinder: The reference center for bacterial insertion sequences. Nucl Acid Res. 34:D32-D36 TE Content Elliott and Gregory, 2015 (BMC Evol Bio) • 54.26% of published genome sequences do not assign TEs down to superfamily level, 25% have little or no reporting of TE content Hoen et al., 2015 (Mob DNA) • Lack of a benchmark for annotation of TEs in genomes • Soliciting community for suggestions TE Classification Piégu et al., 2015 (Mol Phy and Evol) • Classification should reflect common ancestry and include elements in prokaryotes • Lack of communication between various groups of researchers and organizations/databases • Call for the formation of a committee for TE taxonomy TE Resources • Numerous databases with useful features and tools • Varying levels of support for each • Little to no interconnectivity The Future of TE Research • Need for discussion amongst the community to determine interest and those willing to commit time and resources • Re-annotation of genomes using standard methods and annotation of black box genomes, curated data should be freely available to all • Expand support of databases and integration, sharing of data • Perhaps time has come for the formation of a society or organization for researchers working on mobile genetic elements • Provide centralized entity which can enforce standards of annotation, classification, storage and curation of TE information Overview • The study of TEs and mobile DNA in general is at a crossroads in regard to how we annotate, classify , store and curate information • Our knowledge of TE content in genomes needs improvement, and a standardized way of annotating TE across genomes is needed • The classification of TEs needs revision, to better encompass the diversity of more types of mobile DNA from all life and to reflect common ancestry • Useful databases and resources exist online but they often operate in isolation, with little support and interconnectivity • The community would benefit from unifying to discuss these issues and propose a means forward, such as eventually forming the first international society of mobile DNA researchers as a means to propose and enforce standards Department of Integrative Biology, University of Guelph, Ontario, Canada tyleraelliott@gmail.com rgregory@uoguelph.ca

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