W959
Elucidation of Transposable Elements in Conifers and their Effect on Conifer Evolution

Date: Sunday, January 10, 2016
Time: 2:24 PM
Room: Golden Ballroom
Robin Paul , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
Kristian A. Stevens , Department of Evolution and Ecology, University of California, Davis, Davis, CA
Daniel Gonzalez-Ibeas , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
Kevin Pratt , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
Aleksey Zimin , University of Maryland, College Park, MD
James A. Yorke , University of Maryland, College Park, MD
Ann Holtz-Morris , Children's Hospital Oakland Research Institute, Oakland, CA
Maxim Koriabine , Children's Hospital Oakland Research Institute, Oakland, CA
Marc Crepeau , Department of Evolution and Ecology, University of California, Davis, Davis, CA
Daniela Puiu , Johns Hopkins University, School of Medicine, Baltimore, MD
Steven L. Salzberg , Johns Hopkins University, School of Medicine, Baltimore, MD
Pieter J. deJong , Children's Hospital Oakland Research Institute, Oakland, CA
Charles H. Langley , Department of Evolution and Ecology, University of California, Davis, Davis, CA
David B. Neale , Dept. Plant Sciences University of California Davis, Davis, CA
Jill L. Wegrzyn , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
Conifers are the most dominant life forms in boreal and temperate forests. They have important applications towards carbon sequesterization and wood production. Interspersed repeats constitute up to 80% of these typically large and complex genomes (Douglas-fir: 15Gbp, loblolly pine: 23Gbp and sugar pine: 33Gbp) making elucidation of these genomes extremely challenging. A combination of de novo and similarity based methods were used to characterize the repeats in these complex genomes. It was observed that transposable elements constitute about 70%, 74% and 79% of Douglas-fir, loblolly pine and sugar pine genome respectively.  As expected, LTR retrotransposons dominated all three genomes and represent 53.67%, 52.53% and 56.08% of Douglas-fir, loblolly pine and sugar pine genomes respectively. To study the proliferation and diverged nature of the LTRs, dating of LTR retrotransposons were carried out by comparing the nucleotide substitutions of their respective LTR regions. Dating results suggest that transposable element activity has been more recent in sugar pine relative to loblolly pine resulting in the expansion of the sugar pine genome. No major bursts in transposon activity were detected and instead a balanced insertion and removal of transposable elements occurred over the past 15 million years.  Therefore no single repeat element contributed a major portion of the genome. It was also found that gypsy elements in sugar pine were more recent than those in loblolly pine supporting our observation of a gypsy expansion in sugar pine.
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