W352
A Reference Draft Genome for Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco)

Date: Sunday, January 15, 2017
Time: 3:00 PM
Room: Sunrise - Meeting House
U. Uzay Sezen , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
David B. Neale , Dept. Plant Sciences University of California Davis, Davis, CA
Pat McGuire , Department of Plant Sciences, University of California, Davis, Davis, CA
Nicholas Wheeler , Pennsylvania State University, Centralia, WA
Kristian A. Stevens , Department of Evolution and Ecology, University of California, Davis, Davis, CA
Marc Crepeau , Department of Evolution and Ecology, University of California, Davis, Davis, CA
Charis Cardeno , University of California, Davis, Davis, CA
Aleksey Zimin , University of Maryland, College Park, MD
Daniela Puiu , Johns Hopkins University, School of Medicine, Baltimore, MD
Mihaela Pertea , McKusick-Nathans Institute of Genetic Medicine, JHU, Baltimore, MD
Gaurav Sablok , University of Connecticut, Storrs, CT, United States Minor Outlying Islands
Claudio Casola , Texas A & M University, College Station, TX
Tomasz Koralewski , Texas A&M University, College Station, TX
Robin Paul , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
Daniel Gonzalez-Ibeas , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
Sumaira Zaman , University of Connecticut, Storrs, CT
Richard Cronn , USDA Forest Service Pacific Northwest Research Station, Corvallis, OR
M. Yandell , Department of Human Genetics, University of Utah, Salt Lake City, UT
Carson Holt , University of Utah, Salt Lake City, UT
Charles H. Langley , Department of Evolution and Ecology, University of California, Davis, Davis, CA
James A Yorke , University of Maryland, College Park, MD
Steven L. Salzberg , Johns Hopkins University, School of Medicine, Baltimore, MD
Jill L. Wegrzyn , Department of Ecology and Evolutionary Biology - University of Connecticut, Storrs, CT
Douglas-fir (Pseudotsuga menziesii) represents one of 11 genera within the family Pinaceae. As a keystone species, it grows on over 20 million ha across western North America, from British Columbia to Mexico, from the Pacific coast to the eastern slopes of the Rocky Mountains. It occurs at elevations ranging from sea level to 3000 m. Two varieties, one found in the interior west (var. glauca) and the other found along the Pacific slopes (var. menziesii) represent ideal populations for studying the effects of climate change. Until now four conifer genomes in two genera have been de novo sequenced, including Norway spruce (Picea abies), white spruce (Picea glauca), loblolly pine (Pinus taeda), and sugar pine (Pinus lambertiana). Here, we present the 16.6 Gbp draft genome with an N50 scaffold length of 340 Kbp and 47,874 gene models, of which 28,403 are complete (full-length). Analysis of the full-length genes found a maximum intron length of 183 Kbp. Phylogeny-based analyses of gene family evolution showed a faster gene turnover in Pinaceae compared to angiosperms. Multiple genes involved in photosynthesis, including all nuclear genes encoding subunits of the NDH dehydrogenase complex, have been lost in Pinaceae. Additionally, we found several genetic pathways with significant changes in gene family size in Douglas-fir, including a pathway involved in jasmonate regulation and signaling. Inclusion of Douglas-fir transcriptomic resources generated from de novo assemblies of needle tissue enhanced the gene analysis. In specific, light harvesting complex and photoreceptor genes were investigated and compared in shade-intolerant Pinaceae species.
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