W569
Sugar Pine Annotation

Date: Saturday, January 10, 2015
Time: 9:00 AM
Room: Pacific Salon 6-7 (2nd Floor)
Jill Wegrzyn , Department of Ecology and Evolutionary Biology - University of Connecticut, Storrs, CT
Kristian Stevens , Department of Evolution and Ecology, University of California, Davis, Davis, CA
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
Pedro J Martínez-García , Department of Plant Sciences University of California, Davis, CA
John Liechty , Department of Plant Sciences, University of California, Davis, Davis, CA
Hans Vasquez-Gross , University of California Davis, Davis, CA
Sowmya Kuruganti , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
Emily Grau , UC Davis, Davis, CA
Carol Loopstra , Texas A&M University, College Station, TX
Aleksey Zimin , Institute for Physical Science and Technology, University of Maryland, College Park, MD
James A. Yorke , University of Maryland, College Park, MD
Marc Crepeau , Department of Evolution and Ecology, University of California, Davis, Davis, CA
Daniela Puiu , Johns Hopkins University, School of Medicine, Baltimore, MD
Carson Holt , University of Utah, Salt Lake City, UT
Mark Yandell , USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT
Steven L Salzberg , Johns Hopkins University, School of Medicine, Baltimore, MD
Pieter J. deJong , Children's Hospital Oakland Research Institute, Oakland, CA
Keithanne Mockaitis , Indiana University, Bloomington, IN
Dorrie Main , Washington State University, Pullman, WA
Charles H. Langley , Department of Evolution and Ecology, University of California, Davis, Davis, CA
David Neale , Dept. Plant Sciences University of California Davis, Davis, CA
The pathogen Cronartium ribicola, responsible for white pine blister rust, is one of many factors contributing to the decline of several white pine species, including sugar pine (Pinus lambertiana). For conservation of these species and maintenance of genetic diversity, elucidation of the sugar pine genome is essential. Conifer genomes range in size from 6.5-40 gigabases and studies from the first three genomes (Norway spruce, white spruce, and loblolly pine) support that is this is largely due to repetitive sequence. In this study, we have characterized the gene space and repetitive content in the first version of the 34Gb sugar pine genome. To assist in characterizing the coding region, over 30 tissue-specific RNA libraries were sequenced and annotated. Short read technologies (Illumina MiSeq and HiSeq) and the PacBio Iso-Seq technology which yields size-selected transcripts ranging from 1,000 to over 6,000 bp, have been included in the de novo assemblies. A combination of de novo and homology-based methodologies were employed to comprehensively identify both interspersed and tandem repeat content.  Interspersed elements were compared against the RepBase database as well as a library of repeats that was constructed by RepeatModeler. The unclassified interspersed elements identified with RepeatModeler were further characterized using a combination of homology and structural-based approaches.  The MAKER-P application considers the resulting custom repeat libraries, assembled transcriptome resources, and trained gene predictors to generate a preliminary genome annotation.
Back to: Pine Genome Reference Sequence
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