P0988
Genome Annotation and Repeat Sequence Characterization in Sugar Pine (Pinus lambertiana)

Date: Monday, January 12, 2015
Room:
Robin Paul , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
Sowmya Kuruganti , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
Kristian 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
Pedro J Martinez-Garcia , Department of Plant Sciences, University of California, Davis, Davis, CA
John Liechty , Department of Plant Sciences, University of California, Davis, Davis, CA
Hans Vasquez-Gross , Department of Plant Sciences, University of California, Davis, Davis, CA
Emily Grau , Department of Plant Sciences, University of California, Davis, Davis, CA
Carol Loopstra , Dept. of Ecosystem Science and Management, Texas A&M University, College Station, TX
Aleksey Zimin , Institute for Physical Science and Technology, 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
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
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 , Department of Plant Sciences, University of California, Davis, Davis, CA
Jill Wegrzyn , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
The pathogen (Cronartium ribicola) which causes white pine blister rust is one of many factors responsible for the decline in the populations 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. The size of conifer genomes range 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 sequences. As a result, the assembly and annotation of these complex genomes is challenging. In this study, we have characterized the gene space and repetitive content in the first version of the 34Gb sugar pine genome. A combination of de novo and homology-based methodologies have been employed to comprehensively identify both interspersed and tandem repeat content.  Interspersed elements were compared against the plant section of the RepBase database as well as a library of repeats that was constructed de novo by RepeatModeler. The unclassified interspersed elements identified with RepeatModeler were further characterized using a combination of homology and structural-based approaches.  Our preliminary results indicate that the percentage of repeats in the genome is close to 80% which is consistent with previous estimates in loblolly pine. A similar combination of de novo and homology-based approaches was used to characterize the gene space.  The MAKER-P application considers existing transcriptome resources (over 20 libraries complete in sugar pine) and incorporates trained gene predictors to accurately identify genes.
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