W512
Introns, Ancient Transposable Elements and Gene Families Revealed in the Annotation of the Loblolly Pine (Pinus taeda L.) Megagenome

Date: Saturday, January 11, 2014
Time: 5:00 PM
Room: Towne - Meeting House
Jill Wegrzyn , University of Connecticut, Storrs, CT
John Liechty , Department of Plant Sciences, University of California, Davis, Davis, CA
Kristian Stevens , Department of Evolution and Ecology, University of California, Davis, Davis, CA
Carol Loopstra , Texas A&M University, College Station, TX
Hans Vasquez-Gross , University of California Davis, Davis, CA
Brian Lin , University of California, Davis, Davis, CA
Jacob Zieve , University of California, Davis, Davis, CA
Pedro J Martinez-Garcia , Department of Plant Sciences University of California, Davis, CA
Carson Holt , University of Utah, Salt Lake City, UT
Mark Yandell , Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT
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
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
Chuck Langley , University of California, Davis, Davis, CA
David Neale , Dept. Plant Sciences University of California Davis, Davis, CA
The annotation for the first whole-genome shotgun assembly of loblolly pine (P. taeda L.), represents 20.15 Gb of sequence distributed across 14.4 million scaffolds and an N50 scaffold size of 66.9 Kbp. The majority of sequence data was obtained from a single megagametophyte, the haploid tissue from a single pine seed.  The haploid sequence data was supplemented with multiple linking long-fragment mate pair libraries from the parental diploid DNA.  The MAKER2 annotation pipeline combined evidence-based alignments and ab initio predictions to generate 50,172 gene models, of which 15,653 were classified as high confidence. Alignments from PLAZA proteins, a comprehensive transcriptome of 83,271 unique contigs, and other conifer EST resources served as evidence for gene prediction.  The gene models were clustered with 13 other plant species, which resulted in a total of 20,717 gene families, of which 1,554 were predicted to be unique to conifers. Among the conifer gene families, 159 were composed exclusively of loblolly pine members. When compared with 24 fully sequenced plant species, the gene models from loblolly pine had the highest median and mean intron lengths. A total of 1,810 genes with primary introns between 20 and 158 Kbp in length were examined for intron mediated expression signals and repetitive content. Conifer genomes are full of repetitive DNA and the most significant contributions are from long terminal repeat (LTR) retrotransposons. The repetitive content was examined with a combined de novo and similarity approach to generate a genome-wide estimate of approximately 82%.
Back to: Next Generation Genome Annotation and Analysis
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