W562Recent Progress in the Shotgun Sequencing of Conifer Mega-Genomes
Date: Saturday, January 11, 2014
Time: 10:50 AM
Room: Pacific Salon 6-7 (2nd Floor)
Kristian 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
Pedro J Martinez-Garcia
,
Department of Plant Sciences University of California, Davis, CA
Aleksey Zimin
,
Institute for Physical Science and Technology, University of Maryland, College Park, MD
Daniela Puiu
,
Johns Hopkins University, School of Medicine, Baltimore, MD
Maxim Koriabine
,
Children's Hospital Oakland Research Institute, Oakland, CA
Charis Cardeno
,
University of California, Davis, Davis, CA
Ann Holtz-Morris
,
Children's Hospital Oakland Research Institute, Oakland, CA
Pieter J. deJong
,
Children's Hospital Oakland Research Institute, Oakland, CA
Steven L Salzberg
,
Johns Hopkins University, School of Medicine, Baltimore, MD
James A Yorke
,
University of Maryland, College Park, MD
Chuck Langley
,
University of California, Davis, Davis, CA
David Neale
,
Dept. Plant Sciences University of California Davis, Davis, CA
While the conifers are the most ecologically important representatives of the gymnosperms, few published reference genomes exist. The sheer size and complexity of conifer genomes has presented formidable challenges to available reconstruction strategies. We report on progress in sequencing, assembling, and characterizing the genomes of three conifer species: loblolly pine, sugar pine, and Douglas fir.
Whole genome shotgun sequencing of a single haploid megagametophyte results in a dataset of reduced complexity. The resulting haploid data is well suited for additional computational methods of complexity reduction. With limited DNA, paired end megagametophyte coverage is augmented with deep sequencing of multiple long-insert libraries (fosmid DiTags and Illumina mate pair libraries) from the parental diploid DNA. The final datasets have been small enough to be assembled using the classic overlap-layout-consensus approach. We report on recent progress made in applying our strategy to genomes of sugar pine, Douglas fir, as well as our recent and forthcoming loblolly pine genomes.
A complementary approach to complexity reduction based on the sequencing small fosmid pools from the genome of the diploid parent. The effectively haploid assemblies have very high quality scaffolds. We applied this strategy on a small scale to our three conifer genomes for validation and high quality repeat annotation.
To obtain high resolution annotation of recombination rate in loblolly pine, assign scaffolds to chromosomes, and validate our V1.01 assembly, over 600 megagametophytes were genotyped by random shotgun sequencing. We call this strategy Haplotyping by Sequencing (HBS).
