W568A Reference Genome Sequence for Sugar Pine
Date: Saturday, January 10, 2015
Time: 8:30 AM
Room: Pacific Salon 6-7 (2nd Floor)
Kristian Stevens
,
Department of Evolution and Ecology, University of California, Davis, Davis, CA
Jill Wegrzyn
,
Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
Marc Crepeau
,
Department of Evolution and Ecology, University of California, Davis, Davis, CA
Daniela Puiu
,
Johns Hopkins University, School of Medicine, Baltimore, MD
Aleksey Zimin
,
Institute for Physical Science and Technology, University of Maryland, College Park, MD
Charis Cardeno
,
University of California, Davis, Davis, CA
Ann Holtz-Morris
,
Children's Hospital Oakland Research Institute, Oakland, CA
Maxim Koriabine
,
Children's Hospital Oakland Research Institute, Oakland, CA
Pedro J Martínez-García
,
Department of Plant Sciences University of California, Davis, CA
Pieter J. deJong
,
Children's Hospital Oakland Research Institute, Oakland, CA
James A Yorke
,
University of Maryland, College Park, MD
Steven L Salzberg
,
Johns Hopkins University, School of Medicine, Baltimore, MD
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
Sugar pine (
Pinus lambertiana) is considered to be the tallest and most massive member of the genus
Pinus. The estimated 31 billion base pair genome of
P. lambertiana also makes it the largest pine genome reference sequence. With nearly 50 percent more nuclear DNA than the current record holder,
P. taeda (Neale
et al. 2014), it is further notable as the largest genome sequenced and assembled to date. Repetitive elements are the primary driver of the large and variable sizes of the
Pinus genomes, a feature that has traditionally presented formidable challenges to available sequencing and assembly strategies.
The crux of our approach has been to leverage an aspect of conifer biology to reduce the complexity of the assembly problem. We have found that the limited amount of haploid DNA obtainable from of a single megagametophyte can be used to create an ensemble of libraries of sufficient complexity to form the basis of a high quality whole genome shotgun assembly. The resulting haploid sequence data is well suited to additional computational methods for complexity reduction. In this instance error correction was a vital step in reducing the number of erroneous k-mers in the data, making assembly with a de Bruijn graph assembler feasible. For additional contiguity, paired end megagametophyte coverage was augmented with deep coverage from multiple long-insert libraries (mate pair and novel fosmid DiTag libraries) from the parental diploid DNA.
Despite the challenges imposed by a larger and more repetitive genome, a matured procedure delivered assembly contiguity rivaling the smaller P. taeda assembly. For this larger genome, we made advances in the bias, complexity, and composition of the fragment and jumping libraries. The addition of a scaffolding step using full length transcripts from multiple libraries further improves the contiguity of the assembly. To annotate medium copy repeats, a pool of 5000 fosmids were sequenced, assembled, and used for validation and repeat annotation. Finally, we report on recent advances in the utility of single molecule sequencing.
