Assembling the 20 Gb white spruce (Picea glauca)... : Bioinformatics (original) (raw)

ORIGINAL PAPERS: GENOME ANALYSIS

Assembling the 20 Gb white spruce ( Picea glauca ) genome from whole-genome shotgun sequencing data

Inanc Birol
Anthony Raymond
Shaun D. Jackman
Stephen Pleasance
Robin Coope
Greg A. Taylor
Macaire Man Saint Yuen
Christopher I. Keeling
Dana Brand
Benjamin P. Vandervalk
Heather Kirk
Pawan Pandoh
Richard A. Moore
Yongjun Zhao
Andrew J. Mungall
Barry Jaquish
Alvin Yanchuk
Carol Ritland
Brian Boyle
Jean Bousquet
Kermit Ritland
John MacKay
Jörg Bohlmann
Steven J.M. Jones

Bioinformatics

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)

1492

1497

June 15, 2013

| DOI: 10.1093/bioinformatics/btt178

ABSTRACT

White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and providing genomics resources for this commercially valuable tree will help improve forest management and conservation efforts. Sequencing and assembling the large and highly repetitive spruce genome though pushes the boundaries of the current technology. Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software. We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20 356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft assemblies.

Availability:

The Picea glauca genome sequencing and assembly data are available through NCBI (Accession#: ALWZ0100000000 PID: PRJNA83435). http://www.ncbi.nlm.nih.gov/bioproject/83435.

Contact:

[email protected]

Supplementary information:

Supplementary data are available at Bioinformatics online.