Dataset Information

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

ABSTRACT: UNLABELLED: 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.

SUBMITTER: Birol I

PROVIDER: S-EPMC3673215 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature

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Publications

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

Birol Inanc I Raymond Anthony A Jackman Shaun D SD Pleasance Stephen S Coope Robin R Taylor Greg A GA Yuen Macaire Man Saint MM Keeling Christopher I CI Brand Dana D Vandervalk Benjamin P BP Kirk Heather H Pandoh Pawan P Moore Richard A RA Zhao Yongjun Y Mungall Andrew J AJ Jaquish Barry B Yanchuk Alvin A Ritland Carol C Boyle Brian B Bousquet Jean J Ritland Kermit K Mackay John J Bohlmann Jörg J Jones Steven J M SJ

Bioinformatics (Oxford, England) 20130522 12

<h4>Unlabelled</h4>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 ...[more]

PMID: 23698863

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Project description:Tree improvement programs select genotypes for faster growth, at both early and late stages, to increase yields over unimproved material, and the improvement is frequently attributed to genetic control in growth parameters among genotypes. Underutilized genetic variability among genotypes also has the potential to ensure future gains are possible. However, the genetic variation in growth, physiology and hormone control among genotypes generated from different breeding strategies has not been well characterized in conifers. We assessed growth, biomass, gas exchange, gene expression and hormone levels in white spruce seedlings obtained from three different breeding strategies (controlled crosses, polymix pollination, open pollination) using parents grafted into a clonal seed orchard in Alberta, Canada. A pedigree-based best linear unbiased prediction (ABLUP) mixed model was implemented to quantify variability and narrow-sense heritability for target traits and the levels of several hormones and expression of gibberellin-related genes in apical internodes were also determined. Over the first 2-years of development, the estimated heritabilities for height, volume, total dry biomass, above ground dry biomass, root:shoot ratio and root length, varied between 0.10 and 0.21, with height having the highest value. The ABLUP values showed large genetic variability in growth and physiology traits both between families from different breeding strategies, and within families. The principal component analysis showed that developmental and hormonal traits explained 44.2% and 29.4% of the total phenotypic variation between the three different breeding strategies and two growth groups. In general, controlled crosses from the fast growth group showed the best apical growth, with more accumulation of indole-3-acetic acid, abscisic acid, phaseic acid, and a 4-fold greater gene expression of PgGA3ox1 in genotypes from controlled crosses versus those from open pollination, but in some cases, open-pollination from the fast and slow growth groups showed the best root development, higher water use efficiency (iWUE and δ13C) and more accumulation of zeatin and isopentenyladenosine. In conclusion, tree domestication can lead to trade-offs between growth, carbon allocation, photosynthesis, hormone levels and gene expression, and we encourage the use of this phenotypic variation identified in improved and unimproved trees to advance white spruce tree improvement programs.

Dataset Information

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

Publications

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

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