Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data
By Inanç Birol, Anthony Raymond, Shaun D. Jackman, S. Pleasance, R. Coope, G. Taylor, M. Yuen, Christopher I. Keeling, Dana Brand, Benjamin P. Vandervalk and 14 more. Bioinform., 2013
357 citations recorded by the source corpus.
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: ibirol@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online.
Subfields: Cancer Research, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/315b6396b454e85b7012e41873eb03bb7618b5e0
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Citations in the corpus
- MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN] (2013, background): “…and noncoding RNA (ncRNA) genes as revealed through RNA-Seq and proteomics studies (Campbell et al., 2007; Hanada et al., 2007; Jiang et al., 2009; Yang et al., 2009; Li et al., 2010; Lin et al., 2010; Donoghue et al., 2011; Garg et al., 2011; Boerner and McGinnis, 2012; Moghe et al., 2013).”
- Genomic selection in forest tree breeding: the concept and an outlook to the future (2014, background): “White spruce (Picea glauca) genome sequence was completed in 2013 (Birol et al. 2013).”
- Draft genome of the living fossil Ginkgo biloba (2016, background): “glauca DNA was derived from apical shoots [52], which may have introduced considerable heterozygosity.”
- High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species (2015, background): “Recently, genomes of three economically important Pinaceae conifers (Picea abies, P. glauca, and Pinus taeda) have been sequenced (Birol et al. 2013; Neale et al. 2014; Nystedt et al. 2013; Warren et al. 2015), thereby opening a new avenue for investigating genomic evolution of these conifers.”
- ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter (2016, unknown): “For example, ABySS 1.0 was used to assemble the 20-Gbp white spruce genome with 115 cluster nodes and ∼ 4.3 TB of aggregate memory (Birol et al. 2013).”