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

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

来源：Bioinformatics, 2013, 29(12): 1492-1497.

DOI：10.1093/bioinformatics/btt178

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 356bp. 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.

• 出版日期2013-6-15