Developing genomic resources in two Linum species via 454 pyrosequencing and genomic reduction
Article first published online: 18 DEC 2011
© Her Majesty the Queen in Right of Canada 2011, as represented by the Minister of Agriculture and Agri-Food Canada.
Molecular Ecology Resources
Volume 12, Issue 3, pages 492–500, May 2012
How to Cite
FU, Y.-B. and PETERSON, G. W. (2012), Developing genomic resources in two Linum species via 454 pyrosequencing and genomic reduction. Molecular Ecology Resources, 12: 492–500. doi: 10.1111/j.1755-0998.2011.03100.x
- Issue published online: 9 APR 2012
- Article first published online: 18 DEC 2011
- Received 1 July 2011; revision received 31 October 2011; accepted 16 November 2011
- genomic resources;
- next-generation sequencing;
- nonmodel organism;
Recent advances in next-generation DNA sequencing (NGS) have enhanced the development of genomic resources such as contigs or single-nucleotide polymorphisms (SNPs) for evolutionary studies of a nonmodel species with a complex and unsequenced genome. This study presents an application of a NGS technique in combination with genomic reduction and advanced bioinformatics tools to identify contigs and SNPs from multiple samples of two Linum species. A full Roche 454 GS FLX run of 16 diverse Linum samples representing cultivated flax (Linum usitatissimum L.) and its wild progenitor (Linum bienne Mill.) generated approximately 1.6 million sequence reads with a total length of 498 Mbp. Application of the computational pipeline de novo identification of alleles identified 713 contigs and 1067 SNPs. A blast search revealed alignments of all 713 contigs with 491 existing Linum scaffolds and gene annotations associated with 512 contigs. Sanger sequencing confirmed 95% of 79 selected contigs and 94% of 272 SNPs and identified 211 new SNPs and 19 new indels. The scored 454 SNP data were highly imbalanced for assayed samples. These findings not only are useful for evolutionary studies of Linum species but also help to illustrate the utility of NGS technologies in SNP discovery for nonmodel organisms.