Linum spp. genomic resources study
Developing genomic resources in a non-model genus Linum via 454 pyrosequencing and genomic reduction.
/ It is challenging to develop informative genomic resources such as contigs or SNPs for genomic and evolutionary studies of a non-model species with a complex and unsequenced genome. This study applied a next-generation sequencing (NGS) technique in combination with genomic reduction and an advanced bioinformatics tool to identify contigs and SNPs in Linum, a genus with an important agricultural crop, flax. A full Roche 454 GS FLX run of 16 diverse Linum samples representing cultivated flax (L. usitatissimum L.) and its wild progenitor (pale flax; L. bienne Mill.) generated roughly 1.6 million sequence reads with a total length of 498 Mbp. Application of the computational pipeline called DIAL (de novo identification of alleles) identified 713 contigs and 1,067 SNPs. Seventy-five (94.9%) of the selected contigs were validated with Sanger sequencing and 256 (94.1%) of the selected SNPs were confirmed. The Sanger sequencing with 75 primer sets generated 230 (80%) more SNPs and indels than the DIAL prediction on the same contigs. The effective SNP and indel discovery rates were 1.37 SNPs/100bp and 5.9 indels/10,000bp, respectively. These new genomic resources are useful for genomic and evolutionary studies of cultivated flax and its wild relative. Our findings also help to demonstrate the utility of NGS technologies in sampling the complex genomes of non-model organisms.
This study applied a next-generation sequencing (NGS) technique in combination with genomic reduction and an advanced bioinformatics tool to identify contigs and SNPs in Linum, a genus with an important agricultural crop, flax, by examining 16 diverse Linum samples representing cultivated flax (L. usitatissimum L.) and its wild progenitor (pale flax; L. bienne Mill.) using Roche 454 GS FLX Titanium chemistry and the computational pipeline called DIAL (de novo identification of alleles).