Genome-wide microsatellite identification in the fungus Anisogramma anomala using Illumina sequencing and genome assembly.

ABSTRACT: High-throughput sequencing has been dramatically accelerating the discovery of microsatellite markers (also known as Simple Sequence Repeats). Both 454 and Illumina reads have been used directly in microsatellite discovery and primer design (the "Seq-to-SSR" approach). However, constraints of this approach include: 1) many microsatellite-containing reads do not have sufficient flanking sequences to allow primer design, and 2) difficulties in removing microsatellite loci residing in longer, repetitive regions. In the current study, we applied the novel "Seq-Assembly-SSR" approach to overcome these constraints in Anisogramma anomala. In our approach, Illumina reads were first assembled into a draft genome, and the latter was then used in microsatellite discovery. A. anomala is an obligate bi

SUBMITTER: Cai G 

PROVIDER: S-EPMC3842260 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature