Optimizing depth and type of high-throughput sequencing data for microsatellite discovery.

ABSTRACT:

Premise

Simple sequence repeat (SSR) markers (microsatellites) are a mainstay of many labs, especially when working on a limited budget, carrying out preliminary analyses, and in teaching. Whether SSRs mined from plant genomes or transcriptomes are preferred for certain applications, and the depth of sequencing needed to allow efficient SSR discovery, has not been tested.

Methods

I used genome and transcriptome high-throughput sequencing data at a range of sequencing depths to compare efficacy of SSR identification. I then tested primers from tomato for amplification, polymorphism, and transferability to related species.

Results

Small assemblies (two million read pairs) identified ca. 200-2000 potential markers from the genome assemblies and ca. 600-3650 from the tran

SUBMITTER: Chapman MA 

PROVIDER: S-EPMC6858294 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature