文章基本信息

标题：Comparative genomics approach to build a genome-wide database of high-quality, informative microsatellite markers: application on Phytophthora sojae, a soybean pathogen
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作者：Guohong Cai ; Tomara J. Fleury ; Ning Zhang 等
期刊名称：Scientific Reports
电子版ISSN：2045-2322
出版年度：2019
卷号：9
期号：1
页码：1-6
DOI：10.1038/s41598-019-44411-z
出版社：Springer Nature
摘要：Microsatellites are a tract of repetitive, short DNA motifs (usually 1 to 6 bp) abundant in eukaryotic genomes. They are robust molecular markers in many areas of studies. Development of microsatellite markers usually involves three steps: (1) obtaining microsatellite-containing sequences, (2) primer design, and (3) screening microsatellite loci for polymorphism. The first and third steps require considerable resources. Next generation sequencing technologies have greatly alleviated the constraint of the first step. In this study, we leveraged the availability of genome assemblies of multiple individuals in many species and designed a comparative genomics approach to bioinformatically identify polymorphic loci. Our approach can eliminate or greatly reduce the need of experimental screening for polymorphism and ensure that the flanking regions do not have length difference that would confound interpretation of genotyping results using microsatellite markers. We applied this approach on Phytophthora sojae, a soybean pathogen, and identified 157 high-quality, informative microsatellite markers in this oomycete. Experimental validation of 20 loci supported bioinformatics predictions. Our approach can be readily applied to other organisms of which the genomes of multiple individuals have been sequenced.