ArticleScientific reports2019
Comparative genomics approach to build a genome-wide database of high-quality, informative microsatellite markers: application on Phytophthora sojae, a soybean pathogen.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 5 citations in OpenAlex.
- Revisiting the PCR-Based Molecular Approaches for Mycotoxigenic Fusarium Species Detection and Quantification in Wheat.Comprehensive reviews in food science and food safety · 2026Review
- Genome-Wide Informative Microsatellite Markers and Population Structure ofJournal of fungi (Basel, Switzerland) · 2023Article
- Characterization and microsatellite marker development for a common bark and ambrosia beetle associate, Geosmithia obscura.MicrobiologyOpen · 2022Article
- Genotyping by sequencing suggests overwintering of Peronospora destructor in southwestern Québec, Canada.Molecular plant pathology · 2022Article
- Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
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