Microsatellite mining in the genus Colletotrichum

Abstract Genomic data available in the public database are valuable resources for mining microsatellite or simple sequence repeat (SSR) markers. Though microsatellite markers are available for a few Colletotrichum species but their meagre number and species specificity warrants additional search in the publicly available genome databases. Therefore, in the present investigation, eight Colletotrichum genomes belonging to six clades were mined for microsatellites and we developed 57,170 microsatellite markers. Di and tri microsatellite motifs accounted for >80% share while tetra to deca motifs were rare. Ninety-nine percent of the microsatellites produced a single amplicion when subjected to electronic PCR. In silico cross transferability of the microsatellites exhibited specificity to respective species, illustrating the conserved sequences flanking the microsatellite regions. We found maximum microsatellite cross transferability among C. acutatum , C. fioriniae , and C. nymphaeae genomes that belong to acutatum clade. Thus suggesting that the microsatellites developed for one species in a genome clade may amplify other species of same clade. PCR amplification of 150 microsatellite markers confirms the locus specific amplification. Among the 110 microsatellites used for genotyping the 14 diverse races of C. lindemuthianum , 100 markers were polymorphic. Genotyping of 14 diverse bean anthracnose races with 50 SSR markers grouped them as per their geographic location. We report microsatellite markers for eight Colletotrichum genomes that belong to six clades and this is the first study of genome wide microsatellite marker development in the genus. These genome wide SSR markers will provide a useful tool to discover the population structure in Colletotrichum species and evolutionary insights in future.