Genome-wide assessment and characterization of simple sequence repeats (SSRs) makers for Capoeta aculeata (Valenciennes, ۱۸۴۴) using NGS data

The species Capoeta aculeata (Valenciennes, ۱۸۴۴) is one of the most important freshwater species endemics to Iran. However, the investigation of a population genetic structure of this species is limited by the low number of molecular markers currently described. In this study, we implemented next generation sequencing technology to identify polymorphic microsatellite markers and investigate the population genetic structure of C. aculeata sampled from three geographical sites in Iran. We sequenced ۶۰ individuals from three populations occurring in the Zagros basin. We characterized and developed ۳۶ novel polymorphic microsatellite markers and these loci were examined in ۱۲۰ individuals from three populations occurring in the Zagros basin. The average number of alleles per locus varied from ۱.۷ to ۱۶.  (average=۷.۸۹). The results showed that, the polymorphism information content (PIC) of these SSR loci varied from ۰.۲۵۴ to ۰.۸۸۸. The observed heterozygosity (Ho) per locus ranged from ۰.۱۷۰ to ۰.۸۸۱, while the expected heterozygosity (He) per locus was from ۰.۱۷۰ to ۰.۸۸۱. Among these SSR loci, ۲۰ loci deviated significantly from the Hardy–Weinberg equilibrium after Bonferroni correction (p<۰.۰۵). These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeate populations and other closely related species.

Keywords:

Capoeta aculeate , Microsatellite markers , Next generation sequencing (NGS) , Genetic structure