A genome survey sequence (GSS) analysis and microsatellite marker development for Indian mackerel, Rastrelliger kanagurta, using Ion Torrent technology

A next generation sequencing platform (Ion Torrent PGM™) was used to generate a partial genome survey sequence (GSS) dataset to develop microsatellite markers from R. kanagurta genomic DNA. Data generated included a total of 399,794 sequence reads (81.29 Mbp) with 16,209 sequence reads successfully assembled. This produced 327 contigs averaging 677 bp in length in addition to the SSR markers. Results based on GSS BLASTx and BLASTn possessed significant similarity (E value < 10− 6) with available data in public databases, with the majority matching well to previously reported fish sequences. A total of 7891 SSR-containing motif repeats of which 1688 qualified for primer design were generated. After optimization and testing for reproducibility and polymorphism, eight microsatellite markers were deemed suitable for future population genetic analysis in the target species.