Desenvolvimento e caracterização de marcadores microssatélites em Salminus Brasiliensis

Abstract

Salminus brasiliensis is a species of great economic and social importance in artisanal, subsistence, and sport fishing. It is endemic to the Paraná River and Lagoa dos Patos, encompassing five countries including Argentina, Bolivia, Brazil, Paraguay, and Uruguay. The aim of this study was to develop microsatellite molecular markers for this species. Its genome sequence was initially obtained through next-generation sequencing using an Illumina platform. Read quality was analyzed using the FastQC software. De novo assembly was carried out using SOAPdenovo2 and SPAdes programs and microsatellite mining using the MIcroSAtellite Identification Tool (MISA) and EasySSR programs. Batchprimers3 was employed to design the polymerase chain reaction (PCR) primers. The total number of sequenced reads was 411,994 with a length of 36–100 base pairs and Q = 39.06. SOAPdenovo2 yielded an N50 = 731, whereas SPAdes yielded an N50 = 1,649. A total of 56,893 microsatellites, with pentanucleotides predominating at 63.7%, were identified using the MISA program, whereas a total of 29,098 microsatellites, with trinucleotides predominating at 46.3%, were identified using the EasySSR program A total of 89 PCR primers were designed, of which 80 were successful. Thus, next-generation sequencing using the Illumina platform allowed the development of microsatellite markers for future genetic polymorphism studies in S. brasiliensis, where primers were also designed and tested in silico to guide future research.