Development and characterisation of novel polymorphic microsatellite loci in the freshwater mussel Lamellidens marginalis (Lamarck, 1819) using next generation sequencing. (1st October 2020) - Varshney, Shubham
ABSTRACT: The freshwater bivalve Lamellidens marginalis is native to Southeast Asia and one of the most widely used mussels for pearl production in the region. No studies have been carried out on stock characterisation of L. marginalis due to the lack of molecular markers. In the present study, the genome of L. marginalis was sequenced at low coverage using an Illumina paired-end approach. A total of 268, 403 contigs with a size range of 258–13, 308 bp was assembled from 2.5 million high quality reads. The contigs were mined and 26, 877 simple sequence repeats (SSRs) were identified using MIcroSAtellite identification tool software. Among SSRs, di-nucleotide repeats (15, 633 total) were more frequent than the tri- (6306), tetra- (4768), penta- (146) or hexa-nucleotide (24) repeats. Eighteen loci representing di- (eight), tri- (seven) and tetra- (four) nucleotide repeats were characterised using 30 individuals of L. marginalis. All loci showed moderate to high Polymorphic Information Content values. There was no linkage disequilibria between any pair of loci. Fourteen microsatellites were successfully amplified in the closely related species Lamellidens corrianus. These polymorphic microsatellite markers will be useful for genetic selection programs, as well as for studying the population and conservation genetics of L. marginalis and L. corrianus .