Identification of microsatellite loci, gene ontology and functional gene annotations in Indian salmon (Eleutheronema tetradactylum) through nextgeneration sequencing technology using illumina platform

Abstract

Whole genome sequencing was performed on three samples of four finger threadfin Eleutheronema tetradactylum (KET25, KET29 and KET30) using illumina NextSeq500 platform using 2×150 bp chemistry. 8,390,317, 7,085,775 and 8,461,589 high quality reads were obtained after trimming low quality reads and adapter sequence. These high quality reads obtained were used for de novo assembly and obtained a number of scaffolds. From these scaffolds of vast sequenced data, we were able to identify 60246, 46107 and 60907 Simple Sequence Repeats (SSR) markers in KET25, KET29 and KET30 respectively, which will be useful in population genetic analysis and other diversity studies in Indian salmon. The gene prediction on assembled scaffolds predicted 31,943 genes for KET25; 26,487 genes for KET29 and 31,654 genes for KET30 with average gene size of 458bp, 424bp and 459bp respectively. A total of 30,209, 25,107 and 29,943 genes were annotated against the NCBI Nr database for the samples respectively. E. tetradactylum is a commercially important fish species for many countries. This is the first report on the identification of genomic SSR markers in E. tetradactylum using NGS technology. This study provides an insight of baseline knowledge of the genome sequence of Indian salmon for future studies.