Comparative Transcriptome Sequencing Provides a Reference Resource for Expressed Genes and Associated Markers in Giant Tiger Prawn, Penaeus monodon Muscle Tissue

The shrimp industry has seen remarkable growth over the last four decades in India and the culture of P. monodon is experiencing a resurgence due to shifts in market demand, ecological considerations and broodstock and farming management. This study employs a transcriptomics approach to investigate the gene expression profiles of Penaeus monodon from two different origins. Large-scale transcriptomes generated 130,684 super-transcripts (GC 39.18%), with 92.94% BUSCO completeness and 39,974 have functional annotations, and 125 GO terms were identified. A total of 41,108 annotated transcripts examined, 19,637 SSR were identified and SNP mining resulted in identification of 69,028 SNPs with 26,785 indels, which included SNP within the genes of known function were found to be 504 nonsynonymous and 176 synonymous. Differentially expressed 79 genes between two locations fell under 12 GO terms, of which 4 GO terms were under biological process with 5 genes under glycolytic process and 4 under gluconeogenesis. Thus, the cSSRs and cSNP associated with coding genes identified could be a part of the marker set, which would be useful as marker loci or candidate genes to be use in construction of smaller SNP arrays for pedigree analysis and/or genomic selections.