Muscle transcriptome sequencing revealed thermal stress responsive regulatory genes in farmed rohu, Labeo rohita (Hamilton, 1822)

Abstract

Abstract Rohu, Labeo rohita is one of the most important aquaculture species in the Indian subcontinent. The physiological responses to thermal stress or climate change at the molecular level are less understood in rohu. In the present work, transcriptome sequencing was carried out in muscle tissue of the rohu in response to heat stress (35ºC) in comparison with the control (28ºC). A total of 125 Gb of sequence data was generated and the raw-reads were filtered and trimmed, that resulted in 484 million quality reads. Reference-based assembly of reads was performed using L. rohita genome and a total of 90.17% of reads were successfully mapped. A total of 37,462 contigs were assembled with an N50 value of 1854. The differential expression analysis revealed a total of 107 differentially expressed genes (DEGs) (15 up-, 37 down-, and 55 neutrally-regulated) as compared to the control group (Log2FC>2, P<0.05). Gene enrichment analysis of DEGs indicates that transcripts were associated with molecular, biological, and cellular activities. The randomly selected differentially expressed transcripts were validated by RT-qPCR and found consistent expression patterns in line with the RNA-seq data. Several transcripts such as Serpine 1(HSP47), HSP70, HSP90alpha, Rano class II histocompatibility A beta, PGC-1 and ERR-induced regulator, Proto-oncogen c-fos, myozenin2, Alpha-crystallin B chain-like protein, Angiopoietin-like protein 8, Acetyl-CoA carboxylases, etc. have been identified in muscle tissue of rohu that are associated with stress/immunity. This study identified the key biomarker Serpine 1(HSP47), which showed significant up-regulation (~2 to 3-fold) in muscle tissue of rohu exposed to high temperature. This study can pave a path for the identification of stress-responsive biomarkers linked with thermal adaptations in the farmed carps.