Characterization and expression profiles of muscle transcriptome in Schizothoracine fish, Schizothorax prenanti

Abstract

Schizothorax prenanti is a cold-water fish species with great economic importance in aquaculture in Western China, and the underlying mechanisms of muscle development and growth in S. prenanti remain to be elucidated. In this study, deep RNA sequencing was performed to provide an in-depth view of the transcriptome of skeletal muscle of S. prenanti with the specific objective to identify expressed genes in the skeletal muscle of S. prenanti at 30 days post-hatching (S01), 1 year (S02), and 3 years (S03). De novo assembly of high-quality reads generated 132,784 transcripts with an average length of 1282 bp and 67,596 unigenes with an average length of 1559 bp. 2445 unigenes were differentially expressed with 1483 up-regulated and 962 down-regulated in the skeletal muscle of S. prenanti at S01 and S02 stages, and 1936 unigenes were significantly impacted at S02 and S03 stages with 1153 increased and 783 decreased. GO analysis showed that the differentially expressed genes are involved in various biological processes with dominance by cell & cell part, binding & catalytic activity, and cellular process & metabolic process. KEGG enrichment suggested that there are considerable differences in the physiological processes at different stages of muscle development and growth of S. prenanti. PPAR signaling pathway, cardiac muscle contraction, fatty acid metabolism, tight junction, and focal adhesion were the top pathways enriched in comparison between S01 and S02 stages. Whereas significant enrichment of the TCA cycle, fatty acid metabolism, fatty acid elongation in mitochondria, valine, leucine and isoleucine degradation, porphyrin and chlorophyll metabolism, and propanoate metabolism pathway was found in differentially expressed genes identified between S02 and S03 stages. This study provides not only an overall insight into the global gene expression landscape in the skeletal muscle of S. prenanti, but also candidate genes or markers that can be used for further investigations of the underlying mechanisms of skeletal muscle development and growth of S. prenanti.

Keywords: RNA-seq; Schizothorax prenanti; Skeletal muscle.