Transcriptomic analysis of the ark shell Scapharca kagoshimensis: De novo assembly and identification of genes and pathways involved growth

Abstract

To understand the molecular mechanism associated with growth variability in bivalves, we employed Illumina RNA-seq technology to analyze the transcriptomic profiles from fast- and slow-growing individuals in one full-sib family of the ark shell, Scapharca kagoshimensis. De novo assembly of S. kagoshimensis transcriptome yielded 276,082,016 raw reads, which were assembled into 98,502 unique transcripts using the Trinity strategy. A total of 6357 differentially expressed genes (DEGs) were obtained between fast- and slow-growing individuals, with 68 up-regulated genes and 846 down-regulated genes. Functional annotation revealed that most of the DEGs were classified to subunits of the large or small ribosomal protein, all of which showed significantly lower expression levels in the fast-growing group than those in the slow-growing group. Gene Ontology (GO) enrichment analysis indicated that most of the DEGs were involved in biological processes, followed by molecular functions and cellular components. The most Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enriched genes were related to energy metabolism, protein synthesis and degradation. These findings presented the potential links between genes expression and contrasting phenotypes in the ark shell, suggesting that the fast-growing phenotype might be attributed to lower energy demands for metabolism maintenance, and more effective protein biosynthesis and degradation in bivalves.