Transcriptomic analysis identifies candidate genes for shell colour formation in the Venus clam Cyclina sinensis

Some bivalves are important in fisheries and aquaculture, and provide significant economic benefits to humans. The diversity in shell colour among bivalves has received attention due to its potential in breeding and its relevance to the study of speciation and adaptation. In this study, the relationship between whole-genome-scale gene expression and shell coloration in the clam Cyclina sinensis was analysed using high-throughput Illumina sequencing technology. A total of 15,367 annotated genes and 4,425 novel genes were detected based on transcript assembly. The results of the transcriptome analysis show that 49 genes were differentially expressed in the outer mantle fold tissue of purple- vs white-shelled specimens. These genes include three lipoprotein receptor genes, low-density lipoprotein receptor gene (ldlr), low-density lipoprotein receptor-related protein 4 (lrp4) and scavenger receptor cysteine-rich protein gene (srcr). These genes may be involved in the transport of carotenoid pigments. Moreover, as shown by the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, several receptor activity terms and a glycosphingolipid biosynthesis pathway were detected, and these might be involved in shell coloration. Together with the analyses of differentially expressed genes, our results suggest a possible molecular mechanism governing the selective transport of carotenoids in the mantle of purple-shelled clams and shell colour formation. The results of this study may help to elucidate the colour formation mechanism in clam shells.