Transcriptome analysis reveals the pigmentation-related genes in two shell color strains of the Manila clam Ruditapes philippinarum

The Manila clam, Ruditapes philippinarum, is an ecologically and economically important marine bivalve species. In this study, we conducted transcriptomic sequencing of two different shell color strains (O and Z) before color appearance (uncolored juvenile clam) and pigmented shell color (colored juvenile clam) and investigated the analysis of the differential expression patterns of specific genes associated with pigmentation by RNA-seq and time course qPCR analysis. The transcription level of 16 differentially expressed genes (DEGs) related with shell color was analyzed by qRT-PCR to validate the performance of RNA-seq from Illumina sequence data where most of them were up-regulated. Two genes were down-regulated after the occurrence of zebra clam stripes compared with uncolored zebra clam. The trend of gene expression obtained by qPCR was basically consistent with that of RNA-seq. The synthesis of melanin in bivalves plays potential roles in the pigmentation of the shell and is closely related to the formation of the surface pattern. The porphyrin metabolism combined with tyrosinase and melanogenesis signaling pathway is a novel finding in shell color determination of R. philippinarum. This study sheds light on the pigmentation and coloration mechanism of the Manila clam.

Automated summary

This study investigated the relationship between shell color and gene expression in the Manila clam through transcriptomic sequencing and real-time qPCR analysis, revealing the significant role of melanin synthesis in shell pigmentation and its close association with surface pattern formation. The discovery of the porphyrin metabolism combined with tyrosinase and melanogenesis signaling pathway as a novel mechanism in shell color determination of Ruditapes philippinarum sheds light on the pigmentation and coloration process in this species.