Identification of Shell Color-Associated Genes Using Mantle Branch-Specific RNA Sequencing of Yellow-Colored Line of Pearl Oyster Pinctada fucata martensii

The yellow-colored line of pearl oyster Pinctada fucata martensii displays a yellow prismatic layer and a white nacreous layer that can be used as an ideal model for research on shell color formation. Micro-Raman spectroscopy and transcriptome analyses were performed to explore the potential molecular mechanism underlying the phenotype differentiation. The micro-Raman spectroscopy results indicate that the prismatic layer exhibits distinct characteristic peaks of carotenoids, while these peaks are not prominent in the nacreous layer. In the transcriptome comparison of the central zone of mantle and mantle edge tissue, which function in nacreous and prismatic layer formation, respectively, 935 significantly differentially expressed genes (DEGs) were identified, with 385 genes upregulated and 227 genes downregulated (∣log2(Fold change)∣> 1 and false discovery rate < 0.05) in the mantle edge tissue. Among these genes, some were associated with melanoma/melanogenesis, such as tyrosinase, zinc metalloprotease, glutathione S-transferase, and ATP-binding cassette sub-family; some were associated with the carotenoid-related pathway, including scavenger receptors, cytochrome P450 and lipoprotein receptor. Genes associated with porphyrin metabolism, including porphobilinogen deaminase, and copper/zinc superoxide dismutase, and genes associated with shell matrix protein, including amorphous calcium carbonate binding protein, shematrin, PIF, and collagen, also exhibited significantly different expressions. It is speculated that the different colours between prismatic layer and nacreous layer in the yellow-colored line of P. f. martensii might be resulted from melanin, carotenoids and porphyrin metabolism, while genes related to shell structure and biomineralization might also affect coloration. Our results provide new insights to understand the mechanism of shell color formation in mollusca.