Molluscan shell color polymorphism is important in genetic breeding, while the molecular information mechanism for shell coloring is unclear. Here, high-throughput RNA sequencing was used to compare expression profiles of coding and non-coding RNAs (ncRNAs) from Pacific oyster Crassostrea gigas with orange and black shell, which were from an F2 family constructed by crossing an orange shell male with a black shell female. First, 458, 13, and 8 differentially expressed genes (DEGs), lncRNAs (DELs), and miRNAs (DEMs) were identified, respectively. Functional analysis suggested that the DEGs were significantly enriched in 9 pathways including tyrosine metabolism and oxidative phosphorylation pathways. Several genes related to melanin synthesis and biomineralization expressed higher whereas genes associated with carotenoid pigmentation or metabolism expressed lower in orange shell oyster. Then, based on the ncRNA analysis, 163 and 20 genes were targeted by 13 and 8 differentially expressed lncRNAs (DELs) and miRNAs (DEMs), severally. Potential DELs-DEMs-DEGs interactions were also examined. Seven DEMs-DEGs pairs were detected, in which tyrosinase-like protein 1 was targeted by lgi-miR-133-3p and lgi-miR-252a and cytochrome P450 was targeted by dme-miRNA-1-3p. These results revealed that melanin synthesis-related genes and miRNAs-mRNA interactions functioned on orange shell coloration, which shed light on the molecular regulation of shell coloration in marine shellfish.

软体动物壳颜色多态性在遗传育种中具有重要意义，而壳颜色的分子信息机制尚不清楚。在这里，高通量 RNA 测序用于比较来自太平洋牡蛎Crassostrea gigas的编码和非编码 RNA (ncRNA) 的表达谱橙色和黑色外壳，它们来自 F2 家族，由橙色外壳的雄性和黑色外壳的雌性杂交而成。首先，分别鉴定了 458、13 和 8 个差异表达基因 (DEG)、lncRNA (DEL) 和 miRNA (DEM)。功能分析表明，DEGs在酪氨酸代谢和氧化磷酸化途径等9条途径中显着富集。在橙壳牡蛎中，与黑色素合成和生物矿化相关的几个基因表达较高，而与类胡萝卜素色素沉着或代谢相关的基因表达较低。然后，基于 ncRNA 分析，163 和 20 个基因分别被 13 和 8 个差异表达的 lncRNA（DEL）和 miRNA（DEM）靶向。还检查了潜在的 DEL-DEM-DEG 相互作用。检测到七个 DEMs-DEGs 对，其中酪氨酸酶样蛋白 1 被 lgi-miR-133-3p 和 lgi-miR-252a 靶向，细胞色素 P450 被 dme-miRNA-1-3p 靶向。这些结果表明黑色素合成相关基因和 miRNAs-mRNA 相互作用对橙色壳着色起作用，这揭示了海洋贝类壳着色的分子调控。