Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
Mar Biotechnol (NY). 2021 Jun;23(3):417-429. doi: 10.1007/s10126-021-10034-7. Epub 2021 Apr 30.
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.
贝类壳色多态性在遗传育种中很重要，但其壳色形成的分子信息机制尚不清楚。本研究采用高通量 RNA 测序技术，比较了来源于杂交双亲（橙色壳♂×黑色壳♀）的 F2 家系中橙色壳和黑色壳太平洋牡蛎 Crassostrea gigas 的编码 RNA 和非编码 RNA（ncRNA）的表达谱。结果共鉴定到 458 个差异表达基因（DEGs）、13 个差异表达长链非编码 RNA（DELs）和 8 个差异表达 microRNA（DEMs）。功能分析表明，这些 DEGs 显著富集在包括酪氨酸代谢和氧化磷酸化途径在内的 9 条通路中。橙色壳牡蛎中与黑色素合成和生物矿化相关的基因表达水平较高，而与类胡萝卜素色素形成或代谢相关的基因表达水平较低。此外，基于 ncRNA 分析，分别有 163 个和 20 个基因被 13 个和 8 个差异表达 lncRNA（DELs）和 miRNAs（DEMs）靶向调控。还进一步分析了潜在的 DELs-DEMs-DEGs 相互作用，共检测到 7 对 DEMs-DEGs 对，其中 lgi-miR-133-3p 和 lgi-miR-252a 靶向调控 tyrosinase-like protein 1，dme-miRNA-1-3p 靶向调控 cytochrome P450。这些结果表明，黑色素合成相关基因和 miRNA-mRNA 相互作用参与了橙色壳色形成，为海洋贝类壳色的分子调控机制提供了新的见解。
