Table_3_Comparative Transcriptome Analysis Reveals Molecular Basis Underlying Fast Growth of the Selectively Bred Pacific Oyster, Crassostrea gigas.xlsx

Fast growth is one of the most desired traits for all food animals, which affects the profitability of animal production. The Pacific oyster, Crassostrea gigas, is an important aquaculture shellfish around the world with the largest annual production. Growth of the Pacific oyster has been greatly improved by artificial selection breeding, but molecular mechanisms underlying growth remains poorly understood, which limited the molecular integrative breeding of fast growth with other superior traits. In this study, comparative transcriptome analyses between the fast-growing selectively bred Pacific oyster and unselected wild Pacific oysters were conducted by RNA-Seq. A total of 1,303 protein-coding genes differentially expressed between fast-growing oysters and wild controls were identified, of which 888 genes were expressed at higher levels in the fast-growing oysters. Functional analysis of the differentially expressed genes (DEGs) indicated that genes involved in microtubule motor activity and biosynthesis of nucleotides and proteins are potentially important for growth in the oyster. Positive selection analysis of genes at the transcriptome level showed that a significant number of ribosomal protein genes had undergone positive selection during the artificial selection breeding process. These results also indicated the importance of protein biosynthesis and metabolism for the growth of oysters. The alternative splicing (AS) of genes was also compared between the two groups of oysters. A total of 3,230 differential alternative splicing events (DAS) were identified, involved in 1,818 genes. These DAS genes were associated with specific functional pathways related to growth, such as “long-term potentiation,” “salivary secretion,” and “phosphatidylinositol signaling system.” The findings of this study will be valuable resources for future investigation to unravel molecular mechanisms underlying growth regulation in the oyster and other marine invertebrates and to provide solid support for breeding application to integrate fast growth with other superior traits in the Pacific oyster.

快速生长是所有食用动物最受青睐的性状之一，直接影响畜牧水产生产的经济效益。太平洋牡蛎（Pacific oyster, Crassostrea gigas）是全球范围内重要的养殖贝类，年产量位居同类养殖物种之首。尽管通过人工选择育种已大幅提升了太平洋牡蛎的生长性能，但其生长调控的分子机制仍未明晰，这限制了将快速生长与其他优良性状相结合的分子聚合育种工作。本研究通过RNA测序（RNA-Seq）技术，对快速生长选育系太平洋牡蛎与未选育的野生太平洋牡蛎开展了比较转录组分析。研究共鉴定出1303个在快速生长组与野生对照组间存在差异表达的蛋白编码基因，其中888个基因在快速生长牡蛎中呈高表达状态。差异表达基因（differentially expressed genes, DEGs）的功能富集分析显示，参与微管运动活性、核苷酸与蛋白质生物合成的基因，可能对牡蛎的生长具有关键调控作用。转录组水平的基因正选择分析结果表明，在人工选择育种过程中，大量核糖体蛋白基因经历了正选择作用，上述结果同样印证了蛋白质生物合成与代谢在牡蛎生长过程中的重要性。研究还对两组牡蛎的基因可变剪接（alternative splicing, AS）情况进行了比较分析，共鉴定出3230个差异可变剪接事件（differential alternative splicing events, DAS），涉及1818个基因。这些差异可变剪接基因富集于与生长相关的特定功能通路，例如“长时程增强”“唾液分泌”以及“磷脂酰肌醇信号系统”。本研究的结果可为后续解析牡蛎及其他海洋无脊椎动物的生长调控分子机制提供重要参考，并为太平洋牡蛎快速生长与其他优良性状聚合的育种应用提供坚实的理论支撑。