Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China.
Mol Biol Rep. 2024 Oct 29;51(1):1101. doi: 10.1007/s11033-024-10056-z.
The genus Megalobrama holds significant economic value in China, with M. terminalis (Black Amur bream) ranking second in production within this group. However, lacking comprehensive genomic and transcriptomic data has impeded research progress. This study aims to fill this gap through an extensive transcriptomic analysis of M. terminalis.
We utilized PacBio Isoform Sequencing to generate 558,998 subreads, totaling 45.52 Gb, which yielded 22,141 transcripts after rigorous filtering and clustering. Complementary Illumina short-read sequencing corrected 967,114 errors across these transcripts. Our analysis identified 12,426 non-redundant isoforms, with 11,872 annotated in various databases. Functional annotation indicated 11,841 isoforms matched entries in the NCBI non-redundant protein sequences database. Gene Ontology analysis categorized 10,593 isoforms, revealing strong associations with cellular processes and binding functions. Additionally, 8203 isoforms were mapped to pathways in the Kyoto Encyclopedia of Genes and Genomes, highlighting significant involvement in immune system processes and complement cascades. We notably identified key immune molecules such as alpha-2-macroglobulin and complement component 3, each with multiple isoforms, underscoring their potential roles in the immune response. Our analysis also uncovered 853 alternative splicing events, predominantly involving retained introns, along with 672 transcription factors and 426 long non-coding RNAs.
The high-quality reference transcriptome generated in this study provides a valuable resource for comparative genomic studies within the Megalobrama genus, supporting future research to enhance aquaculture stocks.
鳊属鱼类在中国具有重要的经济价值，其中圆口铜鱼（黑背大口鲇）的产量位居该属第二。然而，由于缺乏全面的基因组和转录组数据，研究进展受到了阻碍。本研究旨在通过对圆口铜鱼进行广泛的转录组分析来填补这一空白。
我们利用 PacBio Isoform Sequencing 生成了 558998 条亚读长，总计 45.52Gb，经过严格的过滤和聚类后得到 22141 条转录本。补充的 Illumina 短读测序纠正了这些转录本中的 967114 个错误。我们的分析鉴定了 12426 个非冗余的异构体，其中 11872 个在各种数据库中被注释。功能注释表明，11841 个异构体与 NCBI 非冗余蛋白质序列数据库中的条目匹配。GO 分析将 10593 个异构体分类为与细胞过程和结合功能密切相关的类别。此外，8203 个异构体被映射到京都基因与基因组百科全书（KEGG）中的通路，突出了它们在免疫系统过程和补体级联中的重要参与。我们特别鉴定了关键的免疫分子，如α-2-巨球蛋白和补体成分 3，每个都有多个异构体，这表明它们在免疫反应中具有潜在的作用。我们的分析还揭示了 853 个剪接事件，主要涉及保留的内含子，以及 672 个转录因子和 426 个长非编码 RNA。
本研究生成的高质量参考转录组为鳊属鱼类的比较基因组研究提供了有价值的资源，支持未来的研究以增强水产养殖种群。
