长吻鮠全基因组微卫星分布特征研究

Study on the microsatellite distribution characteristics in the whole genome of Chinese longsnout catfish (Leiocassis longirostris)

摘要

【目的】本研究基于 NCBI 数据库已公开的长吻鮠（Leiocassis longirostris）全基因组数据，利用 MISA 软件开展其全基因组水平微卫星的筛选与分布特征分析。【方法】联合基因组 General Feature Format（GFF）注释文件与 MISA 输出文件，对基因编码区外显子中嵌有微卫星序列的基因进行 Gene Ontology（GO）功能分类注释和 Kyoto Encyclopedia of Genes and Genomes（KEGG）通路富集分析。【结果】在长吻鮠基因组中共筛选出 1 180 545 个微卫星，总长度为 28 807 417 bp，占基因组序列总长度的 4.14%。其中，二碱基类型数量最多（占比 66.59%），其次为单碱基类型（占比 18.08%），六碱基类型数量最少（占比 0.07%）。【结论】初步定位结果显示，有 1 904 个微卫星分布在外显子区，涉及 1 705 个基因。GO 富集最显著的条目为 RNA 结合活性和信号转导过程，提示微卫星关联基因在核酸互作及细胞信号调控中具有重要作用。KEGG 通路富集分析显示前 5 条最显著富集的通路为 MAPK 信号通路、cAMP 信号通路、PI3K-Akt 信号通路、钙信号通路和黏着斑信号通路，这些通路均与细胞信号传导、生长调控及应激响应密切相关。研究结果可为长吻鮠微卫星标记的开发提供基础资料。

Abstract

[Objective] Based on the publicly available whole-genome data ofLeiocassis longirostris in the National Center for Biotechnology Information (NCBI) database, this study aimed to screen microsatellites and analyze their distribution characteristics at the whole-genome level using MISA software. [Method] By integrating the genome's General Feature Format (GFF) annotation files and MISA output files, Gene Ontology (GO) functional classification annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed on genes harboring microsatellite sequences within the exons of coding regions. [Result] A total of 1 180 545 microsatellites were identified in the genome ofL. longirostris, with a total length of 28 807 417 bp, accounting for 4.14% of the total genome sequence length. Among these, dinucleotide microsatellites were the most abundant (66.59%), followed by mononucleotide ones (18.08%), while hexanucleotide microsatellites were the least frequent (0.07%). [Conclusion] The preliminary localization results revealed that 1 904 microsatellites were distributed in exonic regions, involving 1 705 genes. The most significantly enriched GO terms were RNA binding activity and signal transduction processes, suggesting the core role of microsatellite-associated genes in nucleic acid interactions and cellular signal regulation. KEGG pathway enrichment analysis showed that the top five most significantly enriched pathways were the MAPK signaling pathway, cAMP signaling pathway, PI3K-Akt signaling pathway, calcium signaling pathway, and focal adhesion signaling pathway, all of which are closely related to cellular signal transduction, growth regulation, and stress response. These findings provide fundamental data for the development of microsatellite markers inL. longirostris.

关键词

长吻鮠 / 微卫星 / 全基因组分布

Key words

Leiocassis longirostris / microsatellite / genome-wide distribution

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基金资助

淮河干流航道（三河尖至蚌埠闸段）整治工程对淮河淮南段长吻鮠国家级水产种质资源保护区影响生态修复研究项目(2024STBC01)

安徽省重点水域水生生物资源监测项目(2024BFAFZ02936)

安徽省现代农业产业技术体系建设专项(皖农科函[2021]711 号)