彭冶, 李杰, 王涛, 张凯, 宁先会, 暨杰, 尹绍武. 瓦氏黄颡鱼全基因组微卫星的分布特征及其定位的初步研究[J]. 南方水产科学, 2022, 18(1): 90-98. DOI: 10.12131/20210168
引用本文: 彭冶, 李杰, 王涛, 张凯, 宁先会, 暨杰, 尹绍武. 瓦氏黄颡鱼全基因组微卫星的分布特征及其定位的初步研究[J]. 南方水产科学, 2022, 18(1): 90-98. DOI: 10.12131/20210168
PENG Ye, LI Jie, WANG Tao, ZHANG Kai, NING Xianhui, JI Jie, YIN Shaowu. Preliminary study on distribution characteristics and positioning of microsatellites in whole genome of Pelteobagrus vachelli[J]. South China Fisheries Science, 2022, 18(1): 90-98. DOI: 10.12131/20210168
Citation: PENG Ye, LI Jie, WANG Tao, ZHANG Kai, NING Xianhui, JI Jie, YIN Shaowu. Preliminary study on distribution characteristics and positioning of microsatellites in whole genome of Pelteobagrus vachelli[J]. South China Fisheries Science, 2022, 18(1): 90-98. DOI: 10.12131/20210168

瓦氏黄颡鱼全基因组微卫星的分布特征及其定位的初步研究

Preliminary study on distribution characteristics and positioning of microsatellites in whole genome of Pelteobagrus vachelli

  • 摘要: 文章探究了瓦氏黄颡鱼 (Pelteobagrus vachelli) 全基因组微卫星的分布特征及其规律,旨在为相关功能性微卫星分子标记的筛选提供依据。利用MISA (MIcroSAtellite identification tool) 软件对其全基因组微卫星进行筛查和分析,并对外显子中含有微卫星的基因进行了GO (Gene Ontology) 注释和KEGG (Kyoto Encyclopedia of Genes and Genomes) 富集分析。在瓦氏黄颡鱼全基因组 (约663.53 Mb) 中筛查到6种完整型微卫星共417 724个,相对丰度为630 个·Mb−1,在全基因组总长度中占比1.48%。其中二碱基重复类型的微卫星个数最多,占微卫星总数的43.36%,其他依次分别是单碱基 (39.02%)、四碱基 (9.05%)、三碱基 (7.34%)、五碱基 (1.12%)和六碱基 (0.12%)。对筛选得到的完整型微卫星进行初步定位,发现其中10 924个微卫星分布在外显子区,共定位到5 788个基因上。GO分析表明注释到生物过程的基因数量最多,GO富集较为显著的条目为结合活性和细胞大分子代谢过程。KEGG富集表明这些基因共富集到273条通路,其中黄酮与黄酮醇生物合成等通路最为显著 (P=0)。联合分析预测瓦氏黄颡鱼定位到外显子上的微卫星和其体内的生物代谢过程密切相关。

     

    Abstract: In this study, MISA (MIcroSAtellite identification tool) was used to screen and analyze the distribution characteristics of microsatellites in the whole genome of Pelteobagrus vachelli, aiming to provide a basis for the selection of functional microsatellite markers. The genes containing microsatellites in the exon regions were subjected to GO annotation and KEGG enrichment. In the whole genome of P. vachelli (Approximately 663.53 Mb), 417 724 perfect microsatellites were identified, accounting for 1.48% of the total length. The relative abundance of microsatellites in P. vachelli was 630 pcs·Mb−1. Among the six repeat types, dinucleotides were the most frequent, accounting for 43.36% of the total microsatellites, followed by mononucleotides (39.02%), tetranucleotides (9.05%), trinucleotides (7.34%), pentanucleotides (1.12%) and hexanucleotides (0.12%). By investigating the locations of microsatellites in the genome, we found that 10 924 microsatellites which belonged to 5 788 genes were located in the exons. The GO annotation shows that the number of genes annotated to biological process was the largest, mainly associated with binding activity and cellular macromolecular metabolism. KEGG enrichment analysis shows that these genes were enriched in 273 pathways, among which, flavonoids and flavonol biosynthesis (P=0) were the most significantly enriched pathways. Integrated analysis indicates that the microsatellites located in the exons of genes in P. vachelli were closely related to the biological metabolism processes.

     

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