南方农业学报2025，Vol.56Issue(6)：1729-1738,10.DOI:10.3969/j.issn.2095-1191.2025.06.004
中国鲇形目鱼类线粒体基因组密码子偏好性分析
Codon usage bias of mitochondrial genome characteristics in Siluriformes in China
摘要
Abstract
[Objective]This study aimed to analyze the mitochondrial genome characteristics of 91 species of Siluri-formes,explore their phylogenetic relationships,codon usage bias,and the influence of environmental factors on their mitochondrial genome characteristics,which could provide theoretical basis for taxonomic and evolutionary research on Siluriformes.[Method]Mitochondrial genome data of 91 species from 10 families of Siluriformes recorded in China were collected.Protein-coding genes(PCGs)sequences were extracted using PhyloSuite for codon usage analysis.Sequence alignment was conducted using MAFFT,and phylogenetic tree was constructed based on the mitochondrial genome PCGs with IQ-TREE 2.Neutrality plot,ENC-plot and PR2-plot were employed to evaluate the effects of mutation pressure and natural selection on codon usage bias.[Result]The mitochondrial genome lengths of 91 Siluriformes species ranged from 16432 to 16863 bp,with GC content varying between 40.2%and 47.4%,showing no obvious linear correlation.Phyloge-netic analysis based on 13 PCGs indicated that marine species of the family Ariidae formed a monophyletic clade with se-veral freshwater families,including Cranoglanididae,Pangasiidae and Amblycipitidae,which were closely related to Bagridae.The invasive family Loricariidae belonged to a sister lineage with the most recent common ancestor of the other 9 families.Codon usage bias analysis revealed consistent usage patterns across the 91 Siluriformes species.Neutrality plot and ENC-plot results suggested that codon usage bias was primarily driven by natural selection.PR2-plot analysis further showed that,at the third codon position,adenine(A)was more frequently used than thymine(T),and cytosine(C)was more frequently used than guanine(G).[Conclusion]The codon usage bias in the mitochondrial genomes of 91 Siluri-formes species is mainly shaped by natural selection.Marine species of the family Ariidae formed a monophyletic clade with several freshwater families,including Cranoglanididae,Pangasiidae and Amblycipitidae,the invasive family Lori-cariidae belongs to a sister lineage with the most recent common ancestor of the other 9 families,suggesting that geo-graphic isolation plays an important role in the evolutionary dynamics of mitochondrial genomes.关键词
鲇形目/线粒体基因组/系统发育/密码子偏好性Key words
Siluriformes/mitochondrial genome/phylogeny/codon usage bias分类
农业科技引用本文复制引用
熊芳园,李哲,张家俊,胡雪松,林勇,王大鹏..中国鲇形目鱼类线粒体基因组密码子偏好性分析[J].南方农业学报,2025,56(6):1729-1738,10.基金项目
国家自然科学基金地区科学基金项目(31560716) （31560716）
农业农村部财政专项(ZJZX-04) Regional Science Fund Project of National Natural Science Foundation of China(31560716) （ZJZX-04）
Ministry of Agriculture and Rural Affairs Financial Special Project(ZJZX-04) （ZJZX-04）
