Codon usage bias of mitochondrial genome characteristics in Siluriformes in China

【Objective】 This study aimed to analyze the mitochondrial genome characteristics of 91 species of Siluriformes, 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. Phylogenetic analysis based on 13 PCGs indicated that marine species of the family Ariidae formed a monophyletic clade with several 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 Siluriformes 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 Loricariidae belongs to a sister lineage with the most recent common ancestor of the other 9 families, suggesting that geographic isolation plays an important role in the evolutionary dynamics of mitochondrial genomes.