International Journal of Aquaculture, 2025, Vol.15, No.3, 99-115 http://www.aquapublisher.com/index.php/ija 102 rich in G and L chain rich in C (i.e. AT bias, low GC content). The mitochondrial genome of the genus Snakehead also conforms to this rule, showing positive AT bias and negative GC bias, that is, the A content is slightly higher than T, and the C content is lower than G (Fan et al., 2022). This bias is reflected in the distribution of the coding region: for example, the proportion of T at the third codon position of the protein gene is often higher, while G is lower, which may affect the codon usage preference. Analysis of the codon usage of 13 protein genes in Snakehead showed that synonymous codons ending with A or T were preferred, which is a common phenomenon in the high AT background of mitochondrial genome. The position and order of each tRNAgene in the Snakehead genome are basically consistent with those of model fish (such as zebrafish). Each tRNA gene is about 67 bp~75 bp long and can fold into a typical cloverleaf secondary structure, and the anticodon sequence has no abnormal changes. These results further indicate that the arrangement and structure of the mitochondrial genome of Snakehead is highly conserved, providing a good basis for comparing sequence variations in different species. 3 Genome Variation Analysis 3.1 SNPs and InDel distribution patterns By comparing the mitochondrial genome sequences of various species of Snakehead, a large number of single nucleotide polymorphism sites (SNPs) and insertion/deletion variations (InDels) can be identified. In general, the variation density of different regions of the mitochondrial genome varies significantly: the control region has the highest variation frequency, while rRNA and protein-coding genes are relatively conservative. In the comparison between species of Snakehead, there are about hundreds of SNP variations between each pair of species. For example, it is reported that the comparison of the mitochondrial genomes of Channa argus and Channa maculata can detect about 300~400 nucleotide differences, of which the control region and some protein-coding genes account for the majority, while the rRNAgene region has only very few variations (less than 5% of the total). This distribution pattern is related to the importance of different functional regions of mitochondrial genes: the coding region, especially the protein gene, is often subject to strong functional constraints, with fewer variations and most of them are synonymous substitutions; while the control region, as a non-coding regulatory region, can tolerate more neutral mutation accumulation, and thus has a high variation rate. Specifically, among the 13 protein-coding genes, NADH dehydrogenase subunit genes (such as ND2, ND4, and ND5) are usually regions with richer variation, while cytochrome oxidase genes such as COX1 and COX2 are highly conserved. For example, Wang et al. (2023) compared the mitochondrial sequences of five species of snakehead and found that the ND4 gene was about 1 378 bp long, with more than 150 mutation sites, making it one of the most variable coding genes; in contrast, the COX1 gene was about 1 548 bp, with only dozens of mutations. In addition, the third codon position variation of protein genes is far more than the first and second positions, which is related to the fact that codon redundancy makes the third site mutation mostly synonymous mutations. Similarly, in the two rRNAgenes, the 12S and 16S rRNA sequences are very similar between different species of snakehead, with only sporadic base substitutions, indicating that rRNAgenes are under strong structural and functional selection pressure and have a slow evolution rate. InDel mutations are relatively rare in the mitochondrial genome and mostly occur in AT tandem repeat regions or control regions. The insertion/deletion of the mitochondrial genome of the genus Snakehead is mainly concentrated in the control region and some poly T/A regions. For example, an 8 bp tandem repeat was detected in the middle of the control region of Channa maculata. The length difference caused by the variation in the number of replications between different individuals is a typical microsatellite InDel. In the coding region, there are very few insertions and deletions that affect the reading frame. Only occasionally, single-base insertions/deletions are seen at non-critical sites of tRNAgenes, which have no obvious effect on function. In general, the variation of the mitochondrial genome of Snakehead is mainly SNP, supplemented by InDel, and most InDel lengths are very short (1 bp~2 bp) (Fan et al., 2022). These variation markers provide a rich information basis for population genetics and phylogenetic analysis. For example, in the study of different geographical populations of Channa argus, the variation of the mitochondrial control region includes several specific InDels, which can be used as molecular markers to identify different lineages.
RkJQdWJsaXNoZXIy MjQ4ODYzNA==