International Journal of Aquaculture, 2025, Vol.15, No.3, 99-115 http://www.aquapublisher.com/index.php/ija 100 taxonomic status of the genus Snakehead and clarifying the phylogenetic relationship between its species not only has important biodiversity significance, but also provides a scientific basis for aquaculture utilization and invasion prevention and control. Mitochondrial DNA (mtDNA) has become one of the most commonly used molecular markers in animal molecular systematics and phylogenetic geography studies due to its unique genetic characteristics. Compared with the nuclear genome, the mitochondrial genome is maternally unilineal, has no recombination, has a high copy number and a fast evolution rate. These characteristics enable it to have a higher resolution for the closest relationship between species. The typical fish mitochondrial genome is a closed circular double-stranded molecule with a total length of about 16 kb~17 kb, containing 13 protein-coding genes, 22 tRNAgenes, 2 rRNAgenes and 1 non-coding control region (D-loop). The mitochondrial whole genome sequence provides richer and more comprehensive information than a single gene fragment (such as COI, Cyt b, etc.), which can avoid the systematic errors that may exist in a single gene tree (Xu et al., 2024). Especially in the study of fish classification and evolution, the mitochondrial genome can reflect evolutionary characteristics such as gene rearrangement and replication mechanism, providing new ideas for solving the systematic relationship of complex groups. In recent years, with the development of sequencing technology, more and more fish mitochondrial genomes have been determined and used for phylogenetic reconstruction. For example, for the genus Snakehead in the family Channa, many studies have improved the analysis of systematic relationships through mitochondrial genome data, and discovered new species groupings and pedigree structures. These studies have demonstrated the advantages and application prospects of mitochondrial genomes in the study of fish phylogeny and phylogenetic geography (Wang et al., 2023). Mitochondrial DNA also has limitations, such as only representing maternal genetic history, and may cause hybridization or incomplete pedigree sorting. This study will review and analyze the research results on mitochondrial genome variation and phylogeny of Snakehead in recent years, explore the inspiration of mitochondrial genome variation characteristics for clarifying the internal lineage relationship of Snakehead, summarize the basic structural composition of the mitochondrial genome and the characteristics of each functional region of Snakehead, compare the variation distribution law of mitochondrial genome of different species of Snakehead, screen the hypervariable regions and speculate the potential functional impact, and reconstruct the phylogeny based on the mitochondrial whole genome sequence to analyze the phylogeny structure and species differentiation history of Snakehead, compare the mitochondrial variation differences of Snakehead populations in different geographical regions, discuss the influence of geographical isolation and environmental factors on lineage distribution, and deeply explore the ecological adaptation mechanism of Snakehead lineage evolution through typical cases (Channa argus andChanna maculata and samples from different regions). This study hopes to deepen the understanding of the variation law and phylogeny of the mitochondrial genome of Snakehead, and provide a scientific basis for the protection of species diversity, genetic breeding and invasion prevention and control of Snakehead species. 2 Structural Features of the Mitochondrial Genome 2.1 Gene content and coding region organization The mitochondrial genome of snakehead is consistent with that of typical bony fish, presenting a double-stranded circular DNA molecule with a total length of about 16 500 bp~16 900 bp. For example, the reported mitochondrial genome length of Channa argus is about 16 558 bp, and that of Channa maculata is about 16 559 bp, which is almost the same. The mitochondrial genome size of different snakehead species is mainly affected by the difference in the length of the control region, but generally fluctuates around 16.5 kb. The mitochondrial genome of snakehead contains 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes (rRNAs), as well as 1 non-coding control region (D-loop) (Xu et al., 2024). Genes are arranged on two strands: the H strand usually contains most of the coding genes, while the L strand contains only a few genes (such as some tRNA genes and ND6 genes). The order of mitochondrial genes in various species of Snakehead is highly conserved, consistent with the vast majority of bony fish, and no obvious gene rearrangement is observed.
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