International Journal of Aquaculture, 2025, Vol.15, No.3, 99-115 http://www.aquapublisher.com/index.php/ija 109 regulation. For example, mutations in some regulatory regions of the control region sequence of the northern lineage of black snakehead may have changed the regulation of respiration at low temperatures, thereby improving the survival rate over the winter. Similarly, the rapid reproduction characteristics of the southern lineage of snakehead may be related to the improvement of mitochondrial replication rate and energy supply capacity. 6 Case Studies 6.1 Genomic comparison of Channa argus andChanna maculata Channa argus and Channa maculata are the two most widely distributed and economically important snakehead fish in China. The two are morphologically similar, but their ecological habits and geographical distribution are different: Channa argus is cold-resistant and distributed in the north; Channa maculata prefers warmth and is only found in the south. Using mitochondrial genome data, we can deeply compare the genetic differences between these two closely related species. First, from the perspective of the whole genome sequence, the mitochondrial genome lengths of Channa argus and Channa maculata are very similar, both about 16.56 kb, and the gene content and arrangement are exactly the same (Xu et al., 2024). This indicates that they share the ancestral genome structure. However, in terms of sequence, there are obvious base differences between Channa argus and Channa maculata, and the difference rate of the mitochondrial full sequence is about 8%~9%. This difference is enough to distinguish them as two species. These differences are mainly concentrated in the control region and several coding genes: the sequence difference in the control region is more than 15%, while the difference in the COX1 gene is less than 2%. Of particular note, some non-synonymous mutations are fixed between the two species. For example, several amino acid substitutions found in the ND5 gene, all of which are one amino acid in Channa argus and another in Channa maculata, suggest that the two may differ in the function of complex I. Comparisons at the nuclear genome level also provide interesting insights. Recent chromosome-level whole genome sequencing and assembly of Channa argus and Channa maculata revealed that Channa argus has 24 pairs of chromosomes, while Channa maculata has 21 pairs. The Channa maculata genome has three fewer chromosomes, which is due to three chromosome fusion events in the Channa maculata genome. This difference highlights the degree of evolutionary divergence between Channa argus and Channa maculata, which is greater than what can be seen from mitochondrial data (Figure 1) (Ou et al., 2021). Chromosomal fusions may have profound effects on gene expression and adaptability. For example, it is speculated that Channa maculata may have expanded some immune-related genes, making its disease resistance better than that of Channa argus. Correspondingly, mitochondrial genome comparison also supports that Channa maculata may be more resistant to diseases: a mutation in the mitochondrial Cyt b gene of Channa maculata is reported to be related to the regulation of cell apoptosis, which may enhance the ability to cope with pathogens. On the other hand, the advantage of Channa argus in low-temperature environments may partly come from its optimized mitochondrial function. Comparison of the whole mitochondrial genomes of Channa argus and Channa maculata found that there was a unique amino acid substitution in the Channa argus ATP synthase subunit 6 (ATP6) gene that was not found in Channa maculata, which was speculated to improve the efficiency of ATP synthase at low temperatures. Although this speculation needs experimental verification, its corresponding relationship with the stronger cold tolerance of Channa argus is worth further study. As a pair of sister species, Channa argus and Channa maculata have both high similarity and clear variation differences in mitochondrial genomes. These differences are not only indicators of molecular phylogeny, but may also correspond to differences in ecological adaptability between the two. The comparative case of Channa argus and Channa maculata shows that even for closely related species, variations at the mitochondrial and nuclear genome levels can accumulate to a significant degree and subtly affect the physiological and ecological characteristics of the species. 6.2 Phylogenetic positioning of samples from Guangxi, Yunnan, and Indochina Guangxi and Yunnan in China are geographically connected to the Indochina region (Vietnam, Laos, Thailand,
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