International Journal of Aquaculture, 2025, Vol.15, No.3, 99-115 http://www.aquapublisher.com/index.php/ija 99 Research Insight Open Access Mitochondrial Genome Variation in Channa and Its Implications for Phylogenetic Relationships Fei Zhao, Jinni Wu Aquatic Biology Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding authors: 2314548193@qq.com International Journal of Aquaculture, 2025, Vol.15, No.3 doi: 10.5376/ija.2025.15.0011 Received: 19 Apr., 2025 Accepted: 21 May, 2025 Published: 30 May, 2025 Copyright © 2025 Zhao and Wu, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhao F., and Wu J.N., 2025, Mitochondrial genome variation in channa and its implications for phylogenetic relationships, International Journal of Aquaculture, 15(3): 99-115 (doi: 10.5376/ija.2025.15.0011) Abstract The genus Channa is a kind of freshwater fish with important economic value and ecological significance. Its species diversity and phylogenetic relationship have long been concerned. This study systematically sorted and compared the mitochondrial genome sequences of different species and regional populations of the genus Channa, deeply revealed its genome structure composition, variation characteristics and phylogenetic relationship, clarified the lineage differentiation pattern and evolutionary path within the genus Channa, and constructed a high-resolution phylogenetic tree by analyzing genetic variations such as SNP, InDel and non-synonymous mutations. Regional comparison showed that there were significant differences in mitochondrial variation between the southern Chinese and Southeast Asian populations of Channa, and geographical isolation contributed to the formation of lineages in different regions. Case analysis represented byChanna argus andChanna maculatafurther revealed their genomic differences and ecological adaptation mechanisms. This study is expected to provide a theoretical basis for species identification, resource protection and genetic diversity assessment of Channa, and also provide a methodological reference and practical path for studying the phylogenetic relationship of freshwater fish using mitochondrial genome. Keywords Channa; Mitochondrial genome; Phylogeny; Genetic variation; Phylogenetic geography 1 Introduction The genus Channa belongs to the family Channa of the order Perciformes. It is a typical freshwater carnivorous fish, commonly known as "black fish" or "thunder fish". The Channafamily includes the Asian genus Channaand the African genus ParaChanna. Among them, the species of Channa are mainly distributed in East Asia and Southeast Asia, and are widely found in China, the Indian subcontinent and Southeast Asia (Rüber et al., 2020). According to recent statistics, there are four species of Channa in China, namely Channa argus, Channa maculata, Channa asiatica and Channa gachua, which are distributed in northern China, southern China and some local areas respectively. The genus Channa belongs to the suborder Perciformes in taxonomy, and is unique because it has auxiliary respiratory organs that can survive in low-oxygen environments. As a top predator, snakehead fish plays an important role in maintaining the balance of freshwater ecosystems. At the same time, black snakehead and Channa maculatus are also common farmed fish in China, with significant economic value and development potential (Fang et al., 2024). In recent years, due to human activities, snakehead fish have been introduced into some non-native waters and may have an impact on the local ecology. Its invasion risk and species identification have also attracted much attention. The diversity and phylogenetic relationship of snakehead fish have always been one of the hot topics in fish classification and evolution research. Traditional morphological identification is limited by the changes in body color and pattern of snakehead fish at different growth stages and the similar morphology of closely related species, and there is some controversy about species identification and classification status. With the development of molecular systematics, it has become possible to use DNA sequences to solve the problems of species identification and kinship (Kamran et al., 2020). New species of snakehead fish are constantly being discovered and described. For example, new snakehead species have been identified in northeastern India and Myanmar in recent years, indicating that the species diversity of this genus may be underestimated. Therefore, sorting out the
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