Assessment of genetic diversity, detection of strain-specific single nucleotide polymorphisms and identification of the Bangladesh and Vietnam strain of Channa striata by PCR-RFLP analysis of the mitochondrial COI gene fragment

Identification, genetic diversity, and comparative evolution of the striped snakehead Channa striata (Bloch, 1793) in Wallacea, Indonesia

“…Combining C. striata from Wallacea (this study) and other regions (GenBank accessions), this study identified 12 haplotypes and 28 SNPs. Fewer C. striata haplotypes were identified compared to studies in Vietnam and Bangladesh using the primer pair FishF1-FishR1 (Alam et al 2022) which found 15 haplotypes but with just 18 SNPs, far fewer than the 28 haplotypes in this study. Low genetic differentiation is reflected in the low between site FST values, indicating high nucleotide base sequence stability in the COI gene, probably due to the high GC codon usage (>56% at the 1 st position, 42-44% at 2 nd position, and around 37-41% at the 3 rd position).…”

“…The striped snakehead, Channa striata (Bloch 1793), family Channidae, is an economically important freshwater fish in Southeast Asia with a large and growing market demand especially in Indonesia (Muntaziana et al 2013;Hien et al 2015;Alam et al 2022). In certain regions in Indonesia, the striped snakehead was sold at a high price.…”

“…It also has high nutritional content, health benefits, and pharmaceutical properties (Sahu et al 2012). Snakeheads are currently being widely farmed in Southeast Asia (Duong et al 2019;Phan et al 2021;Alam et al 2022) as well as in India (Kumari et al 2018) and Bangladesh (Alam et al 2022). However, snakehead farming is constrained by limited seed availability, and poor recovery or recruitment of young fish (juveniles) to natural stocks/populations (IUCN 2015;Alam et al 2022), the low captive breeding survival rate in the initial period due to huge size variation and cannibalism (Rahman and Awal 2016), and the lack of appropriate formulated diets (Hien et al 2015).…”

“…Snakehead populations are increasingly threatened by the combined effects of climate change, overexploitation, anthropogenic factors, invasive species, and habitat degradation (Arthington et al 2016;Duong et al 2019;Hubert et al 2012). Overexploitation of snakehead populations is caused by high market demand and has resulted in a sharp decline in the quality and abundance of snakehead stocks (Duong et al 2019;Alam et al 2022;Kumar et al 2022). The increasingly intensive exploitation of snakeheads has promoted destructive fishing practices using non-selective and environmentally unfriendly fishing gear (Harianti 2013).…”

“…Current approaches use molecular identification methods and analyze the genetic variation of the fish. This study applied the random amplified polymorphic DNA (RAPD) method, which examines the entire genome, as well as methods that focus on the structural and functional aspects of specific genes in the delineation of species, such as cytochrome b (Rahim et al 2012;Duong et al 2019), mitochondrial Cytochrome Oxidase Subunit I (COI) (Lakra et al 2010;Irmawati et al 2017b;Alam et al 2022), mitochondrial ND2 and tRNA (Li et al 2006), the mitochondrial D-loop (Baisvar et al 2019;Duong et al 2019); mitochondrial 16S RNA (Lakra et al 2010), and metabarcoding that represents a technological advance (Erdozain et al 2019). In particular, the use of the Cytochrome Oxidase Subunit I (COI) gene as a barcode for molecular species identification and the analysis of genetic variation has opened new perspectives in collecting and analyzing genomic resources from a wide variety of taxa (Xu et al 2015;Pappalardo et al 2018;Zhou et al 2019).…”