Whole-Genome Resequencing Reveals the Genetic Diversity and Adaptive Mechanism of Mastacembelus armatus in the Dongjiang and Ganjiang River Sources

To explore the genetic diversity and adaptive evolutionary mechanism of Mastacembelus armatus in the Dongjiang and Ganjiang River Sources, whole-genome resequencing was performed on three populations of M. armatus from Xunwushui (XW) and Jiuqu River (DN) in the Dongjiang River Source, and Taojiang (XF) in the Ganjiang River Source. Population genetics methods were integrated to analyze their genetic structure, differentiation characteristics and selection signals. The results showed that a total of 209.05 Gbp of Clean Data was obtained from the three populations, with the Q30 base percentage reaching 94.42% and the average mapping rate to the reference genome being 97.85%, indicating high reliability of the sequencing data. A mean of 7,459,686 single nucleotide polymorphisms (SNPs) were detected, with a transition/transversion ratio of 1.52 and a heterozygous SNP ratio of 2.22%. The total number of genome-wide insertions and deletions (InDels) was 1,902,722±23,247. Gene Ontology (GO) functional annotation revealed a consistent variation pattern of core genes among the three populations. Phylogenetic tree, Admixture and principal component analysis (PCA) confirmed that the three populations belonged to a single evolutionary clade and shared a genetic origin from two ancestral populations (the lowest cross-validation error at K=2), while significant genetic differentiation was observed among populations: XW and DN populations had similar genetic backgrounds and closer genetic relationships, both biased towards the blue ancestral component, whereas XF population was inclined to the red ancestral component, with the DN population showing the highest degree of genetic admixture. Individuals within the XF population had more distant genetic relationships and the longest linkage disequilibrium (LD) decay distance, which was speculated to be associated with its small population size and low recombination rate; in contrast, the XW population had the shortest LD decay distance, corresponding to the characteristics of large population size and high recombination rate. Analysis of population genetic diversity indicated that XW and DN populations were classified as the high-diversity group (with more than 440,000 polymorphic markers, expected heterozygosity >0.31 and polymorphism information content (PIC) ≈0.25), while the XF population was the low-diversity group (with 342,646 polymorphic markers, expected heterozygosity of 0.2608 and PIC of 0.2073). Only the minor allele frequency (MAF) of the XF population (0.2829) was slightly higher than that of the other two populations. This study systematically elucidated the characteristics of genetic differentiation and diversity differences of M. armatus in the Dongjiang and Ganjiang River Sources, providing a genome-level scientific basis for the conservation of genetic resources, development of molecular markers and analysis of environmental adaptive mechanisms of this species.