Objective To explore the genetic diversity characteristics of Novaculina chinensis populations in the Taojiang River Basin of Fujian Province, and to clarify the genetic differentiation between this local population and conspecific populations from different geographical regions at home and abroad as well as closely related species.

Methods A total of 28 individuals of N. chinensis collected from the Taojiang River Basin in Fujian were used as experimental materials. The mitochondrial cytochrome c oxidase subunit Ⅰ(COⅠ) and 16S rRNA gene sequences of all samples were amplified and sequenced. Multiple bioinformatic software packages , such as PopART and MEGA,were adopted to calculate genetic diversity parameters of the Taojiang population, construct haplotype networks and phylogenetic trees of haplotypes. Combined with homologous sequences of closely related species retrieved from GenBank, comparative analyses were conducted to quantify genetic discrepancies between the N. chinensis population in Taojiang River and other geographical conspecific populations and congeneric species worldwide.

Results The acquired sequence lengths were 595 bp for the COⅠ gene and 389 bp for the 16S rRNA gene, both showing an obvious AT bias. The COⅠ gene exhibited higher genetic diversity than the 16S rRNA gene in the Taojiang River population. A total of 11 COⅠ haplotypes were identified, with 12 variable sites and mutation events detected. The haplotype diversity and nucleotide diversity were 0.862 and 0.00287, respectively. Pairwise genetic distances among all haplotypes ranged from 0.00168 to 0.00852. Hap1 was the dominant haplotype with the highest frequency in the population. Comparative analysis against N. chinensis populations from Poyang Lake (Jiangxi), Qing’an River (Anhui), Xijiang River (Guangdong) and Qiantang River (Zhejiang) revealed that the N. chinensis population from Taojiang River possessed relatively high and unique genetic diversity. The genetic distances between N. chinensis and closely related freshwater razor clam species from Myanmar, the Ganges basin and Thailand ranged from 0.15073 to 0.15880.

Conclusion This study supplements genetic data of Novaculina chinensis inhabiting the Taojiang River basin of Fujian. The findings support the updated taxonomic status of N. chinensis, and provide fundamental data for the conservation and sustainable utilization of its germplasm resources.