Abstract:

The lack of effective molecular markers for germplasm identification and ambiguous genetic diversity characteristics severely restrict the research progress of Hemitrygon bennettii. This study aimed to establish fundamental data for germplasm identification and population genetic diversity evaluation of H. bennettii, and to provide molecular evidence for its phylogenetic analysis, genetic diversity conservation, and fishery resource management. The findings are expected to further promote the in-depth development of conservation genetics research on this species. High-throughput sequencing data and bioinformatics approaches were applied to screen genome-wide single nucleotide polymorphism (SNP) markers and analyze the population demographic history of H. bennettii. Genome-wide microsatellite loci were identified, and high-quality loci were screened for specific primer design. Furthermore, interspecific microsatellite variations between H. bennettii and H. akajei were comparatively analyzed. In addition, the complete mitochondrial genome of H. bennettii was assembled, and its genomic structure and variation characteristics were systematically analyzed. A total of 16150339 SNP loci were screened and annotated. Population demographic analysis based on genome-wide SNPs indicated that the H. bennettii population had experienced two expansion events and one bottleneck contraction event. In total, 521449 microsatellite loci were identified in the genome, with a distribution frequency of 163.02 loci per Mb. After strict screening, 116 high-quality microsatellite loci were obtained with specific primers successfully designed. Meanwhile, 19 microsatellite loci shared by H. bennettii and H. akajei with high interspecific heterogeneity were screened out. The total length of the assembled mitochondrial genome of H. bennettii was 17724 bp. A total of 49 variable sites were detected, and obvious intraspecific length heterogeneity was found in its mitochondrial genome. The SNP markers, microsatellite loci, and complete mitochondrial genome sequence obtained in this study can be effectively applied to subsequent population genetic analysis and germplasm identification of H. bennettii. This study provides reliable molecular baseline data for phylogenetic research, genetic diversity assessment, and scientific conservation and management of H. bennettii germplasm resources.

Key words: Hemitrygon bennettii, molecular marker, single nucleotide polymorphism (SNP), microsatellite, mitochondrial genome