Genome survey analysis, microsatellite site identification and primer development of Barbatia virescens.

Abstract

Background: Due to its red blood and unique taste, Barbatia virescens is considered a species of significant economic value in Chinese coastal cities. With the ever-growing global demand for seafood, human activities have severely damaged the habitat of B. virescens, leading to the degradation of natural resources and a dramatic decline in wild population numbers.

Methods and results: To obtain more information on this species, genome survey sequencing was used. The genomic size of B. virescens was estimated to be 1.426 Gb, with a heterozygosity of 0.589% and a repetitive sequence content of 67.30%. Based on the sequencing data, a draft genome of 1.313 Gb was assembled, and a total of 648,158 microsatellite motifs were identified. Mononucleotide repeats were the most abundant, among which A/T and AC/GT were the dominant repeat units, accounting for 56.45% and 11.27% of the total microsatellite loci, respectively. Microsatellite loci containing 10 repeat units were the most abundant. Using 21 selected polymorphic microsatellite markers, we conducted a genetic diversity analysis of B. virescens. The number of alleles per locus ranged from 8 to 27. The mean observed heterozygosity (Ho) was 0.711, and the mean expected heterozygosity (He) was 0.874. The mean PIC value of the 21 microsatellite primers was 0.865. Thirteen loci showed significant deviations from Hardy-Weinberg equilibrium (P < 0.05).

Conclusion: This study comprehensively explored the genomic characteristics of B. virescens and developed 21 pairs of microsatellite primers, providing valuable data to support future research on its genetic diversity and germplasm conservation of B. virescens.