Scylla paramamosain is a globally important mariculture crab species. However, its resources for simple sequence repeat (SSR) loci remain severely underdeveloped. In the present study, MISA software was employed to systematically detect and characterize SSR loci across the whole genome of S. paramamosain . A total of 3,184,249 SSR loci were identified in the S. paramamosain genome, with a cumulative length of 241,424,069 bp, accounting for 15.62% of the total genome size. The frequency and density of SSRs were 2,059.64 loci/Mb and 156,158.13 bp/Mb, respectively. A total of 259 distinct repeat motifs were detected, with repeat numbers ranging from 5 to 1,551. Mononucleotide repeats were the most abundant type, followed by dinucleotide repeats. Among all repeat motifs, motif A was the most prevalent, followed by the dinucleotide motifs AG and AC. Regarding chromosomal distribution, chromosome 3 had the most SSR loci, while chromosome 44 had the fewest. Notably, chromosome 44 exhibited the highest SSR frequency and density. In total, 2,382,227 SSR markers were developed; among these, 72.82% were located in intergenic regions, 20.15% in introns, and 7.03% in exons. Sixteen SSR markers were amplified in 32 S. paramamosain individuals, among which eight markers possessed high polymorphism. To the best of our knowledge, this is the first chromosome-level genome-wide SSR analysis in S. paramamosain . These findings provide valuable genetic resources and a theoretical basis for subsequent genetic breeding and germplasm improvement of S. paramamosain .
范嗣刚 et al. (2026) studied this question.