Evolutionary Patterns of Microsatellite Distribution in Cricket Genomes: Insights from Comparative Genomics of Five Gryllidae Species

Microsatellites or simple sequence repeats (SSRs) are valuable markers for understanding genome structure, function, and evolution. However, their distribution and characteristics remain largely unexplored in cricket species. We conducted a genome-wide identification and analysis of SSRs (P-SSRs, C-SSRs, and I-SSRs) across five cricket genomes. The total number of SSRs ranged from 2,350,765 to 3,299,527, representing 5.37%–7.27% of the genomes. Abundance followed the pattern I-SSRs > P-SSRs > C-SSRs across genomic regions (genome, intergenic, intronic, and CDSs). The total SSR number showed a strong but statistically non-significant positive correlation with genome size, whereas SSR length, abundance, and density showed no correlation. Trinucleotide repeats were consistently the most common P-SSR type. The (AAT)n motif predominated in genome, intergenic, and intron regions, while (CCG)n was most frequent in CDSs. Consequently, AT-rich repeats dominated non-coding regions, whereas GC-rich repeats were enriched in CDSs. Coefficient of variation (CV) analysis of repeat copy numbers (RCN) revealed distinct trends in P-SSR distribution across regions and species. Functional annotation of CDSs containing P-SSRs indicated involvement in binding, signal transduction, and transcription. This study represents, to our knowledge, the first comprehensive family-level comparative analysis of SSRs in crickets, providing new insights into their genomic architecture.