Genome-wide analysis on the diversity and abundance of simple sequence repeats (SSRs) in the tri-spine horseshoe crab, Tachypleus tridentatus

The tri-spine horseshoe crab Tachypleus tridentatus, listed by the IUCN as an endangered marine species, is often referred to as a “living fossil” due to its ancient lineage and evolutionary significance. Despite its importance, the genomic landscape of this species, particularly regarding simple sequence repeats (SSRs), remains insufficiently explored. SSRs are key markers for assessing genomic diversity and hold promise for informing conservation strategies. This study systematically classifies and quantifies SSRs across the T. tridentatus genome using data generated from high-throughput sequencing. For a detailed analysis of composite SSRs, Tseng's system was applied to enhance structural characterization. The results revealed that SSRs fall into three major categories: perfect (92.85%), interrupted perfect (1.61%), and composite repeats (5.54%). A negative correlation was observed between motif length and the frequency of perfect SSRs. Mononucleotide and dinucleotide motifs dominated the dataset, accounting for 93.10% of all perfect SSRs. Composite SSRs were further subdivided into four categories: interrupted compound, compound, interrupted complex, and complex SSRs, with interrupted compound SSRs being the most prevalent. This comprehensive classification and quantification of SSRs in the T. tridentatus genome not only enriches our understanding of sequence diversity and genomic architecture but also highlights the potential of SSRs as molecular tools for conservation genetics, population monitoring, and evolutionary studies in this marine arthropod.