AquaSSR: A Lightweight Python Tool for Taxon-Specific SSR Marker Development in Aquatic Organisms

Simple sequence repeats (SSRs) are fundamental molecular markers in aquaculture genetics. Most existing SSR mining tools, however, were built for general-purpose use and apply identical detection criteria regardless of the organism, thereby overlooking the distinct genomic features of aquaculture species. Crustacean genomes, for example, are extremely AT-rich, while bivalve genomes show exceptionally high SSR density. Conventional tools account for neither feature. Here, we present AquaSSR, a lightweight SSR analysis tool that implements taxon-specific mining rules and primer design parameters tailored to three major taxonomic groups in aquaculture: bony fish, crustaceans, and bivalve mollusks. AquaSSR adopts an aquaculture-oriented screening strategy that excludes mononucleotide repeats (a methodological choice suited to conventional genotyping platforms), applies a three-tier dinucleotide threshold adapted to each group’s genome composition (≥6 for fish, ≥8 for AT-rich crustaceans, ≥7 for high-density bivalves), and optimizes primer GC scoring centers for taxon-specific base composition. The complete pipeline, from FASTA input through SSR detection, primer design, and optional in silico e-PCR validation to Excel and figure output, runs with a single command and requires only four pip-installable Python libraries, with no external command-line bioinformatics programs. Validation on transcriptome datasets of Larimichthys crocea (fish), Litopenaeus vannamei (crustacean), and Magallana gigas (bivalve) identified 8398, 5471, and 2287 SSR loci, respectively, demonstrating that the taxon-specific thresholds effectively shaped the motif composition profiles across species.