Development of CypriSSR: a genome-wide, chromosome-level microsatellite database for multiple cyprinidae species

The family Cyprinidae represents the most taxonomically diverse group of freshwater fishes, encompassing over 3 000 species of ecological and economic importance in aquaculture, conservation, and ecological monitoring. Simple sequence repeats (SSRs), also known as microsatellites, are highly informative molecular markers widely used for genetic diversity analysis, population structure assessment, and marker-assisted breeding. However, comprehensive genome-wide SSR resources for cyprinids remain limited. Existing databases, such as FishMicrosat, provide restricted taxonomic coverage and lack standardized chromosome-level datasets suitable for comparative genomic analyses. To address this gap, we developed CypriSSR, a genome-wide SSR database encompassing 11 representative cyprinid species. Chromosome-level genome assemblies were retrieved from NCBI. SSR loci were identified using MISA, and primer pairs were designed using Primer3. In total, over 7.8 million SSR loci were identified. Mononucleotide repeats were the most abundant class (39-53%), followed by dinucleotide and trinucleotide motifs. SSRs were predominantly distributed in genic regions (54%-71% across species), suggesting potential functional roles. Each database entry includes repeat type, genomic coordinates, primer sequences, melting temperatures, and predicted PCR product sizes. The CypriSSR web interface enables flexible querying of SSR markers based on species, chromosome, motif class, and genomic location, and supports sequence similarity searches through an integrated BLAST module along with data export options. CypriSSR provides a comprehensive and standardized multi-species microsatellite resource for cyprinid genomes and supports applications in population genetics, molecular breeding, and conservation genomics. Database URL:  http://46.202.167.198/fishssr/.