Draft genome data of Pediococcus acidilactici strain AP1 isolated from common carp (Cyprinus carpio)

This data article presents the whole-genome sequencing and associated genomic datasets of Pediococcus acidilactici strain AP1, isolated from the intestinal tract of a healthy common carp (Cyprinus carpio) obtained from a fish farm in the Tashkent region, Uzbekistan. The datasets comprise raw paired-end sequencing reads, a draft genome assembly, genome-quality assessment reports, structural and functional annotations, and phylogenomic outputs. Whole-genome sequencing was performed using the Illumina MiSeq i100 Plus System with paired-end 2 × 151 bp chemistry. De novo assembly generated a draft genome comprising 19 contigs, with a total length of 2,015,983 bp, an N50 of 388,737 bp, an L50 of 2, and a GC content of 42.02%. CheckM2 estimated 99.99% genome completeness and 0.5% contamination, whereas BUSCO recovered 99.2% of the conserved bacterial single-copy orthologs. Annotation with Prokka v1.15.6 identified 1,897 protein-coding sequences, 52 tRNA genes, four rRNA genes, and one tmRNA. Genome-based phylogenetic and digital DNA-DNA hybridization analyses supported the assignment of strain AP1 to P. acidilactici. Functional annotations generated using Prokka, RAST, eggNOG-mapper, and InterProScan indicated genes putatively associated with carbohydrate fermentation, stress adaptation, exopolysaccharide biosynthesis, peptide transport and proteolysis, cell-surface interactions, and CRISPR-Cas defense. Gene-based functional assignments represent predictions and require experimental validation. The publicly available datasets can support comparative genomic investigations of fish-associated Pediococcus strains and future experimental studies of host-associated and probiotic-relevant traits.