Genome annotation resources for Pelophylax nigromaculatus

This dataset contains protein-coding gene annotation resources for the chromosome-level genome assembly of the black-spotted frog Pelophylax nigromaculatus (NCBI Assembly GCA_054643415.1; BioProject PRJNA1335551). The primary annotation was generated using MAKER+PASA and contains 32,557 protein-coding genes; this annotation was used for all downstream analyses in the associated manuscript. For protein-level completeness assessment, the longest predicted protein isoform was retained for each MAKER+PASA gene, yielding BUSCO v5.1.2 results of C:90.2% [S:85.5%, D:4.7%], F:5.2%, M:4.6% using vertebrata_odb10. An independent BRAKER3 v3.0.8 annotation, containing 21,448 protein-coding genes, is provided as an alternative annotation and was not used for downstream analyses. Under the same representative-protein BUSCO assessment, BRAKER3 yielded C:94.1% [S:90.0%, D:4.1%], F:1.3%, M:4.6%. The deposited files include GFF3 annotations, CDS and protein FASTA files, representative longest-isoform sets, and BUSCO summaries.