Gene-Miner protein-coding gene catalogues for four reference genomes (Oryza sativa, Glycine max, Drosophila melanogaster, Caenorhabditis elegans)

Protein-coding gene catalogues produced by Gene-Miner (https://github.com/k821209/gene-miner), an evidence-integrating Nextflow pipeline that unions three gene-prediction streams (RNA-seq/StringTie+TransDecoder, AUGUSTUS, GeneMark-ETP) and applies a taxonomic and a transposable-element quality-control filter. Two files per genome: union.final.gff3.gz (structural annotation) and union.final.pep.fa.gz (proteins for all transcripts). Genomes and gene counts: Oryza sativa cv. Nipponbare (IRGSP-1.0) 41,509; Glycine max cv. Williams 82 (Glycine_max_v2.1 / Wm82.a2.v1) 43,941; Drosophila melanogaster (RefSeq Release 6) 13,400; Caenorhabditis elegans (RefSeq WBcel235) 18,272. Companion manuscript: 'Gene-Miner: an evidence-integrating Nextflow pipeline for protein-coding gene annotation in non-model genomes.'