Gene models and functional annotations for Cloeon dipterum (clodip_v4)

This dataset provides the structural, functional, and orthology annotations for the mayfly Cloeon dipterum CLODIP2 reference genome (GCA_902829235.1).Annotation version 4 (updated October 2025) integrates RNA-seq evidence, protein homology, and functional inference.All files use open, standard formats (GFF3, GTF, FASTA, TSV, BED) and are organised for reproducibility and reuse. Folder Description 01_GeneModels/ Structural genome annotation for C. dipterum. Contains gene, transcript, exon and CDS features, gene-level BED file, and transcription-start-site positions. 02_Sequences/ Nucleotide and protein sequences derived from the gene models: full transcripts, CDS regions, and the canonical (longest-isoform) proteome. 03_FunctionalAnnotation/ Functional annotation results: InterProScan domain predictions, Gene Ontology assignments, and a list of putative transcription factors identified by motif and orthology. 04_EquivalenceTables/ Cross-species equivalence tables linking C. dipterum genes to D. melanogaster and FlyBase identifiers, including manually curated and Broccoli-based mappings. 05_Orthology/ Complete Broccoli output used to infer orthologous relationships: similarity searches, phylogenies, network extraction, and final orthologous-group tables.