Gene annotation set for the Castanopsis sieboldii (Makino) Hatus. ex T. Yamaz. et Mashiba subsp. sieboldii (Fagaceae) draft genome (GFF3, CDS, and protein sequences)

This repository provides the gene annotation files for the Castanopsis sieboldii draft genome (Tokumoto & Kijidani (2025)) generated in Tokumoto et al. (submitted). The annotation was generated following a standard workflow combining repeat masking, evidence‑guided gene prediction, and functional annotation. The genome assembly was soft‑masked using RepeatModeler v2.0.1 and RepeatMasker v4.1.1, implemented within the EDTA pipeline (Ou et al. 2019). As transcriptional evidence, we incorporated leaf and inflorescence RNA‑seq datasets previously sequenced on the DNBSEQ‑T7 platform (paired‑end; accessions DRR586675 and DRR586676). These reads were aligned to the masked genome using hisat2 v2.2.1 (Kim et al. 2019). Protein‑coding gene models were predicted with BRAKER v3.0.8, using (i) spliced read alignments (BAM files), (ii) plant protein homologs from OrthoDB v12, and (iii) the soft‑masked assembly. Predicted amino‑acid and CDS sequences were extracted from the resulting GFF3 annotation using gffread v0.12.7 (Pertea & Pertea 2020). Included files Csieboldii.annotation.braker.gff3 — Gene structural annotation (gene / mRNA / CDS / exon features) Csieboldii.cds.braker.fasta — Coding sequences of predicted protein‑coding genes Csieboldii.protein.braker.fasta — Predicted protein sequences