Variant discovery datasets for Castanopsis sieboldii (Takaoka isolate): SNP VCF, de novo assembly, and structural variant calls

This repository provides the variant discovery datasets for the Castanopsis sieboldii Takaoka isolate. These datasets were produced for the comparative genomic analyses in Tokumoto et al. (submitted) and were used to identify species‑specific and shared genomic variants between C. sieboldii and C. cuspidata. For small variants (SNPs and short indels <1 kb), cleaned short reads from the Takaoka isolate were mapped to the C. sieboldii draft genome (Koshi individual; Tokumoto & Kijidani 2025) using minimap2 v2.28. Variants were called with bcftools mpileup and filtered by quality (QUAL <20), depth (DP <10), and mapping quality (MQ <30). For structural variant (SV) discovery (≥1 kb), the Takaoka isolate reads were assembled de novo using SPAdes v4.2.0 with multiple k‑mer sizes (21–127). Contigs <1,000 bp were removed. Because the Takaoka isolate belongs to the same species as the reference draft genome, scaffolding was performed with RagTag v2.1.0, using the correct, scaffold, and patch modules. Assembly completeness was assessed using BUSCO (embryophyta_odb). SVs were detected by aligning the de novo assembly to the C. sieboldii draft genome with minimap2, followed by svim‑asm v1.0.3. Species‑specific and shared variants were extracted with bcftools isec, and combined with SNP calls for downstream variant‑effect prediction (snpEff) and Gene Ontology enrichment. Included files Csieboldii_Takaoka.smallvariants.vcf.gz — SNP and short indel calls Csieboldii_Takaoka.assembly.fasta — de novo assembly used for SV detection Csieboldii_Takaoka.structural_variants.vcf.gz — structural variant (SV) calls from svim‑asm These files constitute the complete C. sieboldii Takaoka variant dataset used in the study.