Variant discovery datasets for Castanopsis cuspidata: SNP VCF, de novo assembly, and structural variant calls

This repository provides the variant discovery datasets for Castanopsis cuspidata generated in Tokumoto & Kijidani (submitted). These files were used to identify species‑specific and shared genomic variants between C. cuspidata and C. sieboldii in the comparative genomic analyses. For small variants (SNPs and short indels <1 kb), cleaned short reads of C. cuspidata were aligned to the C. sieboldii draft genome 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) detection (≥1 kb), the C. cuspidata reads were assembled de novo using SPAdes v4.2.0 with multiple k‑mer sizes (21–127). Contigs shorter than 1,000 bp were removed, and scaffolding was performed with RagTag v2.1.0 (using only the scaffold function to avoid cross‑species over‑correction). SVs were then 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 using bcftools isec, and these datasets were used for downstream variant‑effect prediction and Gene Ontology analyses. Included files Ccusp_smallvariants.vcf.gz — SNP and short indel calls Ccusp_assembly.fasta — de novo assembly used for SV identification Ccusp_structural_variants.vcf.gz — structural variant (SV) calls from svim‑asm