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本仓库提供了Tokumoto与Kijidani（已投稿）研究中生成的锥栗（Castanopsis cuspidata）变异检测数据集，上述文件可用于比较基因组分析中鉴定锥栗与西氏锥（C. sieboldii）的物种特异性变异及共有基因组变异。 针对小变异（单核苷酸多态性（Single Nucleotide Polymorphism, SNP）与长度小于1 kb的短插入缺失（insertion-deletion, indel）），将锥栗的清洁短读长序列比对至西氏锥的基因组草图，通过minimap2 v2.28完成序列比对。随后采用bcftools mpileup进行变异识别，并基于质量阈值（QUAL <20）、测序深度阈值（DP <10）及比对质量阈值（MQ <30）完成过滤。 针对长度≥1 kb的结构变异（structural variant, SV）检测，使用SPAdes v4.2.0，以多种k-mer长度（21–127）对锥栗的读长序列进行从头组装。移除长度小于1000 bp的重叠群（contig），并采用RagTag v2.1.0进行支架组装（仅启用其支架功能以避免跨物种过度校正）。随后通过minimap2将从头组装序列比对至西氏锥的基因组草图，再结合svim-asm v1.0.3完成结构变异检测。 采用bcftools isec提取物种特异性变异与共有变异，上述数据集可用于后续的变异效应预测及基因本体（Gene Ontology, GO）分析。 包含文件： Ccusp_smallvariants.vcf.gz — 单核苷酸多态性与短插入缺失变异集 Ccusp_assembly.fasta — 用于结构变异鉴定的从头组装序列 Ccusp_structural_variants.vcf.gz — 经svim-asm v1.0.3检测得到的结构变异集