Data for: Complete plastid genome assembly, annotation, and SNP variations of Fritillaria thunbergii

Understanding how climatic fluctuations and human activities jointly influence genetic diversity is essential for conserving medicinal plants. In this study, we generated a genome-wide SNP dataset for Fritillaria thunbergii using ddRAD-seq, identifying 18,029 high-quality markers for downstream population genomic analyses , demographic inference, and species distribution modeling, supplemented by complete plastid genomes.