A population-scale chloroplast genome dataset for the endangered orchids Cypripedium taibaiense and C. flavum.

Abstract

Many Cypripedium orchids are threatened and legally protected, restricting destructive or large-scale wild sampling and leaving population-scale plastome resources scarce. Using small leaf samples collected with permission and assistance from local reserve staff, we assembled and annotated 62 complete chloroplast genomes from total genomic DNA sequencing data, representing 53 Cypripedium taibaiense and 9 C. flavum individuals. The plastomes were 191,252 to 204,050 bp long and retained the typical quadripartite structure. In the final GenBank annotations, unique intact CDS content was consistent within each species (79 genes in C. taibaiense and 75 in C. flavum), and the four canonical rRNA genes were each present in two copies. A phylogeny based on concatenated nucleotide alignments of protein-coding sequences recovered the two species as reciprocal monophyletic, whereas whole-plastome analyses including non-coding regions captured population-level variation. Across the dataset, we detected 5,574 SNPs and 60,941 indels, mainly in the large and small single-copy regions. This population-scale plastome dataset provides a practical reference for phylogeographic analysis, marker development, and conservation genomic studies in Cypripedium.