The distribution of suitable habitats for medicinal plants is affected by climate, soil, land use, and other factors. Arnebiae Radix, an important traditional Chinese medicinal resource in Xinjiang, includes Arnebia euchroma (Royle) I. M. Johnst. and Arnebia guttata Bunge and is at risk of over-exploitation. This study predicted suitable planting areas by integrating habitat and phytochemical suitability using the MaxEnt model and ArcGIS. The AUC values for A. euchroma and A. guttata were 0.977 and 0.952, with TSS values of 0.829 and 0.725, respectively, validating the high accuracy of the prediction model. Under the current scenario, the areas of suitable habitats for A. euchroma and A. guttata were 108,914 and 176,445 km², mainly distributed along the main mountains in Xinjiang. Under future climate scenarios, the suitable habitat area of A. euchroma increased by 11–18%, except in the ssp126-2090s scenario, while the suitable habitat area of A. guttata area decreased by 3–18%. Both species were influenced by land use/land cover and soil available nitrogen content; additionally, A. euchroma was affected by the precipitation in the driest month, and A. guttata by the mean diurnal range. The content of secondary metabolites was positively correlated with habitat suitability, with soil factors contributing 35.25% to the total secondary metabolite content. Their suitable habitats predominantly occur in grasslands (42–82%). As habitat and phytochemical suitability distributions aligned, the eastern and western sides of the northern Kunlun Mountain Pass emerged as key areas for cultivation. This research can provide a scientific foundation for selecting optimal planting regions for the two Arnebia species.

Cypripedium is renowned for its high morphological diversity and complex genetic and evolutionary characteristics. The chloroplast genome serves as a valuable tool for investigating phylogenetic relationships and evolutionary processes in plants. Currently, research on the evolution of the chloroplast genome within the Cypripedium genus is limited due to insufficient large-scale sampling and a lack of comprehensive understanding. Consequently, the mechanisms underlying the significant differences in chloroplast genome size among Cypripedium species remain poorly understood. In this study, we conducted a comprehensive comparative analysis of the chloroplast genomes of 29 Cypripedium species. The lengths of these genomes ranged from 162,092 to 246,177 base pairs (bp) and contained between 127 and 134 genes. Our results indicate that, while the overall structure of the chloroplast genomes in Cypripedium species is relatively conserved, significant differences were observed among the large single-copy (LSC), small single-copy (SSC), and inverted repeat (IR) regions. Several genes, including psaC, rpl32, ycf1, and psbK, exhibited higher levels of variability and may serve as molecular markers in taxonomic studies. The results of our correlation analysis suggest that the expansion of the LSC region, the increase in simple sequence repeats (SSRs), and tandem repeats (TRs) have significantly enlarged the size of the chloroplast genome in Cypripedium species. Phylogenetic signal testing supports the notion that genetic variation has driven species divergence within the genus. Overall, our findings provide insights into the substantial differences in chloroplast genome length observed among Cypripedium species. However, the relationship between diversification and the evolutionary mechanisms affecting Cypripedium, including ecological adaptive evolution, incomplete lineage sorting (ILS), hybridization, and reticulate events, requires further investigation.