Henckelia longisepala (H. W. Li) D. J. Middleton & Mich. Möller is a rare and endangered plant species found only in Southeastern Yunnan, China, and Northern Vietnam. It is listed as a threatened species in China and recognized as a plant species with extremely small populations (PSESP), while also having high ornamental value and utilization potential. This study used ddRAD-seq technology to quantify genetic diversity and structure for 32 samples from three extant populations of H. longisepala. The H. longisepala populations were found to have low levels of genetic diversity (Ho = 0.1216, He = 0.1302, Pi = 0.1731, F_IS = 0.1456), with greater genetic differentiation observed among populations (F_ST = 0.3225). As indicated by genetic structure and phylogenetic analyses, samples clustered into three distinct genetic groups that corresponded to geographically separate populations. MaxEnt modeling was used to identify suitable areas for H. longisepala across three time periods and two climate scenarios (SSP1-2.6, SSP5-8.5). High-suitability areas were identified in Southeastern Yunnan Province, Northern Vietnam, and Eastern Laos. Future H. longisepala distribution was predicted to remain centered in these areas, but with a decrease in the total amount of suitable habitat. The present study provides key data on H. longisepala genetic diversity, as well as a theoretical basis for the conservation, development, and utilization of its germplasm resources.

Papilionanthe Schltr. (Vandeae, Epidendroideae, Orchidaceae) is distinguished by its terete leaves and showy flowers, with significant horticultural and medicinal values. However, its systematic position in Aeridinae has been controversial and not been paid attention to or clarified. This study is focused on the complete chloroplast (cp) genomic data of P. biswasiana and P. teres in order to provide some genomic data for its phylogenetic relationship. The cp genomes of two Papilionanthe were 148,183 bp (P. biswasiana) and 148,145 bp (P. teres) in length, with similar GC content (36.5–36.6%). Comparative cp genomes of two Papilionanthe species and the other eight related taxa revealed differences in sequence analysis and statistics. A phylogenetic analysis based on CDS from complete cp genomes supported the notion that Papilionanthe is a monophyletic clade and closer to Luisia than to Paraphalaenopsis. It was obvious that there are four well-supported clades in Aeridinae, which could hold a significant implication for the phylogenetic relationship between Papilionanthe and other alliances in Aeridinae. Furthermore, the taxonomic positions of V. flabellata and H. himalacia were also reconfirmed herein by phylogenetic analysis of the cp genomes.