Background: Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. Results: The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT^(GGU), and trnT^(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions: Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

Despite having a generally conserved structure, chloroplast genome data have been helpful for plant population genetics and evolution research. To mine Pueraria montana chloroplast genome variation architecture and phylogeny, we investigated the chloroplast variation architecture of 104 P. montana accessions from across China. P. montana’s chloroplast genome showed high diversity levels, with 1674 variations, including 1118 single nucleotide polymorphisms and 556 indels. The intergenic spacers, psbZ-trnS and ccsA-ndhD, are the two mutation hotspot regions in the P. montana chloroplast genome. Phylogenetic analysis based on the chloroplast genome dataset supported four P. montana clades. P. montana variations were conserved among and within clades, which showed high gene flow levels. Most P. montana clades were estimated to have diverged at 3.82–5.17 million years ago. Moreover, the East Asian summer monsoon and South Asian summer monsoon may have accelerated population divergence. Our results show that chloroplast genome sequences were highly variable and can be used as molecular markers to assess genetic variation and relationships in P. montana.

Hawthorns (Crataegus L.) are one of the most important processing and table fruits in China, due to their medicinal properties and health benefits. However, the interspecific relationships and evolution history of cultivated Crataegus in China remain unclear. Our previously published data showed C. bretschneideri may be derived from the hybridization of C. pinnatifida with C. maximowiczii, and that introgression occurs between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. In the present study, chloroplast sequences were used to further elucidate the phylogenetic relationships of cultivated Crataegus native to China. The chloroplast genomes of three cultivated species and one related species of Crataegus were sequenced for comparative and phylogenetic analyses. The four chloroplast genomes of Crataegus exhibited typical quadripartite structures and ranged from 159,607 bp (C. bretschneideri) to 159,875 bp (C. maximowiczii) in length. The plastomes of the four species contained 113 genes consisting of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Six hypervariable regions (ndhC-trnV(UAC)-trnM(CAU), ndhA, atpH-atpI, ndhF, trnR(UCU)-atpA, and ndhF-rpl32), 196 repeats, and a total of 386 simple sequence repeats were detected as potential variability makers for species identification and population genetic studies. In the phylogenomic analyses, we also compared the entire chloroplast genomes of three published Crataegus species: C. hupehensis (MW201730.1), C. pinnatifida (MN102356.1), and C. marshallii (MK920293.1). Our phylogenetic analyses grouped the seven Crataegus taxa into two main clusters. One cluster included C. bretschneideri, C. maximowiczii, and C. marshallii, whereas the other included C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. Taken together, our findings indicate that C. maximowiczii is the maternal origin of C. bretschneideri. This work provides further evidence of introgression between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major, and suggests that C. pinnatifida var. major might have been artificially selected and domesticated from hybrid populations, rather than evolved from C. pinnatifida.

Background: Epimedii Folium is well known for its medicinal value. Four Epimedium species—Euphorbia brevicornu, E. sagittatum, E. pubescens, and E. koreanum—are the designated original plants of Epimedii Folium. Objective: The objective of this study is to facilitate the identification of the four Epimedium species and clarify their distributional responses to climate change. Methods: In this study, we assessed the genetic divergence of the four species and identified the molecular markers for species identification by using chloroplast genome sequences. Furthermore, we forecasted the distribution of potentially suitable regions of the four species Folium under climate change. Results: The authors obtained 26 chloroplast genome sequences of the four species and identified 1393 variable sites and 273 indel events. Genetic divergence analyses revealed that E. koreanum had long genetic distance from the other three species. Compared with the complete chloroplast genome, six hypervariable markers were discovered, and both rps4-trnL and ndhF were chosen as Epimedii Folium-specific DNA barcodes. Climate change is expected to influence the geographical distribution of the four Epimedium species, which were primarily found in China, South Korea, and Japan, leading to both expansion and contraction of their distribution ranges. Conclusion: Two identification markers were selected as the specific DNA barcodes for all four original plant species of Epimedii Folium. In addition, the shift of potential suitable area in various climate scenarios has been predicted. With the support of identification markers and the dynamics of suitable distribution areas, we are able to establish a foundation for the sustainable utilization of medicinal Epimedium resources in the future.

Chinese hawthorn (Crataegus pinnatifida) offers both medicinal and nutritional benefits due to its bioactive compounds. However, the combined effects of environmental and anthropogenic factors on its geographic distribution and medicinal quality remain insufficiently explored. Species distribution modeling (Biomod2) was integrated with ArcGIS-based spatial analysis to systematically model suitable habitats for C. pinnatifida across varying environmental and anthropogenic conditions, while concurrently assessing the spatial distribution patterns of medicinally active compounds. Furthermore, multi-scenario climate simulations were utilized to predict the impacts of future climate change on the spatial distribution patterns of this species. Anthropogenic activities strongly influence C. pinnatifida habitat suitability, followed by BIO18 (Precipitation of Warmest Quarter) and BIO4 (Temperature Seasonality). Bioactive compound heterogeneity is driven by anthropogenic activities, AWC (Soil Available Water Content), BIO12 (Annual Precipitation), and BIO4. High-suitability/high-quality areas are concentrated in Shandong Province. Under SSP126 (low emissions), high-suitability areas remain stable (2050s–2090s) with northeastward centroid shifts; under SSP585 (high emissions), they contract with southeastward centroid migration. Shandong is the optimal long-term cultivation region across scenarios. These findings establish a critical basis for cultivating C. pinnatifida with enhanced medicinal properties, developing adaptive management strategies to strengthen conservation, and ensuring sustainable utilization amid global climate change.