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Abstract Paphiopedilum armeniacum, Paphiopedilum wenshanense and Paphiopedilum emersonii are critically endangered wild orchids. Their populations are under severe threat, with a dramatic decline in the number of their natural distribution sites. Ex situ conservation and artificial breeding are the keys to maintaining the population to ensure the success of ex situ conservation and field return in the future. The habitat characteristics and soil nutrient information of the last remaining wild distribution sites of the three species were studied. ITS high-throughput sequencing was used to reveal the composition and structure of the soil fungal community, analyze its diversity and functional characteristics, and reveal its relationship with soil nutrients. The three species preferred to grow on low-lying, ventilated and shaded declivities with good water drainage. There were significant differences in soil alkali-hydrolyzed nitrogen and available phosphorus among the three species. There were 336 fungal species detected in the samples. On average, there were different dominant groups in the soil fungal communities of the three species. The functional groups of soil fungi within their habitats were dominated by saprophytic fungi and ectomycorrhizae, with significant differences in diversity and structure. The co-occurrence network of habitat soil fungi was mainly positive. Soil pH significantly affected soil fungal diversity within their habitats of the three paphiopedilum species. The study confirmed that the dominant groups of soil fungi were significantly correlated with soil nutrients. The three species exhibit comparable habitat inclinations, yet they display substantial variations in the composition, structure, and diversity of soil fungi. The fungal functional group is characterized by a rich presence of saprophytic fungi, a proliferation of ectomycorrhizae, and a modest occurrence of orchid mycorrhizae. The symbiotic interactions among the soil fungi associated with these three species are well-coordinated, enhancing their resilience against challenging environmental conditions. There is a significant correlation between soil environmental factors and the composition of soil fungal communities, with pH emerging as a pivotal factor regulating fungal diversity. Our research into the habitat traits and soil fungal ecosystems of the three wild Paphiopedilum species has established a cornerstone for prospective ex situ conservation measures and the eventual reestablishment of these species in their native landscapes.

Abstract Background The sect. Chrysantha Chang of plants with yellow flowers of Camellia species as the “Queen of the Tea Family”, most of these species are narrowly distributed endemics of China and are currently listed Grde-II in National Key Protected Wild Plant of China. They are commercially important plants with horticultural medicinal and scientific research value. However, the study of the sect. Chrysantha species genetics are still in its infancy, to date, the mitochondrial genome in sect. Chrysantha has been still unexplored. Results In this study, we provide a comprehensive assembly and annotation of the mitochondrial genomes for four species within the sect. Chrysantha. The results showed that the mitochondrial genomes were composed of closed-loop DNA molecules with sizes ranging from 850,836 bp (C. nitidissima) to 1,098,121 bp (C. tianeensis) with GC content of 45.71–45.78% and contained 48–58 genes, including 28–37 protein-coding genes, 17–20 tRNA genes and 2 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the four species. Then, we performed a comprehensive comparison of their basic structures, GC contents, codon preferences, repetitive sequences, RNA editing sites, Ka/Ks ratios, haplotypes, and RNA editing sites. The results showed that these plants differ little in gene type and number. C. nitidissima has the greatest variety of genes, while C. tianeensis has the greatest loss of genes. The Ka/Ks values of the atp6 gene in all four plants were greater than 1, indicating positive selection. And the codons ending in A and T were highly used. In addition, the RNA editing sites differed greatly in number, type, location, and efficiency. Twelve, six, five, and twelve horizontal gene transfer (HGT) fragments were found in C. tianeensis, Camellia huana, Camellia liberofilamenta, and C. nitidissima, respectively. The phylogenetic tree clusters the four species of sect. Chrysantha plants into one group, and C. huana and C. liberofilamenta have closer affinities. Conclusions In this study, the mitochondrial genomes of four sect. Chrysantha plants were assembled and annotated, and these results contribute to the development of new genetic markers, DNA barcode databases, genetic improvement and breeding, and provide important references for scientific research, population genetics, and kinship identification of sect. Chrysantha plants.

Abstract Sect. tuberculata plant belongs to the Camellia genus and is named for the “tuberculiform protuberance on the surface of the ovary and fruit”. It is a species of great ornamental value and potential medicinal value. However, little has been reported on the metabolites of C. tuberculata seeds. Therefore, this study was conducted to investigate the metabolites of C. tuberculata seeds based on UPLC/ESI-Q TRAP-MS/MS with extensively targeted metabolomics. A total of 1611 metabolites were identified, including 107 alkaloids, 276 amino acids and derivatives, 283 flavonoids, 86 lignans and coumarins, 181 lipids, 68 nucleotides and derivatives, 101 organic acids, 190 phenolic acids, 10 quinones, 4 steroids, 17 tannins, 111 terpenoids, and 177 other metabolites. We compared the different metabolites in seeds between HKH, ZM, ZY, and LY. The 1311 identified different metabolites were classified into three categories. Sixty-three overlapping significant different metabolites were found, of which lignans and coumarins accounted for the largest proportion. The differentially accumulated metabolites were enriched in different metabolic pathways between HKH vs. LY, HKH vs. ZM, HKH vs. ZY, LY vs. ZY, ZM vs. LY and ZM vs. ZY, with the most abundant metabolic pathways being 4, 2, 4, 7, 7 and 5, respectively (p

Abstract Background Sect. Tuberculata belongs to Camellia, and its members are characterized by a wrinkled pericarp and united filaments. All the plants in this group, which are endemic to China, are highly valuable for exploring the evolution of Camellia and have great potential for use as an oil source. However, due to the complex and diverse phenotypes of these species and the difficulty of investigating them in the field, their complex evolutionary history and interspecific definitions have remained largely unelucidated. Results Therefore, we newly sequenced and annotated 12 chloroplast (cp) genomes and retrieved the published cp genome of Camellia anlungensis Chang in sect. Tuberculata. In this study, comparative analysis of the cp genomes of the thirteen sect. Tuberculata species revealed a typical quadripartite structure characterized by a total sequence length ranging from 156,587 bp to 157,068 bp. The cp.genome arrangement is highly conserved and moderately differentiated. A total of 130 to 136 genes specific to the three types were identified by annotation, including protein-coding genes (coding sequences (CDSs)) (87–91), tRNA genes (35–37), and rRNA genes (8). The total observed frequency ranged from 23,045 (C. lipingensis) to 26,557 (C. anlungensis). IR region boundaries were analyzed to show that the ycf1 gene of C. anlungensis is located in the IRb region, while the remaining species are present only in the IRa region. Sequence variation in the SSC region is greater than that in the IR region, and most protein-coding genes have high codon preferences. Comparative analyses revealed six hotspot regions (tRNA-Thr(GGT)-psbD, psbE-petL, ycf15-tRNA-Leu(CAA), ndhF-rpl32, ndhD, and trnL(CAA)-ycf15) in the cp genomes that could serve as potential molecular markers. In addition, the results of phylogenetic tree construction based on the cp genomes showed that the thirteen sect. Tuberculata species formed a monophyletic group and were divided into two evolutionarily independent clades, confirming the independence of the section. Conclusions In summary, we obtained the cp genomes of thirteen sect. Tuberculata plants and performed the first comparative analysis of this group. These results will help us better characterize the plants in this section, deepen our understanding of their genetic characteristics and phylogenetic relationships, and lay the theoretical foundation for their accurate classification, elucidation of their evolutionary changes, and rational development and utilization of this section in the future.

Wild plants are an important part of the natural ecological system, and China is one of the countries with the most abundant wild plant species. It is of great significance to study the distribution characteristics, protection status and potential distribution areas of National Key Protected Wild Plants for supporting and formulating biodiversity conservation strategies. Based on 1 032 species (belonging to 315 genera, 129 families) of National Key Protected Wild Plants, this study used the top 5% richness algorithm to identify hotspots, and superimposed with nature reserves to evaluate the conservation effectiveness and determine conservation gaps of current nature reserves. Furthermore, this study used maximum entropy (MaxEnt) model to predict the potential distribution and range shifts of National Key Protected Wild Plants. The results were as follows: (1) The areas with the highest species richness of the National Key Protected Wild Plants mainly confined to the south and southwest of China, especially in central Sichuan, southern and southeastern Yunnan, northern Guangxi, northern Guangdong and Hainan. (2) The conservation effectiveness of hotspot grids showed that 171 (85.50%) hotspot grids were efficient protection (including 80.50% of total species), and 29 hotspot grids (14.50%) were not effectively protected (including 51.20% of total species). (3) By comparing the potential distribution area of National Key Protected Wild Plants under current and future climate scenarios, it is found that potential distribution area would expand to southeastern of Xizang, southwestern Guangxi, southern Guangdong, and southern Fujian in the future, while those around Sichuan Basin, southern Yunnan and southern Guizhou would shrink. Therefore, it is necessary to strengthen the dynamic monitoring of biodiversity and pay continuous attention to the impact of climate change on National Key Protected Wild Plants in the region. Based on the analysis results of hotspot grids, conservation effectiveness and potential distribution areas identified in this study, strong data support and reference can be provided for the identification of diversity priority protected areas for National Key Protected Wild Plants and the formulation of conservation policies.

Species of the subgenus Brachypetalum are the most primitive, most ornamental and most threatened group in the Orchid. This study revealed the ecological characteristics, soil nutrient characteristics and soil fungal community structure of habitats of the subgenus Brachypetalum in Southwest China. Lays a foundation for research on the wild populations and conservation Brachypetalum. The results showed that species of the subgenus Brachypetalum preferred a cool and humid environment, grew in scattered or aggregated form in narrow negative terrain, mainly in humic soil. The soil physical and chemical properties and soil enzyme activity indexes of the habitats were significantly different among different species, and the soil properties of different distribution points of the same species also varied greatly. There were significant differences in the soil fungal community structure among the habitats of different species. Basidiomycetes and ascomycetes were the main fungi in habitats of subgenus Brachypetalum species, and their relative abundance varied among different species. The functional groups of soil fungi were mainly symbiotic fungi and saprophytic fungi. LEfSe analysis found that there were different numbers and species of biomarkers in the habitats of subgenus Brachypetalum species, indicating that the habitat preference characteristics of each species in subgenus Brachypetalum were reflected in the fungal community. It was found that environmental factors had an impact on the changes in soil fungal communities in the habitats of subgenus Brachypetalum species, with climatic factors having the highest explanation rate (20.96%). Soil properties were significantly positively or negatively correlated with a variety of dominant soil fungal groups. Conclusions: The results of this study lay the foundation for the study of the habitat characteristics of wild populations of subgenus Brachypetalum and provides data to support in situ and ex situ conservation in the future.

To reveal the potential distribution characteristics of Phoebe zhennan in Guizhou Province and its response mode to environmental factors. Based on the geographical distribution points of P. zhennan in Guizhou Province, this study used MaxEnt and ArcGIS methods combining with 30 environmental factors such as climate, soil and topography to predict the potential habitat of P. zhennan in Guizhou Province and analyze the main environmental factors affecting the growth of P. zhennan. The results were as follows: (1) The AUC of MaxEnt model had an average value of 0.843, which indicated that it could well predict the geographical distribution of P. zhennan in Guizhou Province. The northeast of Guizhou Province was the key area of it’s potential habitat, with a decreasing trend from north to south and from east to west. The high suitable areas were mainly located in Tongren City, northeastern Guizhou Province and mid-eastern Zunyi City, northern Guizhou Province. The middle suitable and low suitable areas were concentrated in northern Tongren City, north-central Miao and Dong autonomous prefecture in southeastern Guizhou Province, Guiyang, northeastern Bijie City and northeastern Buyi and Miao autonomous prefecture in southern Guizhou Province. Other areas were not suitable for P. zhennan to grow. (2) The potential distribution area of P. zhennan in Guizhou Province was 80 013.47 km2, which accounted for 45.4% of the whole province's land area. The high suitable area covered 30 565.66 km2, and the share of high suitable area was 17.4%. (3) Environmental factors including isothermality (Bio3), precipitation of the warmest quarte (Bio18), precipitation of the wettest month (Bio13), precipitation of the driest month (Bio14), min temperature of the coldest month (Bio6) and temperature seasonality (Bio4) were the main environmental factors affecting the potential distribution of P. zhennan in Guizhou Province. In conclusion, the results elucidate that the geographical distribution of P. zhennan in Guizhou Province and the main environmental factors affecting its distribution are of great significance. The results of this study will provide a scientific basis for seedling expansion, afforestation promotion, development and utilization of P. zhennan in Guizhou Province.

Endangered plants are essential components of most forest ecosystems and reflect the ecological integrity of forests. The study of the population structure and spatial pattern of Alsophila spinulosa is of great significance for its conservation. In the subtropical Chishui Tree fern valley in China, we studied the best structure of A. spinulosa to reflect the environmental change, the range of the most intense spatial aggregation change, and the spatial relationship with the community structure, and explored the survival characteristics of A. spinulosa. Our results showed that the variation in tree height structure was the most obvious response to the change in community type. The spatial aggregation degree of A. spinulosa had the most obvious change in the range of 1–5 m. There was an obvious spatial correlation between the dominant plants, the vertical structure of the community, and the distribution of A. spinulosa. These findings provided a reference for exploring the population structure, distribution pattern, and the influence of community types on A. spinulosa populations.

Geodorum eulophioides is a unique and endangered species belonging to the Orchidaceae family in China. It has great potential as an ornamental horticultural plant. However, little is known about its genetic diversity and reasons for being endangered due to its narrow distribution and few populations in the wild. To effectively evaluate and conserve available resources, the genetic diversity and population structure of G. eulophioides were analyzed in this study. A total of 94 individuals from 10 natural populations were studied using site-specific amplified fragment sequencing (SLAF-seq). Based on the 76,340 SNPs detected by SLAF-seq, genetic diversity analysis was performed and markers associated with environmental variables were determined. The results showed that the level of genetic diversity in the 10 natural populations studied was low, with PIC values ranging from 0.1874 to 0.2156. FIS values ranged from −0.2376 to 0.2658, with excess and deficiency in heterozygotes. FST values ranged from 0.0482 to 0.3144, with genetic variation among populations. AMOVA results showed that the genetic variation among populations accounted for 21.35% of the total variation, and the remaining genetic variation among individuals within populations was 78.65%. The results of the population structure analysis showed that 94 individuals were classified into three major groups and two subgroups. Environmental association analysis using Bayenv2 and LFMM yielded thirty and eighteen putative adaptive loci, respectively, and five specific functional genes were annotated. In summary, this study provides further insight into the genetic structure of G. eulophioides and provides a reference for protection and restoration.

Abstract To understand the distribution of biodiversity and its determinants, particularly that of ecologically sensitive ones, has long been intriguing to the science community and will help formulate conservation strategies under future climate changes. To this end, we conducted extensive field surveys on the distribution of orchid flora in the Beipan River Basin in Guizhou Province, which is one of the biodiversity conservation priorities in China. The data we acquired, together with those published previously, were converted into orchid species richness for each of the 3 km × 3 km grid cells covering the study region. Redundancy analysis (RDA) and geographically weighted regression (GWR) were then applied to determine which of the 30 environmental factors are potentially critical for the spatial distribution of orchid flora we have observed. Despite a moderate spatial extent, we found that the Beipan River Basin harbors about 249 native orchid species belonging to 74 genera, equivalent to 14.5% of orchid flora of China. Orchid species richness in this area follows a descending gradient from the southeast to the northwest, 70.41% of its variation among grid cells can be explained by environmental factors and spatial variables, and spatial variables accounted for 63.90% of the spatial variation of orchid distribution, indicating that spatial variables played a dominant role in the distribution of wild Orchidaceae species richness. In addition, the main environmental driver is the mean temperature of the wettest quarter. Our study provides a good example for revealing the main drivers of orchid distribution characteristics and has a certain reference value for the development of orchid conservation strategies.

Dendrobium comatum is a rare orchid plant. To further its research and conservation, we reported and characterized its complete chloroplast (cp) genome by using Illumina paired-end sequencing data. We also analyzed its characteristics and studied its clustering relationships. The total chloroplast genome size was 158,008 bp, including inverted repeats (IRs) of 27,032 bp separated by a large single copy (LSC) region and a small single copy (SSC) region of 85,592 and 18,352 bp, respectively. A total of 132 genes, including 38 tRNA, 8 rRNA, and 87 protein-coding genes, were identified. Phylogenetic analysis showed that D. comatum is sister to D. kingianum with sufficient support.

The determination of the geographic distributions of orchid species and their relationships with environmental factors are considered fundamental to their conservation. Paphiopedilum subgenus Brachypetalum is one of the most primitive, ornamental, and threatened groups of Orchidaceae. However, little is known about the distribution of Brachypetalum orchids and how they are influenced by environmental factors. In this study, we developed a database on the geographical distribution of Brachypetalum orchids based on a large-scale field investigation in the Guangxi, Guizhou, and Yunnan provinces of southwest China (2019–2020). Using this database, we first adopted the nonparametric Mann–Whitney U test to analyze the differences in the geographical distributions and growth environments of Brachypetalum orchids. In addition, we also used the method of principal component analysis (PCA) to explore distribution patterns of Brachypetalum orchids in relation to environmental factors (topography, climate, anthropogenic disturbance, productivity, and soil) in southwest China. Our results indicated that Brachypetalum orchid species were mainly distributed in the karst limestone habitats of southwest China. In general, there were 194 existing localities with the occurrence of seven target orchids in the investigated area. Of the discovered species in our study, 176 locations (~90.7%) were distributed primarily in the karst habitat. Among them, the range of 780–1267 m was the most concentrated elevation of Brachypetalum orchids. In addition, the findings also suggested that the distribution of Brachypetalum orchids in southwest China was relatively scattered in geographical space. However, the density of the distribution of Brachypetalum orchids was high, between 104° and 108° E and between 25° and 26° N. The results of the Mann–Whitney U test revealed that there are obviously different geographical distributions and growth environments of Brachypetalum in southwest China. More specifically, we found some extremely significant differences (p < 0.001) in elevation, mean diurnal range, precipitation of coldest quarter, solar radiation, and exchangeable Ca2+ between the provinces of southwest China. The PCA analysis revealed that elevation, solar radiation, temperature (mean diurnal range, annual temperature range) and precipitation (precipitation seasonality, precipitation of the warmest quarter) were found to be the most significant factors in determining Brachypetalum orchids’ distribution. These findings have implications in assessing conservation effectiveness and determining niche breadth to better protect the populations of these Brachypetalum orchid species in the future.

Catalyzed oxidative C-C bond coupling reactions play an important role in the chemical synthesis of complex natural products of medicinal importance. However, the poor functional group tolerance renders them unfit for the synthesis of naturally occurring polyphenolic flavones. We find that molecular oxygen in alkaline water acts as a hydrogen atom acceptor and oxidant in catalyst-free (without added catalyst) oxidative coupling of luteolin and other flavones. By this facile method, we achieve the synthesis of a small collection of flavone dimers and trimers including naturally occurring dicranolomin, philonotisflavone, dehydrohegoflavone, distichumtriluteolin, and cyclodistichumtriluteolin. Mechanistic studies using both experimental and computational chemistry uncover the underlying reasons for optimal pH, oxygen availability, and counter-cations that define the success of the reaction. We expect our reaction opens up a green and sustainable way to synthesize flavonoid dimers and oligomers using the readily available monomeric flavonoids isolated from biomass and exploiting their use for health care products and treatment of diseases.