Conservation genetics and potential geographic distribution modeling of Corybas taliensis, a small 'sky Island' orchid species in China.

BACKGROUND: Corybas taliensis is an endemic species of sky islands in China. Its habitat is fragile and unstable, and it is likely that the species is threatened. However, it is difficult to determine the conservation priority or unit without knowing the genetic background and the overall distribution of this species. In this study, we used double digest restriction-site associated DNA-sequencing (ddRAD-seq) to investigate the conservation genomics of C. taliensis. At the same time, we modeled the extent of suitable habitat for C. taliensis in present and future (2030 and 2090) habitat using the maximum-entropy (MaxEnt) model. RESULTS: The results suggested that the related C. fanjingshanensis belongs to C. taliensis and should not be considered a separate species. All the sampling locations were divided into three genetic groups: the Sichuan & Guizhou population (SG population), the Hengduan Mountains population (HD population) and Himalayan population (HM population), and we found that there was complex gene flow between the sampling locations of HD population. MT was distinct genetically from the other sampling locations due to the unique environment in Motuo. The genetic diversity (π, He) of C. taliensis was relatively high, but its contemporary effective population size (Ne) was small. C. taliensis might be currently affected by inbreeding depression, although its large population density may be able to reduce the effect of this. The predicted areas of suitable habitat currently found in higher mountains will not change significantly in the future, and these suitable habitats are predicted to spread to other higher mountains under future climate change. However, suitable habitat in relatively low altitude areas may disappear in the future. This suggests that C. taliensis will be caught in a 'summit trap' in low altitude areas, however, in contrast, the high altitude of the Himalaya and the Hengduan Mountains are predicted to act as 'biological refuges' for C. taliensis in the future. CONCLUSIONS: These results not only provide a new understanding of the genetic background and potential resource distribution of C. taliensis, but also lay the foundation for its conservation and management.

The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP).

Magnolia sinica (Magnoliaceae) is a highly threatened tree endemic to southeast Yunnan, China. In this study, we generated for the first time a high-quality chromosome-scale genome sequence from M. sinica, by combining Illumina and ONT data with Hi-C scaffolding methods. The final assembled genome size of M. sinica was 1.84 Gb, with a contig N50 of ca. 45 Mb and scaffold N50 of 92 Mb. Identified repeats constituted approximately 57% of the genome, and 43,473 protein-coding genes were predicted. Phylogenetic analysis shows that the magnolias form a sister clade with the eudicots and the order Ceratophyllales, while the monocots are sister to the other core angiosperms. In our study, a total of 21 individuals from the 5 remnant populations of M. sinica, as well as 22 specimens belonging to 8 related Magnoliaceae species, were resequenced. The results showed that M. sinica had higher genetic diversity (θw = 0.01126 and θπ = 0.01158) than other related species in the Magnoliaceae. However, population structure analysis suggested that the genetic differentiation among the 5 M. sinica populations was very low. Analyses of the demographic history of the species using different models consistently revealed that 2 bottleneck events occurred. The contemporary effective population size of M. sinica was estimated to be 10.9. The different patterns of genetic loads (inbreeding and numbers of deleterious mutations) suggested constructive strategies for the conservation of these 5 different populations of M. sinica. Overall, this high-quality genome will be a valuable genomic resource for conservation of M. sinica.

Genomic Data Reveals Population Genetic and Demographic History of Magnolia fistulosa (Magnoliaceae), a Plant Species With Extremely Small Populations in Yunnan Province, China.

Elucidating the genetic background of threatened species is fundamental to their management and conservation, and investigating the demographic history of these species is helpful in the determination of the threats facing them. The woody species of the genus Magnolia (Magnoliaceae) have high economic, scientific and ecological values. Although nearly half of all Magnolia species have been evaluated as threatened, to date there has been no population genetic study employing Next Generation Sequencing (NGS) technology in this genus. In the present study, we investigate the conservation genomics of Magnolia fistulosa, a threatened species endemic to the limestone area along the Sino-Vietnamese border, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. To increase the reliability of our statistical inferences, we employed two approaches, Stacks and ipyrad, for SNP calling. A total of 15,272 and 18,960, respectively, putatively neutral SNPs were generated by Stacks and ipyrad. Relatively high genetic diversity and large population divergence were detected in M. fistulosa. Although higher absolute values were calculated using the ipyrad data set, the two data sets showed the same trends in genetic diversity (π, H e), population differentiation (F ST) and inbreeding coefficients (F IS). A change in the effective population size of M. fistulosa within the last 1 Ma was detected, including a population decline about 0.5-0.8 Ma ago, a bottleneck event about 0.2-0.3 Ma ago, population fluctuations during the last glacial stage, and the recovery of effective population size after the last glacial maximum. Our findings not only lay the foundation for the future conservation of this species, but also provide new insights into the evolutionary history of the genus Magnolia in southeastern Yunnan, China.

Two new species of Oreocharis (Gesneriaceae) from karst regions in Yunnan and notes on O. tetraptera and O. brachypoda from China.

Two new species of Gesneriaceae, Oreocharis aimodisca and O. longipedicellata, from the limestone area of Yunnan Province, China, are described and illustrated. Their morphological relationship with similar species is discussed and colour photographs, detailed descriptions, distribution and habitat, as well as the IUCN endangered status are provided. We also discuss the accuracy of the scientific names of the described species O. tetrapterus from Guangxi, China in 2019 and O. brachypodus from Guizhou, China, in 2015, and put forward corrections related to name form.

Oreocharis wumengensis, a new species of Gesneriaceae from northeastern Yunnan, China.

A new species of Gesneriaceae, Oreocharis wumengensis Lei Cai & Z.L.Dao from Wumeng Mountain area, Yanjin County, Yunnan Province, China, is described. The new species is morphologically similar to O. panzhouensis Lei Cai, Y.Guo & F.Wen in the shape of corolla, number of stigma and stamens, but it can be easily distinguished from this species by the leaf shape and indumentum characters of leaf blade, calyx and stamens. Detailed descriptions with photographs of the plant and holotype, and comparisons with morphologically similar species, are also provided.

Two new species of Henckelia (Gesneriaceae) from Southeastern Yunnan, China.

Two new species of Gesneriaceae, Henckelia nanxiheensis Lei Cai & Z.L.Dao, sp. nov. and H. multinervia Lei Cai & Z.L.Dao, sp. nov. from southeastern Yunnan, China, are described with color photos. The diagnostic characters of the two new species, together with photographs, detailed descriptions, distribution and habitat, as well as comparisons with morphologically similar species, are also provided.

De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China.

BACKGROUND: Acer yangbiense is a newly described critically endangered endemic maple tree confined to Yangbi County in Yunnan Province in Southwest China. It was included in a programme for rescuing the most threatened species in China, focusing on "plant species with extremely small populations (PSESP)". FINDINGS: We generated 64, 94, and 110 Gb of raw DNA sequences and obtained a chromosome-level genome assembly of A. yangbiense through a combination of Pacific Biosciences Single-molecule Real-time, Illumina HiSeq X, and Hi-C mapping, respectively. The final genome assembly is ∼666 Mb, with 13 chromosomes covering ∼97% of the genome and scaffold N50 sizes of 45 Mb. Further, BUSCO analysis recovered 95.5% complete BUSCO genes. The total number of repetitive elements account for 68.0% of the A. yangbiense genome. Genome annotation generated 28,320 protein-coding genes, assisted by a combination of prediction and transcriptome sequencing. In addition, a nearly 1:1 orthology ratio of dot plots of longer syntenic blocks revealed a similar evolutionary history between A. yangbiense and grape, indicating that the genome has not undergone a whole-genome duplication event after the core eudicot common hexaploidization. CONCLUSION: Here, we report a high-quality de novo genome assembly of A. yangbiense, the first genome for the genus Acer and the family Aceraceae. This will provide fundamental conservation genomics resources, as well as representing a new high-quality reference genome for the economically important Acer lineage and the wider order of Sapindales.

Isolation and characterization of 21 microsatellite loci in Cardiocrinum giganteum var. yunnanense (Liliaceae), an important economic plant in China.

Twenty-one microsatellite markers from the genome of Cardiocrinum giganteum var. yunnanense, an important economic plant in China, were developed with a fast isolation protocol by amplified fragment length polymorphism of sequences containing repeats (FIASCO). Polymorphism within each locus was assessed in 24 wild individuals from Gaoligong Mountains in western Yunnan Province, China. The number of alleles per locus ranged from 2 to 4 with a mean of 2.9. The expected and observed levels of heterozygosity ranged from 0.042 to 0.726 and from 0.000 to 1.000, with averages of 0.44 and 0.31, respectively. These polymorphic microsatellite markers should prove useful in population genetics studies and assessments of genetic variation to develop conservation and management strategies for this species.

Development of ten polymorphic microsatellite loci for Fosbergia shweliensis (Rubiaceae), a potentially crisis endangered tree.

PREMISE OF THE STUDY: Fosbergia shweliensis (Anth.) Tirveng. & Sastre (Rubiaceae) is a potentially endangered tree endemic to China. Microsatellite markers were developed to investigate population genetics of this plant. METHODS AND RESULTS: Ten polymorphic microsatellite loci were identified and screened in 32 individuals from four wild populations of F. shweliensis. Alleles numbered 2 to 5, and their levels of observed heterozygosity and expected heterozygosity ranged from 0.0564 to 0.7214 and from 0.2794 to 0.7912, respectively. CONCLUSIONS: These new microsatellite loci will facilitate further studies of the population genetics of F. shweliensis, allowing us to design reasonable conservation and management strategies.

Genetic variation and conservation assessment of Chinese populations of Magnolia cathcartii (Magnoliaceae), a rare evergreen tree from the South-Central China hotspot in the Eastern Himalayas.

Nine natural populations of the rare evergreen tree Magnolia cathcartii (Magnoliaceae) were sampled across its natural range, and amplified fragment length polymorphism (AFLP) markers were used to assess genetic variation within and among populations. Three ex situ populations were also surveyed to determine whether conservation plantings include the entire genetic diversity of the species. Genetic diversity within the natural populations was very low (0.122 for Nei's gene diversity), and the southeast populations had the highest diversity. The ex situ populations had a lower diversity than the mean diversity for all populations, and none of the ex situ populations reached the levels of diversity found in their source populations. Genetic differentiation was high among natural populations (G st = 0.247), and an isolation-by-distance pattern was detected. Habitat fragmentation, restricted gene flow, and geitonogamy are proposed to be the primary reasons for the low genetic diversity and high genetic differentiation. More protection is needed, especially for the southeast populations, which possess the highest numbers of unique alleles according to AFLP fragment analyses. The ex situ program was a good first step towards preserving this species, but the current ex situ populations preserve only a limited portion of its genetic diversity. Future ex situ efforts should focus on enhancing the plantings with individuals from southeastern Yunnan.

Medicinal plants used by Tibetans in Shangri-la, Yunnan, China.

BACKGROUND: Medicinal plants used by the local people in Xizang (Tibet) have been investigated since the 1960s. The others out of Xizang, however, have been less understood, although they may be easily and strongly influenced by the various local herbal practices, diverse environments, local religious beliefs and different prevalent types of diseases. In 2006, two ethnobotanical surveys were organized in the county of Shangri-la, Yunnan Province, SW China, to document the traditional medicinal plants used by the Tibetan people. METHODS: After literature surveying, four local townships were selected to carry out the field investigation. Three local healers were interviewed as key informants. The methods of ethnobotany, anthropology and participatory rural appraisal (PRA) were used in the field surveys. Plant taxonomic approach was adopted for voucher specimen identification. RESULTS: Sixty-eight medicinal plant species in 64 genera of 40 families were recorded and collected. Among them, 23 species were found to have medicinal values that have not been recorded in any existing Tibetan literatures before, and 31 species were recorded to have traditional prescriptions. Moreover, the traditional preparations of each species and some folk medicinal knowledge were recorded and analyzed. These traditional prescriptions, preparations, new medicinal plants and folk medicinal knowledge and principles were discovered and summarized by local traditional Tibetan healers through times of treatment practices, and were passed down from generation to generation. CONCLUSION: As a part of the cultural diversity of Tibetan community, these traditional medicinal knowledge and experiences may provide data and information basis for the sustainable utilization and development of Tibetan medicine, and may contribute to the local economic development. However, for many reasons, they are disappearing gradually as time goes by. Our study showed that there were abundant traditional Tibetan medicinal prescriptions and using methods. It implies that more Tibetan medicinal plants and traditional knowledge can be discovered. Further research should be done to save the wealth of these traditional medicinal knowledge and experiences before they are dying out.