1
|
Jin XH, Wang YC, Li D, Li Y, He HY, Zhang HB. Diverse Mycena Fungi and Their Potential for Gastrodia elata Germination. J Microbiol Biotechnol 2024; 34:1249-1259. [PMID: 38938004 PMCID: PMC11239410 DOI: 10.4014/jmb.2401.01009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/29/2024]
Abstract
It remains to be determined whether there is a geographical distribution pattern and phylogenetic signals for the Mycena strains with seed germination of the orchid plant Gastrodia elata. This study analyzed the community composition and phylogenetics of 72 Mycena strains associated with G. elata varieties (G. elata. f. glauca and G. elata. f. viridis) using multiple gene fragments (ITS+nLSU+SSU). We found that (1) these diverse Mycena phylogenetically belong to the Basidiospore amyloid group. (2) There is a phylogenetic signal of Mycena for germination of G. elata. Those strains phylogenetically close to M. abramsii, M. polygramma, and an unclassified Mycena had significantly higher germination rates than those to M. citrinomarginata. (3) The Mycena distribution depends on geographic site and G. elata variety. Both unclassified Mycena group 1 and the M. abramsii group were dominant for the two varieties of G. elata; in contrast, the M. citrinomarginata group was dominant in G. elata f. glauca but absent in G. elata f. viridis. Our results indicate that the community composition of numerous Mycena resources in the Zhaotong area varies by geographical location and G. elata variety. Importantly, our results also indicate that Mycena's phylogenetic status is correlated with its germination rate.
Collapse
Affiliation(s)
- Xiao-Han Jin
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan, Kunming, P.R. China
- School of Ecology and Environmental Science, Yunnan University, Kunming, P.R. China
| | - Yu-Chuan Wang
- Gastrodia Tuber Research Institute of Zhaotong, P.R. China
| | - Dong Li
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan, Kunming, P.R. China
- School of Ecology and Environmental Science, Yunnan University, Kunming, P.R. China
| | - Yu Li
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan, Kunming, P.R. China
| | - Hai-Yan He
- The Agriculture and Life Sciences College, Zhaotong University, Zhaotong, P.R. China
- Yunnan Key Laboratory of Gastrodia elata and Fungus Symbiotic Biology, Zhaotong, P.R. China
| | - Han-Bo Zhang
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan, Kunming, P.R. China
| |
Collapse
|
2
|
Hu J, Feng Y, Zhong H, Liu W, Tian X, Wang Y, Tan T, Hu Z, Liu Y. Impact of climate change on the geographical distribution and niche dynamics of Gastrodia elata. PeerJ 2023; 11:e15741. [PMID: 37520262 PMCID: PMC10373646 DOI: 10.7717/peerj.15741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/20/2023] [Indexed: 08/01/2023] Open
Abstract
Background Gastrodia elata is widely used in China as a valuable herbal medicine. Owing to its high medicinal and nutrient value, wild resources of G. elata have been overexploited and its native areas have been severely damaged. Understanding the impacts of climate change on the distribution of this endangered species is important for the conservation and sustainable use of G. elata. Methods We used the optimized maximum entropy model to simulate the potential distribution of G. elata under contemporary and future time periods (1970-2000, 2050s, 2070s, and 2090s) and different climate change scenarios (SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5). Under these conditions, we investigated the key environmental factors influencing the distribution of G. elata as well as the spatial and temporal characteristics of its niche dynamics. Results With high Maxent model accuracy (AUCmean = 0.947 ± 0.012, and the Kappa value is 0.817), our analysis revealed that annual precipitation, altitude, and mean temperature of driest quarter are the most important environmental factors influencing the distribution of G. elata. Under current bioclimatic conditions, the potentially suitable area for G. elata in China is 71.98 × 104 km2, while the highly suitable region for G. elata growth is 7.28 × 104 km2. Our models for three future periods under four climate change scenarios indicate that G. elata can maintain stable distributions in southern Shaanxi, southwestern Hubei, and around the Sichuan basin, as these areas are highly suitable for its growth. However, the center of the highly suitable areas of G. elata shift depending on different climatic scenarios. The values of niche overlap for G. elata show a decreasing trend over the forecasted periods, of which the niche overlap under the SSP3-7.0 scenario shows the greatest decrease. Discussions Under the condition of global climate change in the future, our study provides basic reference data for the conservation and sustainable utilization of the valuable and endangered medicinal plant G. elata. It is important to carefully choose the protection area of G. elata wild resources according the suitable area conditions modeled. Moreover, these findings will be valuable for providing insights into the breeding and artificial cultivation of this plant, including the selection of suitable areas for planting.
Collapse
Affiliation(s)
- Juan Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Ying Feng
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Haotian Zhong
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Wei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xufang Tian
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yehong Wang
- Wufeng Tujia Autonomous County Agricultural Science and Technology Demonstration Center, Yichang, China
| | - Tao Tan
- Wufeng Tujia Autonomous County Herbal Medicine Development Center, Yichang, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| |
Collapse
|
3
|
Zhou Z, Shi R, Zhang Y, Xing X, Jin X. Orchid conservation in China from 2000 to 2020: Achievements and perspectives. PLANT DIVERSITY 2021; 43:343-349. [PMID: 34816060 PMCID: PMC8591184 DOI: 10.1016/j.pld.2021.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/03/2021] [Accepted: 06/11/2021] [Indexed: 06/01/2023]
Abstract
We review achievements in the conservation of orchid diversity in China over the last 21 years. We provide updated information on orchid biodiversity and suggestions for orchid conservation in China. We outline national policies of biodiversity conservation, especially of orchid conservation, which provide general guidelines for orchid conservation in China. There are now approximately 1708 known species of Orchidaceae in 181 genera in China, including five new genera and 365 new species described over the last 21 years. The assessment of risk of extinction of all 1502 known native orchid species in China in 2013 indicated that 653 species were identified as threatened, 132 species were treated as data-deficient, and four species endemic to China were classified as extinct. Approximately 1100 species (ca. 65%) are protected in national nature reserves, and another ~66 species in provincial nature reserves. About 800 native orchid species have living collections in major botanical gardens. The pollination biology of 74 native orchid species and the genetic diversity and spatial genetic structure of 29 orchid species have been investigated at a local scale and/or across species distributions. The mycorrhizal fungal community composition has been investigated in many genera, such as Bletilla, Coelogyne, Cymbidium, Cypripedium, and Dendrobium. Approximately 292 species will be included in the list of national key protected wild plants this year. Two major tasks for near future include in situ conservation and monitoring population dynamics of endangered species.
Collapse
Affiliation(s)
- Zhihua Zhou
- Department of Wildlife Conservation, National Forestry and Grassland Administration, No. 18, Hepingli Dongjie, Beijing, 100714, China
| | - Ronghong Shi
- Department of Wildlife Conservation, National Forestry and Grassland Administration, No. 18, Hepingli Dongjie, Beijing, 100714, China
| | - Yu Zhang
- Beijing Botanical Garden, Wofosi Rd, Xiangshan, Beijing, 100093, China
| | - Xiaoke Xing
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193, China
| | - Xiaohua Jin
- Institute of Botany, Chinese Academy of Sciences (IBCAS), Nanxincun 20, Xiangshan, Beijing, 100093, PR China
| |
Collapse
|
4
|
Alves MF, Pinheiro F, Nunes CEP, Prosdocimi F, Sarzi DS, Furtado C, Mayer JLS. Reproductive development and genetic structure of the mycoheterotrophic orchid Pogoniopsis schenckii Cogn. BMC PLANT BIOLOGY 2021; 21:332. [PMID: 34253186 PMCID: PMC8276481 DOI: 10.1186/s12870-021-03118-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/29/2021] [Indexed: 05/17/2023]
Abstract
BACKGROUND Pogoniopsis schenckii Cogn. is a mycoheterotrophic orchid that can be used as a model to understand the influence of mycoheterotrophy at different stages of the reproductive cycle. We aimed to verify the presence of endophytic and epiphytic fungi at each stage of the reproductive process and investigated how the breeding system may relate to genetic structure and diversity of populations. In this study we performed anatomical and ultrastructural analyses of the reproductive organs, field tests to confirm the breeding system, and molecular analysis to assess genetic diversity and structure of populations. RESULTS During the development of the pollen grain, embryo sac and embryogenesis, no fungal infestation was observed. The presence of endophytic fungal hyphae was observed just within floral stems and indehiscent fruit. Beyond assuring the presence of fungus that promote seed germination, specific fungi hyphae in the fruit may affect other process, such as fruit ripening. As other mycoheterotrophic orchids, P. schenckii is autogamous, which may explain the low genetic diversity and high genetic structure in populations. CONCLUSIONS We discuss an interesting interaction: fungal hyphae in the indehiscent fruit. These fungal hyphae seem to play different roles inside fruit tissues, such as acting in the fruit maturation process and increasing the proximity between fungi and plant seeds even before dispersion occurs. As other mycoheterotrophic orchids, P. schenckii is autogamous, which may explain the low genetic diversity and high genetic structure in populations. Altogether, our findings provide important novel information about the mechanisms shaping ecology and evolution of fragmented populations of mycoheterotrophic plant.
Collapse
Affiliation(s)
- Mariana Ferreira Alves
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil.
| | - Fabio Pinheiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil
| | | | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Deise Schroder Sarzi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carolina Furtado
- Departamento de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | |
Collapse
|
5
|
Andriamihaja CF, Ramarosandratana AV, Grisoni M, Jeannoda VH, Besse P. Drivers of population divergence and species differentiation in a recent group of indigenous orchids ( Vanilla spp.) in Madagascar. Ecol Evol 2021; 11:2681-2700. [PMID: 33767829 PMCID: PMC7981232 DOI: 10.1002/ece3.7224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 11/21/2022] Open
Abstract
With over 25,000 species, orchids are among families with remarkable high rate of diversification. Since Darwin's time, major advances attributed the exceptional diversity of orchids to plant-pollinator interactions. However, unraveling the processes and factors that determine the phenotypic and genotypic variation of natural orchid populations remains a challenge. Here, we assessed genetic population structure and floral differentiation in recently diverged leafless Vanilla species in a world biodiversity hotspot, Madagascar, using seven microsatellite loci and 26 morphometric variables. Additionally, analyses were performed to test for the occurrence of any patterns of isolation by distance, isolation by environment, and isolation by adaptation and to detect possible physical barriers that might have caused genetic discontinuities between populations. Positive inbreeding coefficients detected in 22 populations were probably due to the presence of null alleles, geitonogamy and/or some admixture (sympatric species). In contrast, the only high-altitude population showed an important rate of clonality leading to heterozygote excess. Genetic diversity was maximum in western populations, suggesting a postglacial colonization to the north and south. Clustering analyses identified seven genetic groups characterized by specific floral traits that matched five botanical descriptions in the literature. A contribution of montane refugia and river barriers on population differentiation was detected. We also detected combined effects of IBD/IBE and IBE/IBA on genetic differentiation and suggested this pattern is more likely determined by ecological isolation, although pollinator-mediated divergent selection could not be ruled out for some of the species. Overall, this study provides further insights on speciation in orchids, a group for which Madagascar shows one of the world's highest level of endemism and confirms the importance of the peculiar biogeography of the island in shaping species differentiation.
Collapse
Affiliation(s)
- Cathucia F. Andriamihaja
- Université de la RéunionUMR PVBMTSt PierreFrance
- Department of Plant Biology and EcologyUniversity of AntananarivoAntananarivoMadagascar
| | | | | | | | | |
Collapse
|
6
|
Jain A, Sarsaiya S, Chen J, Wu Q, Lu Y, Shi J. Changes in global Orchidaceae disease geographical research trends: recent incidences, distributions, treatment, and challenges. Bioengineered 2020; 12:13-29. [PMID: 33283604 PMCID: PMC8806279 DOI: 10.1080/21655979.2020.1853447] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Many of the Orchidaceae species are threatened due to environmental changes and over exploitation for full fill global demands. The main objective of this article was critically analyzed the recent global distribution of Orchidaceae diversity, its disease patterns, microbial disease identification, detection, along with prevention and challenges. Critical analysis findings revealed that Orchidaceae growth and developments were affected indirectly or directly as a result of complex microbial ecological interactions. Studies have identified many species associated with orchids, some are pathogenic and cause symptoms such as soft rot, brown rot, brown spot, black rot, wilt, foliar, root rot, anthracnose, leaf spot. The review was provided the comprehensive data to evaluate the identification and detection of microbial disease, which is the most important challenge for sustainable cultivation of Orchidaceae diversity. Furthermore, this article is the foremost of disease triggering microbes, orchid relations, and assimilates various consequences that both promoted the considerate and facts of such disease multipart, and will permit the development of best operative disease management practices.
Collapse
Affiliation(s)
- Archana Jain
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi, Guizhou, China
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi, Guizhou, China.,Bioresource Institute for Healthy Utilization, Zunyi Medical University , Zunyi, Guizhou, China.,Laboratory, CES Analytical and Research Services India Private Limited (Formerly Known as Creative Enviro Services) , Bhopal, Madhya Pradesh, India
| | - Jishuang Chen
- Bioresource Institute for Healthy Utilization, Zunyi Medical University , Zunyi, Guizhou, China
| | - Qin Wu
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi, Guizhou, China
| | - Yuanfu Lu
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi, Guizhou, China
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi, Guizhou, China
| |
Collapse
|
7
|
Wu Q, Zang F, Ma Y, Zheng Y, Zang D. Analysis of genetic diversity and population structure in endangered Populus wulianensis based on 18 newly developed EST-SSR markers. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01329] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
8
|
Yun SA, Son HD, Im HT, Kim SC. Genetic diversity and population structure of the endangered orchid Pelatantheria scolopendrifolia (Orchidaceae) in Korea. PLoS One 2020; 15:e0237546. [PMID: 32790795 PMCID: PMC7425873 DOI: 10.1371/journal.pone.0237546] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/28/2020] [Indexed: 01/02/2023] Open
Abstract
Due to substantial population decline, the Korean orchid P. scolopendrifolia is considered endangered and highly threatened. Like many endangered species, it is vulnerable to biological and anthropogenic threats that can lead to the loss of genetic diversity and, ultimately, extinction. Therefore, the assessment of genetic diversity and population genetic structure is imperative for conservation. In this study, we newly developed 15 polymorphic microsatellite markers. Analyses of genetic diversity and population genetic structure that included 182 samples from 11 populations were conducted using microsatellite markers and four noncoding regions of chloroplast DNA. Our study revealed a relatively low level of genetic diversity (Ho = 0.529, He = 0.356), albeit harboring with private alleles based on microsatellite genotyping data, and high haplotype diversities based on chloroplast DNA sequences data. The results of STRUCTURE and PCoA based on microsatellite genotyping data showed population differentiations. An AMOVA based on chloroplast DNA sequence data further corroborated these conclusions, indicating about 70% of variations found among populations. Low genetic diversity and divergence among the population might have been caused by factors, such as asexual reproduction, demographic events (bottleneck and population expansion), geographic isolation, and low gene flow. The development and implication of conservation strategies and management of P. scolopendrifolia are proposed based on these results.
Collapse
Affiliation(s)
- Seon A. Yun
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
| | | | - Hyoung-Tak Im
- Department of Biological Sciences, Chonnam National University, Gwangju, Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
| |
Collapse
|
9
|
Wang Y, Shahid MQ, Ghouri F, Baloch FS. De Novo Assembly and Annotation of the Juvenile Tuber Transcriptome of a Gastrodia elata Hybrid by RNA Sequencing: Detection of SSR Markers. Biochem Genet 2020; 58:914-934. [DOI: 10.1007/s10528-020-09983-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 06/25/2020] [Indexed: 02/08/2023]
|
10
|
Genetic Diversity and Population Genetic Structure of Cinnamomum camphora in South China Revealed by EST-SSR Markers. FORESTS 2019. [DOI: 10.3390/f10111019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cinnamomum camphora is a valuable broad-leaf tree indigenous to South China and East Asia and has been widely cultivated and utilized by humans since ancient times. However, owing to its overutilization for essential oil extraction, the Transplanting Big Trees into Cities Program, and over deforestation to make furniture, its wild populations have been detrimentally affected and are declining rapidly. In the present study, the genetic diversity and population structure of 180 trees sampled from 41 populations in South China were investigated with 22 expressed sequence tag-simple sequence repeat (EST-SSR) markers. In total, 61 alleles were harbored across 180 individuals, and medium genetic diversity level was inferred from the observed heterozygosity (Ho), expected heterozygosity (He), and Nei’ gene diversity (GD), which were 0.45, 0.44, and 0.44, respectively. Among the 41 wild populations, C. camphora had an average of 44 alleles, 2.02 effective alleles, and He ranging from 0.30 (SC) to 0.61 (HK). Analysis of molecular variance (AMOVA) showed that 17% of the variation among populations and the average pairwise genetic differentiation coefficient (FST) between populations was 0.162, indicating relatively low genetic population differentiations. Structure analysis suggested two groups for the 180 individuals, which was consistent with the principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA). Populations grouped to cluster I were nearly all distributed in Jiangxi Province (except population XS in Zhejiang Province), and cluster II mainly comprised populations from other regions, indicating a significant geographical distribution. Moreover, the Mantel test showed that this geographical distance was significantly correlated with genetic distance. The findings of this research will assist in future C. camphora conservation management and breeding programs.
Collapse
|
11
|
Wang Y, Shahid MQ, Ghouri F, Ercişli S, Baloch FS. Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome. 3 Biotech 2019; 9:292. [PMID: 31321198 DOI: 10.1007/s13205-019-1823-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 06/23/2019] [Indexed: 01/28/2023] Open
Abstract
Tianma (Gastrodia elata Blume) has unique biological characteristics and high medicinal value. The wild resource of G. elata is being overutilized and should be conserved as it is already included in the list of endangered species in China. The population size of cultivated G. elata is small because of domestication bottleneck. Therefore, it is of utmost importance to evolve high-quality varieties and conserve wild resources of G. elata. In this study, we sequenced tuber transcriptomes of three major cultivated sub-species of Gastrodia elata, namely G. elata BI. f. elata, G. elata Bl. f. glauca S. Chow, and G. elata Bl. f. Viridis, and obtained about 7.8G clean data. The assembled high-quality reads of three sub-species were clustered into 56,884 unigenes. Of these, 31,224 (54.89%), 25,733 (45.24%), 22,629 (39.78%), and 11,856 (20.84%) unigenes were annotated by Nr, Swiss-Port, Eukaryotic Ortholog Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Here, a total of 3766 EST-SSRs and 128,921 SNPs were identified from the unigenes. The results not only offer huge number of genes that were responsible for the growth, development, and metabolism of bioactive components, but also a large number of molecular markers were detected for future studies on the conservation genetics and molecular breeding of G. elata.
Collapse
|
12
|
Chen L, Wang YC, Qin LY, He HY, Yu XL, Yang MZ, Zhang HB. Dynamics of fungal communities during Gastrodia elata growth. BMC Microbiol 2019; 19:158. [PMID: 31291888 PMCID: PMC6617676 DOI: 10.1186/s12866-019-1501-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 05/31/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gastrodia elata is a widely distributed achlorophyllous orchid and is highly valued as both medicine and food. Gastrodia elata produces dust-like seeds and relies on mycorrhizal fungi for its germination and growth. In its life cycle, G. elata is considered to switch from a specific single-fungus relationship (Mycena) to another single-fungus relationship (Armillaria). However, no studies have investigated the changes in the plant-fungus relationship during the growth of G. elata in the wild. In this study, high-throughput sequencing was used to characterize the fungal community of tubers in different growth phases as well as the soils surrounding G. elata. RESULTS The predominant fungi were Basidiomycota (60.44%) and Ascomycota (26.40%), which exhibited changes in abundance and diversity with the growth phases of G. elata. Diverse basidiomycetes in protocorms (phase P) were Hyphodontia, Sistotrema, Tricholoma, Mingxiaea, Russula, and Mycena, but the community changed from a large proportion of Resinicium bicolor (40%) in rice-like tubers (phase M) to an unidentified Agaricales operational taxonomic unit 1(OTU1,98.45%) in propagation vegetation tubers (phase B). The soil fungi primarily included Simocybe, Psathyrella, Conocybe, and Subulicystidium. Three Mycena OTUs obtained in this study were differentially distributed among the growth phases of G. elata, accounting for less than 1.0% of the total reads, and were phylogenetically close to Mycena epipterygia and M. alexandri. CONCLUSIONS Our data indicated that G. elata interacts with a broad range of fungi beyond the Mycena genus. These fungi changed with the growth phases of G. elata. In addition, these data suggested that the development of the fungal community during the growth of G. elata was more complex than previously assumed and that at least two different fungi could be involved in development before the arrival of Armillaria.
Collapse
Affiliation(s)
- Lin Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
- School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yu-Chuan Wang
- Gastrodia Tuber Research Institute of Zhaotong, Zhaotong, 657000, Yunnan Province, China
| | - Li-Yuan Qin
- School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Hai-Yan He
- Gastrodia Tuber Research Institute of Zhaotong, Zhaotong, 657000, Yunnan Province, China
| | - Xian-Lun Yu
- Gastrodia Tuber Research Institute of Zhaotong, Zhaotong, 657000, Yunnan Province, China
| | - Ming-Zhi Yang
- School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Han-Bo Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China.
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.
- School of Life Sciences, Yunnan University, Kunming, 650091, China.
| |
Collapse
|
13
|
Wang X, Chen W, Luo J, Yao Z, Yu Q, Wang Y, Zhang S, Liu Z, Zhang M, Shen Y. Development of EST-SSR markers and their application in an analysis of the genetic diversity of the endangered species Magnolia sinostellata. Mol Genet Genomics 2018; 294:135-147. [PMID: 30255205 DOI: 10.1007/s00438-018-1493-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 09/18/2018] [Indexed: 12/13/2022]
Abstract
Magnolia sinostellata is an endemic species of Magnoliaceae that is narrowly distributed in the south of Zhejiang Province, China. To explore the genetic diversity and population structure of this endangered species, this study developed sequence tag-simple sequence repeat (EST-SSR) markers based on transcriptome data of M. sinostellata. In total, 25472 SSRs were identified among 110644 unique assembled sequences with a total of 90.83 Mb and an average frequency of 23.02%. The mononucleotide (33.53%) and dinucleotide (42.08%) motifs appeared to be the most abundant. In total, 150 potential loci were randomly selected to validate the quality of the developed SSR markers; an effective PCR rate of 32.00% and a polymorphism rate of 15.33% were obtained for these loci. After performing sequencing and cloning for validation, 23 pairs of SSR primers were retained and used to characterize the genetic diversity and population structure of M. sinostellata. Overall, 204 alleles were amplified. The results of Shannon's information index (I), heterozygosity (Ho), heterozygosity (He) and Nei's expected heterozygosity (H) indicated rich genetic diversity in M. sinostellata. However, the high inbreeding coefficient and differential coefficient suggest that serious genetic drift occurred within populations, and genetic differentiation is apparent among the populations. Consequently, although M. sinostellata has high genetic diversity among populations, it is still in a serious and dangerous condition. Habitat destruction caused by human activities is the main threat to this species, and enhancing the species abundance by adopting some conservation measures should be favourable for saving the species.
Collapse
Affiliation(s)
- Xingli Wang
- School of Landscape and Architecture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China
| | - Wenchong Chen
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China
| | - Jia Luo
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China
| | - Zhangxiu Yao
- Shenzhen Fairy Lake Botanical Garden, 160# Xianhu Road, Shenzhen, 518004, Guangdong, China
| | - Qin Yu
- School of Landscape and Architecture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China
| | - Yaling Wang
- Xi'an Botanical Garden of Shaanxi Academy of Science, 17# Cuihua South Road, Xi'an, 710061, Shaanxi, China
| | - Shouzhou Zhang
- Shenzhen Fairy Lake Botanical Garden, 160# Xianhu Road, Shenzhen, 518004, Guangdong, China
| | - Zhigao Liu
- School of Landscape and Architecture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China
| | - Mingru Zhang
- School of Landscape and Architecture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China
| | - Yamei Shen
- School of Landscape and Architecture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China.
| |
Collapse
|
14
|
Roy SC, Moitra K, De Sarker D. Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:169-183. [PMID: 28250593 PMCID: PMC5313405 DOI: 10.1007/s12298-016-0401-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/27/2016] [Indexed: 05/22/2023]
Abstract
Genetic diversity was assessed in the four orchid species using NGS based ddRAD sequencing data. The assembled nucleotide sequences (fastq) were deposited in the SRA archive of NCBI Database with accession number (SRP063543 for Dendrobium, SRP065790 for Geodorum, SRP072201 for Cymbidium and SRP072378 for Rhynchostylis). Total base pair read was 1.1 Mbp in case of Dendrobium sp., 553.3 Kbp for Geodorum sp., 1.6 Gbp for Cymbidium, and 1.4 Gbp for Rhynchostylis. Average GC% was 43.9 in Geodorum, 43.7% in Dendrobium, 41.2% in Cymbidium and 42.3% in Rhynchostylis. Four partial gene sequences were used in DnaSP5 program for nucleotide diversity and phylogenetic relationship determination (Ycf2 gene of Dendrobium, matK gene of Geodorum, psbD gene of Cymbidium and Ycf2 gene of Ryhnchostylis). Nucleotide diversity (per site) Pi (π) was 0.10560 in Dendrobium, 0.03586 in Geodorum, 0.01364 in Cymbidium and 0.011344 in Rhynchostylis. Neutrality test statistics showed the negative value in all the four orchid species (Tajima's D value -2.17959 in Dendrobium, -2.01655 in Geodorum, -2.12362 in Rhynchostylis and -1.54222 in Cymbidium) indicating the purifying selection. Result for these gene sequences (matK and Ycf2 and psbD) indicate that they were not evolved neutrally, but signifying that selection might have played a role in evolution of these genes in these four groups of orchids. Phylogenetic relationship was analyzed by reconstructing dendrogram based on the matK, psbD and Ycf2 gene sequences using maximum likelihood method in MEGA6 program.
Collapse
Affiliation(s)
- Subhas Chandra Roy
- Plant Genetics and Molecular Breeding Laboratory, Department of Botany, University of North Bengal, PO-NBU, Siliguri, WB 734013 India
| | - Kaushik Moitra
- Plant Genetics and Molecular Breeding Laboratory, Department of Botany, University of North Bengal, PO-NBU, Siliguri, WB 734013 India
| | - Dilip De Sarker
- Department of Botany, Raiganj University, Raiganj, WB 733134 India
| |
Collapse
|
15
|
Matias M, Silvestre S, Falcão A, Alves G. Gastrodia elata and epilepsy: Rationale and therapeutic potential. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2016; 23:1511-1526. [PMID: 27765372 DOI: 10.1016/j.phymed.2016.09.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 08/29/2016] [Accepted: 09/03/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND Gastrodia elata Blume (G. elata) is a traditional Chinese herb used for centuries in folk medicine. Due to the claimed anticonvulsant properties of G. elata, it is expected that this herb continues to be a target of research, aiming to deepen the available knowledge on its biological activity and safety. PURPOSE The current review aims to discuss the most recent advances on the elucidation of the phytochemical composition and anticonvulsant potential of G. elata. METHODS Available literature was reviewed from PubMed, ISI Web of Knowledge and Science Direct, using combinations of the following keywords: Gastrodia elata, tianma, epilepsy, anticonvulsant and pharmacokinetics. Abstracts and full texts were evaluated for their clarity and scientific merit. RESULTS G. elata rhizome, as well as specific phenolic compounds isolated from this herb, have demonstrated anticonvulsant potential in a variety of in vitro and in vivo models. The pharmacological mechanisms potentially involved in the anticonvulsant activity have been extensively studied, being similar to the known mechanisms claimed for the available antiepileptic drugs. In addition, the pharmacokinetics of the main bioactive component of G. elata (gastrodin) has also been studied. CONCLUSION Due to its recognised therapeutic properties, G. elata has gained an increasing interest within the scientific community and, therefore, new medicinal preparations containing G. elata rhizome itself or its bioactive components are expected to be developed in the coming years. Moreover, specific phytochemical constituents isolated from G. elata may also be considered to integrate programs of discovery and development of new anticonvulsant drug candidates.
Collapse
Affiliation(s)
- Mariana Matias
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Rua Marquês d'Ávila e Bolama, 6201-001 Covilhã, Portugal; CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Samuel Silvestre
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Rua Marquês d'Ávila e Bolama, 6201-001 Covilhã, Portugal; CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Amílcar Falcão
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; Department of Pharmacology, Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
| | - Gilberto Alves
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Rua Marquês d'Ávila e Bolama, 6201-001 Covilhã, Portugal; CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal.
| |
Collapse
|
16
|
Blambert L, Mallet B, Humeau L, Pailler T. Reproductive patterns, genetic diversity and inbreeding depression in two closely related Jumellea species with contrasting patterns of commonness and distribution. ANNALS OF BOTANY 2016; 118:93-103. [PMID: 26944785 PMCID: PMC4934390 DOI: 10.1093/aob/mcw014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 09/11/2015] [Accepted: 11/13/2015] [Indexed: 05/23/2023]
Abstract
BACKGROUNDS AND AIMS Theory predicts that the long-term persistence of plant populations exposed to size reduction can be threatened by a loss of genetic diversity and increased inbreeding. However, several life-history and ecological traits can influence the response to population size reduction. The reproductive patterns, levels of genetic diversity and magnitude of inbreeding depression of the rare and fragmented Jumellea fragrans and of its widespread congener J. rossii were studied. The aim was to evaluate the effects of over-collection and fragmentation on J. fragrans and to enhance our knowledge of the biology and ecology of the two species, used for their aromatic and medicinal properties on Réunion. METHODS Hand pollination experiments were conducted to determine the breeding system and to evaluate the potential for inbreeding depression in both species. Nuclear microsatellite markers were used to investigate selfing rates and levels of genetic diversity. KEY RESULTS Jumellea rossii revealed a mixed-mating system, and inbreeding depression at the germination stage (δ = 0·66). Levels of genetic diversity were relatively high [allelic richness (AR) = 8·575 and expected heterozygosity (He) = 0·673]. In J. fragrans, selfing rates suggest a mainly outcrossing mating system. Genetic diversity was lower than in J. rossii, but not yet critically low (AR = 4·983 and He = 0·492), probably because of the mainly outcrossing mating system and the relatively high density of individuals in the studied population. Jumellea fragrans did not show inbreeding depression, and it is hypothesized that the population had progressively purged its genetic load during successive fragmentation events. CONCLUSIONS Even if the persistence of the J. fragrans population is not threatened in the short term, its genetic diversity has probably been reduced by fragmentation and over-collection. In situ conservation actions for J. fragrans and ex situ cultivation of both species are recommended in order to meet the demand of local people.
Collapse
Affiliation(s)
- Laury Blambert
- UMR Peuplements Végétaux et Bio-agresseurs en Milieu Tropical, Université de la Réunion, Ile de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex 9, Réunion, France
| | - Bertrand Mallet
- UMR Peuplements Végétaux et Bio-agresseurs en Milieu Tropical, Université de la Réunion, Ile de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex 9, Réunion, France
| | - Laurence Humeau
- UMR Peuplements Végétaux et Bio-agresseurs en Milieu Tropical, Université de la Réunion, Ile de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex 9, Réunion, France
| | - Thierry Pailler
- UMR Peuplements Végétaux et Bio-agresseurs en Milieu Tropical, Université de la Réunion, Ile de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex 9, Réunion, France
| |
Collapse
|
17
|
Pellegrino G, Bellusci F, Palermo AM. Effects of population structure on pollen flow, clonality rates and reproductive success in fragmented Serapias lingua populations. BMC PLANT BIOLOGY 2015; 15:222. [PMID: 26377667 PMCID: PMC4573484 DOI: 10.1186/s12870-015-0600-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 09/02/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Fragmentation of habitats by roads, railroads, fields, buildings and other human activities can affect population size, pollination success, sexual and asexual reproduction specially in plants showing pollinator limitation, such as Mediterranean orchids. In this study, we assessed pollen flow, selfing rates, vegetative reproduction and female reproductive success and their correlations with habitat characters in nine fragmented subpopulations of Serapias lingua. To improve understanding of population structure effects on plant biology, we examined genetic differentiation among populations, pollen flow, selfing rates and clonal reproduction using nuclear microsatellite markers. RESULTS Smaller populations showed a significant heterozygote deficit occurred at all five nuclear microsatellite loci, the coefficient of genetic differentiation among populations was 0.053 and pairwise FST was significantly correlated with the geographical distance between populations. Paternity analysis of seeds showed that most pollen flow occurred within a population and there was a positive correlation between percentage of received pollen and distance between populations. The fruit production rate varied between 5.10 % and 20.30 % and increased with increasing population size, while the percentage of viable seeds (78-85 %) did not differ significantly among populations. The extent of clonality together with the clonal and sexual reproductive strategies varied greatly among the nine populations and correlated with the habitats where they occur. The small, isolated populations tended to have high clonal diversity and low fruit production, whereas the large populations with little disturbance were prone to have reductions in clonal growth and increased sexual reproduction. CONCLUSIONS We found that clonality offers an advantage in small and isolated populations of S. lingua, where clones may have a greater ability to persist than sexually reproducing individuals.
Collapse
Affiliation(s)
- Giuseppe Pellegrino
- Dept. of Biology, Ecology and Earth Sciences, University of Calabria, I-87036, Rende, (CS), Italy.
| | - Francesca Bellusci
- Dept. of Biology, Ecology and Earth Sciences, University of Calabria, I-87036, Rende, (CS), Italy.
| | - Anna Maria Palermo
- Dept. of Biology, Ecology and Earth Sciences, University of Calabria, I-87036, Rende, (CS), Italy.
| |
Collapse
|
18
|
Ueno S, Rodrigues JF, Alves-Pereira A, Pansarin ER, Veasey EA. Genetic variability within and among populations of an invasive, exotic orchid. AOB PLANTS 2015; 7:plv077. [PMID: 26162896 PMCID: PMC4564003 DOI: 10.1093/aobpla/plv077] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/27/2015] [Indexed: 06/04/2023]
Abstract
Despite the fact that invasive species are of great evolutionary interest because of their success in colonizing and spreading into new areas, the factors underlying this success often remain obscure. In this sense, studies on population genetics and phylogenetic relationships of invasive species could offer insights into mechanisms of invasions. Originally from Africa, the terrestrial orchid Oeceoclades maculata, considered an invasive plant, is the only species of the genus throughout the Americas. Considering the lack of information on population genetics of this species, the aim of this study was to evaluate the genetic diversity and structure of Brazilian populations of O. maculata. We used 13 inter-simple sequence repeat primers to assess the genetic diversity of 152 individuals of O. maculata distributed in five sampled sites from three Brazilian states (São Paulo, Mato Grosso and Paraná). Low diversity was found within samples, with estimates of the Shannon index (H) ranging from 0.0094 to 0.1054 and estimates of Nei's gene diversity (He) ranging from 0.0054 to 0.0668. However, when evaluated together, the sampling locations showed substantially higher diversity estimates (H = 0.3869, He = 0.2556), and most of the genetic diversity was found among populations (ΦST = 0.933). Both clustering and principal coordinate analysis indicate the existence of five distinct groups, corresponding to the sampled localities, and which were also recovered in the Bayesian analysis. A substructure was observed in one of the localities, suggesting a lack of gene flow even between very small distances. The patterns of genetic structure found in this study may be understood considering the interaction of several probable reproductive strategies with its history of colonization involving possible genetic drift, selective pressures and multiple introductions.
Collapse
Affiliation(s)
- Sueme Ueno
- Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, CP 83, Piracicaba, São Paulo 13418-900, Brazil
| | - Jucelene Fernandes Rodrigues
- Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, CP 83, Piracicaba, São Paulo 13418-900, Brazil
| | - Alessandro Alves-Pereira
- Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, CP 83, Piracicaba, São Paulo 13418-900, Brazil
| | - Emerson Ricardo Pansarin
- Departamento de Biologia, FFCLRP, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-901, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, CP 83, Piracicaba, São Paulo 13418-900, Brazil
| |
Collapse
|