1
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Xu T, Wang R, La Q, Yonezawa T, Huang X, Sun K, Song Z, Wang Y, Bartish IV, Zhang W, Cheng S. Climate heterogeneity shapes phylogeographic pattern of Hippophae gyantsensis (Elaeagnaceae) in the east Himalaya-Hengduan Mountains. Ecol Evol 2023; 13:e10182. [PMID: 37304372 PMCID: PMC10251425 DOI: 10.1002/ece3.10182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/13/2023] Open
Abstract
The interaction of recent orographic uplift and climate heterogeneity acted as a key role in the East Himalaya-Hengduan Mountains (EHHM) has been reported in many studies. However, how exactly the interaction promotes clade diversification remains poorly understood. In this study, we both used the chloroplast trnT-trnF region and 11 nuclear microsatellite loci to investigate the phylogeographic structure and population dynamics of Hippophae gyantsensis and estimate what role geological barriers or ecological factors play in the spatial genetic structure. The results showed that this species had a strong east-west phylogeographic structure, with several mixed populations identified from microsatellite data in central location. The intraspecies divergence time was estimated to be about 3.59 Ma, corresponding well with the recent uplift of the Tibetan Plateau. Between the two lineages, there was significant climatic differentiation without geographic barriers. High consistency between lineage divergence, climatic heterogeneity, and Qingzang Movement demonstrated that climatic heterogeneity but not geographic isolation drives the divergence of H. gyantsensis, and the recent regional uplift of the QTP, as the Himalayas, creates heterogeneous climates by affecting the flow of the Indian monsoon. The east group of H. gyantsensis experienced population expansion c. 0.12 Ma, closely associated with the last interglacial interval. Subsequently, a genetic admixture event between east and west groups happened at 26.90 ka, a period corresponding to the warm inter-glaciation again. These findings highlight the importance of the Quaternary climatic fluctuations in the recent evolutionary history of H. gyantsensis. Our study will improve the understanding of the history and mechanisms of biodiversity accumulation in the EHHM region.
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Affiliation(s)
- Ting Xu
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Ruixue Wang
- College of Life SciencesNorthwest Normal UniversityLanzhouChina
| | - Qiong La
- Department of BiologyTibet UniversityLhasaChina
| | - Takahiro Yonezawa
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Xinyi Huang
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Kun Sun
- College of Life SciencesNorthwest Normal UniversityLanzhouChina
| | - Zhiping Song
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Yuguo Wang
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Igor V. Bartish
- Institute of Botany of the Czech Academy of SciencesPruhoniceCzech Republic
| | - Wenju Zhang
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Shanmei Cheng
- Laboratory of Subtropical BiodiversityJiangxi Agricultural UniversityNanchangChina
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2
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Ahmad W, Asaf S, Al-Rawahi A, Al-Harrasi A, Khan AL. Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae). Sci Rep 2023; 13:7436. [PMID: 37156827 PMCID: PMC10167353 DOI: 10.1038/s41598-023-34477-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/02/2023] [Indexed: 05/10/2023] Open
Abstract
The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp-typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in both Tetraena species. An unusual shrinkage of IR regions 16-24 kb was identified. This resulted in the loss of 16 genes, including 11 ndh genes which encode the NADH dehydrogenase subunits, and a significant size reduction of Tetraena plastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes, matK, rbcL, and cssA genes exhibited identical topologies, indicating that both species are sisters to the genus Tetraena and may not belong to Zygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence of Zygophyllum and Tetraena was 36.6 Ma and 34.4 Ma, respectively. Tetraena stem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely related Tetraena and Zygophyllum species. It can be potentially used as a universal super-barcode for identifying plants.
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Affiliation(s)
- Waqar Ahmad
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman.
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA.
- Department of Biology and Biochemistry, University of Houston, Houston, USA.
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3
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Zhai Y, Zhang T, Guo Y, Gao C, Zhou L, Feng L, Zhou T, Xumei W. Phylogenomics, phylogeography and germplasms authentication of the Rheum palmatum complex based on complete chloroplast genomes. JOURNAL OF PLANT RESEARCH 2023; 136:291-304. [PMID: 36808315 DOI: 10.1007/s10265-023-01440-0] [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: 10/26/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
As a traditional Chinese medicine, rhubarb is used to treat several diseases such as severe acute pancreatitis, sepsis and chronic renal failure. However, few studies focused on the authentication of germplasm for the Rheum palmatum complex, and no studies have been conducted to elucidate the evolutionary history of the R. palmatum complex using plastome datasets. Hence, we aim to develop the potential molecular markers to identify the elite germplasms of rhubarb and explore the divergence and biogeographic history of the R. palmatum complex based on the newly sequenced chloroplast genome datasets. Chloroplast genomes of thirty-five the R. palmatum complex germplasms were sequenced, and the length ranged from 160,858 to 161,204 bp. The structure, gene content and gene order were highly conserved across all genomes. Eight InDels and sixty-one SNPs loci could be used to authenticate the high-quality germplasms of rhubarb in specific areas. Phylogenetic analysis revealed that all rhubarb germplasms were clustered in the same clade with high bootstrap support values and Bayesian posterior probabilities. According to the molecular dating result, the intraspecific divergence of the complex occurred in the Quaternary, which might be affected by climatic fluctuation. The biogeography reconstruction indicated that the ancestor of the R. palmatum complex might originate from the Himalaya-Hengduan Mountains or/and Bashan-Qinling Mountains, and then spread to surrounding areas. Several useful molecular markers were developed to identify rhubarb germplasms, and our study will provide further understanding on speciation, divergence and biogeography of the R. palmatum complex.
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Affiliation(s)
- Yunyan Zhai
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tianyi Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yanbing Guo
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Chenxi Gao
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Lipan Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Wang Xumei
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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4
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Ma Y, Mao X, Wang J, Zhang L, Jiang Y, Geng Y, Ma T, Cai L, Huang S, Hollingsworth P, Mao K, Kang M, Li Y, Yang W, Wu H, Chen Y, Davis CC, Shrestha N, Ree RH, Xi Z, Hu Q, Milne RI, Liu J. Pervasive hybridization during evolutionary radiation of Rhododendron subgenus Hymenanthes in mountains of southwest China. Natl Sci Rev 2022; 9:nwac276. [PMID: 36687562 PMCID: PMC9844246 DOI: 10.1093/nsr/nwac276] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/04/2022] Open
Abstract
Radiations are especially important for generating species biodiversity in mountainous ecosystems. The contribution of hybridization to such radiations has rarely been examined. Here, we use extensive genomic data to test whether hybridization was involved in evolutionary radiation within Rhododendron subgenus Hymenanthes, whose members show strong geographic isolation in the mountains of southwest China. We sequenced genomes for 143 species of this subgenus and 93 species of four other subgenera, and found that Hymenanthes was monophyletic and radiated during the late Oligocene to middle Miocene. Widespread hybridization events were inferred within and between the identified clades and subclades. This suggests that hybridization occurred both early and late during diversification of subgenus Hymenanthes, although the extent to which hybridization, speciation through mixing-isolation-mixing or hybrid speciation, accelerated the diversification needs further exploration. Cycles of isolation and contact in such and other montane ecosystems may have together promoted species radiation through hybridization between diverging populations and species. Similar radiation processes may apply to other montane floras in this region and elsewhere.
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Affiliation(s)
| | | | | | - Lei Zhang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuying Geng
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Tao Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Liming Cai
- Department of Organismic and Evolutionary Biology and Harvard University Herbaria, Harvard University, Cambridge, MA 02138, USA
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | | | - Kangshan Mao
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Minghui Kang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yiling Li
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wenlu Yang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Haolin Wu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yang Chen
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology and Harvard University Herbaria, Harvard University, Cambridge, MA 02138, USA
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Richard H Ree
- Negaunee Integrative Research Center, Field Museum, Chicago, IL 60605, USA
| | - Zhenxiang Xi
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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5
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Liu HR, Khan G, Gao Q, Zhang F, Liu W, Wang Y, Fang J, Chen S, Afridi SG. Dispersal into the Qinghai-Tibet plateau: evidence from the genetic structure and demography of the alpine plant Triosteum pinnatifidum. PeerJ 2022; 10:e12754. [PMID: 35178292 PMCID: PMC8815373 DOI: 10.7717/peerj.12754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/15/2021] [Indexed: 01/07/2023] Open
Abstract
Triosteum pinnatifidum Maxim., an alpine plant, is traditionally used for several medicinal purposes. Here, both chloroplast DNA sequences and nuclear low copy sequence markers were used to investigate the genetic diversity and population structure of T. pinnatifidum. Materials were collected from thirteen localities in the northeast Qinghai-Tibet Plateau (QTP) and adjacent highlands and advanced analytical toolkits were used to access their origin and range shifts. The results revealed a higher level of population differentiation based on chloroplast DNA (cpDNA) concatenated sequences compared with the nuclear DNA sequences (F ST = 0.654 for cpDNA, F ST = 0.398 for AT103), indicating that pollen flow was still extensive in T. pinnatifidum. A decline in haplotype variation was observed from the plateau edge and adjoining highlands toward the platform of the QTP. The hypothesis "dispersal into the QTP," proposing that T. pinnatifidum experienced migration from the plateau edge and adjacent highlands to the platform, was supported. These results were in line with the hypothesis that multiple refugia exist on the plateau edge and adjacent highlands rather than on the plateau platform. Our unimodal mismatch distribution, star-like network supported a recent expansion in T. pinnatifidum.
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Affiliation(s)
- Hai Rui Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai Province, China,College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai Province, China,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Lower Saxony, Germany
| | - Qingbo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China
| | - Wenhui Liu
- Department of Geological Engineering, Qinghai University, Xining, Qinghai Province, China
| | - Yingfang Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai Province, China
| | - Jie Fang
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai Province, China
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China
| | - Sahib Gul Afridi
- Department of Biochemistry, Abdul Wali Khan University Mardan, Marden, Khyber-Pakhtunkhwa, Pakistan
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6
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Khan MA, Kassianos AJ, Hoy WE, Alam AK, Healy HG, Gobe GC. Promoting Plant-Based Therapies for Chronic Kidney Disease. J Evid Based Integr Med 2022; 27:2515690X221079688. [PMID: 35243916 PMCID: PMC8902019 DOI: 10.1177/2515690x221079688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Chronic kidney disease (CKD) is debilitating, increasing in incidence worldwide, and a financial and social burden on health systems. Kidney failure, the final stage of CKD, is life-threatening if untreated with kidney replacement therapies. Current therapies using commercially-available drugs, such as angiotensin-converting enzyme inhibitors, angiotensin II receptor blockers and calcium channel blockers, generally only delay the progression of CKD. This review article focuses on effective alternative therapies to improve the prevention and treatment of CKD, using plants or plant extracts. Three mechanistic processes that are well-documented in CKD pathogenesis are inflammation, fibrosis, and oxidative stress. Many plants and their extracts are already known to ameliorate kidney dysfunction through antioxidant action, with subsequent benefits on inflammation and fibrosis. In vitro and in vivo experiments using plant-based therapies for pre-clinical research demonstrate some robust therapeutic benefits. In the CKD clinic, combination treatments of plant extracts with conventional therapies that are seen as relatively successful currently may confer additive or synergistic renoprotective effects. Therefore, the aim of recent research is to identify, rigorously test pre-clinically and clinically, and avoid any toxic outcomes to obtain optimal therapeutic benefit from medicinal plants. This review may prove to be a filtering tool to researchers into complementary and alternative medicines to find out the current trends of using plant-based therapies for the treatment of kidney diseases, including CKD.
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Affiliation(s)
- Muhammad Ali Khan
- NHMRC CKD CRE (CKD.QLD), Univ of Queensland, Brisbane, Australia.,School of Biomedical Sciences, Faculty of Medicine, Univ of Queensland, Australia.,Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Brisbane, Queensland, Australia.,Kidney Disease Research Collaborative, Princess Alexandra Hospital and Univ of Queensland, Translational Research Institute, Brisbane, Australia.,Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Bangladesh
| | - Andrew J Kassianos
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Brisbane, Queensland, Australia.,Centre for Chronic Disease, Faculty of Medicine, Univ of Queensland, Brisbane, Australia.,Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Australia.,IHBI, Queensland Univ of Technology, Brisbane, Australia
| | - Wendy E Hoy
- NHMRC CKD CRE (CKD.QLD), Univ of Queensland, Brisbane, Australia.,Centre for Chronic Disease, Faculty of Medicine, Univ of Queensland, Brisbane, Australia
| | | | - Helen G Healy
- NHMRC CKD CRE (CKD.QLD), Univ of Queensland, Brisbane, Australia.,Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Brisbane, Queensland, Australia.,Centre for Chronic Disease, Faculty of Medicine, Univ of Queensland, Brisbane, Australia.,Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Glenda C Gobe
- NHMRC CKD CRE (CKD.QLD), Univ of Queensland, Brisbane, Australia.,School of Biomedical Sciences, Faculty of Medicine, Univ of Queensland, Australia.,Kidney Disease Research Collaborative, Princess Alexandra Hospital and Univ of Queensland, Translational Research Institute, Brisbane, Australia
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7
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Wang RH, Yang ZP, Zhang ZC, Comes HP, Qi ZC, Li P, Fu CX. Plio-Pleistocene climatic change drives allopatric speciation and population divergence within the Scrophularia incisa complex (Scrophulariaceae) of desert and steppe subshrubs in Northwest China. FRONTIERS IN PLANT SCIENCE 2022; 13:985372. [PMID: 36212368 PMCID: PMC9532938 DOI: 10.3389/fpls.2022.985372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/19/2022] [Indexed: 05/07/2023]
Abstract
Numerous temperate plants and animals on the Qinghai-Tibet Plateau (QTP) are hypothesized to have differentiated due to vicariant allopatric speciation associated with the geologic uplifts. However, this hypothesis has rarely been tested through a phylogeographic study of relative species in a broader geographic context, including the QTP, Tianshan Mountains, Mongolian Plateau, and surrounding regions. To understand the speciation and diversification process of plants across this wide area, phylogeographic analysis were examined from Scrophularia incisa and two other closely relative species comprising S. kiriloviana and S. dentata. Thirty-two populations of the three close relatives were genotyped using chloroplast DNA fragments and nuclear microsatellite loci to assess population structure and diversity, supplemented by phylogenetic dating, ancestral area reconstructions and species distribution modelings, as well as niche identity tests. Our chloroplast DNA (cpDNA) phylogeny showed that this monophyletic group of desert and steppe semi-shrub is derived from a Middle Pliocene ancestor of the Central Asia. Lineages in Central Asia vs. China diverged through climate/tectonic-induced vicariance during Middle Pliocene. Genetic and ENM data in conjunction with niche differentiation analyses support that the divergence of S. incisa, S. dentata and S. kiriloviana in China lineage proceeded through allopatric speciation, might triggered by early Pleistocene climate change of increase of aridification and enlargement of deserts, while subsequent climate-induced cycles of range contractions/expansions enhanced the geographical isolation and habit fragmentation of these taxa. These findings highlight the importance of the Plio-Pleistocene climate change in shaping genetic diversity and driving speciation in temperate steppes and deserts of Northwestern China.
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Affiliation(s)
- Rui-Hong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhao-Ping Yang
- Key Laboratory of Biological Resources and Conservation and Application, College of Life Sciences, Tarim University, Alaer, China
| | - Zhi-Cheng Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Hans Peter Comes
- Department of Biosciences, Salzburg University, Salzburg, Austria
| | - Zhe-Chen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- *Correspondence: Zhe-Chen Qi,
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
- Pan Li,
| | - Cheng-Xin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
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8
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Zhang L, Wang S, Su C, Harris AJ, Zhao L, Su N, Wang JR, Duan L, Chang ZY. Comparative Chloroplast Genomics and Phylogenetic Analysis of Zygophyllum (Zygophyllaceae) of China. FRONTIERS IN PLANT SCIENCE 2021; 12:723622. [PMID: 34630471 PMCID: PMC8500179 DOI: 10.3389/fpls.2021.723622] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/24/2021] [Indexed: 05/25/2023]
Abstract
The genus Zygophyllum comprises over 150 species within the plant family Zygophyllaceae. These species predominantly grow in arid and semiarid areas, and about 20 occur in northwestern China. In this study, we sampled 24 individuals of Zygophyllum representing 15 species and sequenced their complete chloroplast (cp) genomes. For comparison, we also sequenced cp genomes of two species of Peganum from China representing the closely allied family, Nitrariaceae. The 24 cp genomes of Zygophyllum were smaller and ranged in size from 104,221 to 106,286 bp, each containing a large single-copy (LSC) region (79,245-80,439 bp), a small single-copy (SSC) region (16,285-17,146 bp), and a pair of inverted repeat (IR) regions (3,792-4,466 bp). These cp genomes contained 111-112 genes each, including 74-75 protein-coding genes (PCGs), four ribosomal RNA genes, and 33 transfer RNA genes, and all cp genomes showed similar gene order, content, and structure. The cp genomes of Zygophyllum appeared to lose some genes such as ndh genes and rRNA genes, of which four rRNA genes were in the SSC region, not in the IR regions. However, the SC and IR regions had greater similarity within Zygophyllum than between the genus and Peganum. We detected nine highly variable intergenic spacers: matK-trnQ, psaC-rps15, psbZ-trnG, rps7-trnL, rps15-trnN, trnE-trnT, trnL-rpl32, trnQ-psbK, and trnS-trnG. Additionally, we identified 156 simple sequence repeat (cpSSR) markers shared among the genomes of the 24 Zygophyllum samples and seven cpSSRs that were unique to the species of Zygophyllum. These markers may be useful in future studies on genetic diversity and relationships of Zygophyllum and closely related taxa. Using the sequenced cp genomes, we reconstructed a phylogeny that strongly supported the division of Chinese Zygophyllum into herbaceous and shrubby clades. We utilized our phylogenetic results along with prior morphological studies to address several remaining taxonomic questions within Zygophyllum. Specifically, we found that Zygophyllum kaschgaricum is included within Zygophyllum xanthoxylon supporting the present treatment of the former genus Sarcozygium as a subgenus within Zygophyllum. Our results provide a foundation for future research on the genetic resources of Zygophyllum.
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Affiliation(s)
- Ling Zhang
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
- College of Life Science, Tarim University, Alar, China
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin Xinjiang Production & Construction Group, Alar, China
| | - Shu Wang
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Chun Su
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - AJ Harris
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Liang Zhao
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Na Su
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Jun-Ru Wang
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Lei Duan
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zhao-Yang Chang
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
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9
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In Vitro Propagation Method for Production of Phenolic-Rich Planting Material of Culinary Rhubarb 'Malinowy'. PLANTS 2021; 10:plants10091768. [PMID: 34579301 PMCID: PMC8469749 DOI: 10.3390/plants10091768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/16/2022]
Abstract
Culinary rhubarb is a popular vegetable crop, valued for its long, thickened stalks, very rich in different natural bioactive ingredients. Tissue cultures are a useful tool for vegetative propagation of virus-free rhubarb plants and rapid multiplication of valuable selected genotypes. The aim of this study was to develop an effective method for in vitro propagation of selected genotypes of Polish rhubarb ‘Malinowy’ characterized by high yield and straight, thick and intensive red stalks. Identification and quantification of anthocyanins and soluble sugars by the HPLC method in shoot cultures and ex vitro established plantlets were also performed. Shoot cultures were established from axillary buds isolated from dormant, eight-year-old rhizomes. Effective shoot multiplication of rhubarb ‘Malinowy’ was obtained in the presence of 6.6 µM benzylaminopurine or 12.4 µM meta-topolin. Both cytokinins stimulated shoot formation in a manner that depended on sucrose concentration. Increasing the sucrose concentration from 59 to 175 mM decreased the production of shoots and outgrowth of leaves by 3-fold but enhanced shoot length, single shoot mass and callus formation at the base of shoots. This coincided with increased accumulation of soluble sugars (fructose, glucose) and anthocyanins-cyanidin-3-O-rutinoside (max. 208.2 mg·100 g−1 DM) and cyanidin-3-O-glucoside (max. 47.7 mg·100 g−1 DM). The highest rooting frequency (94.9%) and further successful ex vitro establishment (100%) were observed for shoots that were earlier rooted in vitro in the presence of 4.9 µM indole-3-butyric acid. Our results indicated that anthocyanin contents in leaf petioles were influenced by developmental stage. Under in vitro conditions, it is possible to elicit those pigments by sucrose at high concentration and meta-topolin.
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Abstract
Taxonomy is the science that explores, describes, names, and classifies all organisms. In this introductory chapter, we highlight the major historical steps in the elaboration of this science, which provides baseline data for all fields of biology and plays a vital role for society but is also an independent, complex, and sound hypothesis-driven scientific discipline.In a first part, we underline that plant taxonomy is one of the earliest scientific disciplines that emerged thousands of years ago, even before the important contributions of the Greeks and Romans (e.g., Theophrastus, Pliny the Elder, and Dioscorides). In the fifteenth-sixteenth centuries, plant taxonomy benefited from the Great Navigations, the invention of the printing press, the creation of botanic gardens, and the use of the drying technique to preserve plant specimens. In parallel with the growing body of morpho-anatomical data, subsequent major steps in the history of plant taxonomy include the emergence of the concept of natural classification , the adoption of the binomial naming system (with the major role of Linnaeus) and other universal rules for the naming of plants, the formulation of the principle of subordination of characters, and the advent of the evolutionary thought. More recently, the cladistic theory (initiated by Hennig) and the rapid advances in DNA technologies allowed to infer phylogenies and to propose true natural, genealogy-based classifications.In a second part, we put the emphasis on the challenges that plant taxonomy faces nowadays. The still very incomplete taxonomic knowledge of the worldwide flora (the so-called taxonomic impediment) is seriously hampering conservation efforts that are especially crucial as biodiversity has entered its sixth extinction crisis. It appears mainly due to insufficient funding, lack of taxonomic expertise, and lack of communication and coordination. We then review recent initiatives to overcome these limitations and to anticipate how taxonomy should and could evolve. In particular, the use of molecular data has been era-splitting for taxonomy and may allow an accelerated pace of species discovery. We examine both strengths and limitations of such techniques in comparison to morphology-based investigations, we give broad recommendations on the use of molecular tools for plant taxonomy, and we highlight the need for an integrative taxonomy based on evidence from multiple sources.
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Affiliation(s)
- Germinal Rouhan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France.
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France
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Ethnobotanical Uses, Phytochemistry and Pharmacology of Different Rheum Species (Polygonaceae): A Review. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1308:309-352. [PMID: 33861453 DOI: 10.1007/978-3-030-64872-5_22] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Today, there is an increased tendency to use herbal remedies. Rhubarb refers to several species of the genus Rheum L. in the Polygonaceae family. This species-rich genus is mainly distributed in Asian countries. Several medicinal effects have been attributed to the Rheum spp. in the traditional and modern medicine such as healing lungs, liver, kidney, womb and bladder diseases, cancer, diabetes, insect bites, relapsing fevers, diarrhea and constipation. Various in vitro, in vivo and clinical studies have investigated the therapeutic effect of extracts, fractions and pure compounds isolated from different species of this genus. Considering the positive findings, several pharmaceutical formulations containing rhubarb extract like capsules, drops, mouthwashes and different topical formulations are now present in the market. However, there are other traditional therapeutic effects of rhubarb that have not been studied yet and it is of great importance to perform confirmatory experiments or clinical investigations. The current review summarizes general information regarding botany, phytochemistry, ethnobotany and pharmacological aspects of Rheum spp. It is hoped that the present review could motivate subsequent research on the other medicinal properties of these plants that have been neglected until today.
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Liu M, Xu R. Complete chloroplast genome sequence of an alpine rhubarb Rheum likiangense. Mitochondrial DNA B Resour 2020; 5:3681-3682. [PMID: 33367058 PMCID: PMC7646595 DOI: 10.1080/23802359.2020.1832930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/01/2020] [Indexed: 10/24/2022] Open
Abstract
Rheum likiangense Samuelsson (Polygonaceae) is an endangered alpine rhubarb in the Qinghai-Tibet Plateau. In this study we report the complete chloroplast genome sequence (plastome) of Rh. likiangense. The assembled plastome is 162,291 bp in length with 31,741 bp inverted repeat (IR) regions and 128 annotated genes, including 34 tRNA genes, 8 rRNA genes, and 86 protein-coding genes. Phylogenetic analyses based on the full plastome sequences suggest the close relationship of Rh. likiangense with Rh. acuminatum and Rh. nobile. The plastome reported here is highly useful for designing plastome SSR markers to conduct a further conservation genetic study of this endangered rhubarb.
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Affiliation(s)
- Mingyu Liu
- College of Basic Education, National University of Defense Technology, Changsha, China
| | - Renping Xu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
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Zhou T, Zhu H, Wang J, Xu Y, Xu F, Wang X. Complete chloroplast genome sequence determination of Rheum species and comparative chloroplast genomics for the members of Rumiceae. PLANT CELL REPORTS 2020; 39:811-824. [PMID: 32221666 DOI: 10.1007/s00299-020-02532-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/13/2020] [Indexed: 05/10/2023]
Abstract
Complete plastomes of Rheum species facilitated to clarify the phylogeny of Polygonaceae, and comparative chloroplast genomics contributed to develop genetic markers for the authentication of Rheum species. Rheum (Polygonaceae) is widely distributed throughout the temperate and subtropical areas of Asian interior. Rheum species are usually perennial herbs, and half of them are endemic to China with important medicinal properties. On account of similar morphological characteristics, species delimitation of Rheum still remains unclear. Chloroplast genomes of eight Rheum species, Rumex crispus and Oxyria digyna were characterized. Based on the comparison of genome structure of these species and the two published Rheum species, it is shown that plastome sequences of these species are relatively conserved with the same gene order, and three Sect. Palmata species remarkably showed high sequence similarities. Some hotspots could be used to discriminate the Rheum species, and 17 plastid genes were subject to positive selection. The phylogenetic analyses indicated that all the Polygonaceae species were clustered in the same group and showed that Rheum species, except for Rheum wittrockii, formed a monophyletic group with high maximum parsimony/maximum likelihood bootstrap support values and Bayesian posterior probabilities. The molecular dating based on plastomes indicated that the divergences within Polygonaceae species were dated to the Upper Cretaceous period [73.86-77.99 million years ago (Ma)]. The divergence of Sect. Palmata species was estimated to have occurred around 1.60 Ma, indicating that its diversification was affected by the repeated climatic fluctuation in the Quaternary.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
- Key Laboratory of Qiyao Resources and Anti-Tumor Activities, Shaanxi Administration of Traditional Chinese Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Honghong Zhu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jian Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yucan Xu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Fusheng Xu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
- Key Laboratory of Qiyao Resources and Anti-Tumor Activities, Shaanxi Administration of Traditional Chinese Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
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Zong D, Gan P, Zhou A, Zhang Y, Zou X, Duan A, Song Y, He C. Plastome Sequences Help to Resolve Deep-Level Relationships of Populus in the Family Salicaceae. FRONTIERS IN PLANT SCIENCE 2019; 10:5. [PMID: 30723484 PMCID: PMC6349946 DOI: 10.3389/fpls.2019.00005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/07/2019] [Indexed: 05/30/2023]
Abstract
Populus, a core genus of Salicaceae, plays a significant ecological role as a source of pioneer species in boreal forests. However, interspecific hybridization and high levels of morphological variation among poplars have resulted in great difficulty in classifying species for systematic and comparative evolutionary studies. Here, we present phylogenetic analyses of 24 newly sequenced Populus plastomes and 36 plastomes from GenBank, which represent seven genera of Salicaceae, in combination with a matrix of eighteen morphological characters of 40 Populus taxa to reconstruct highly supported relationships of genus Populus. Relationships among the 60 taxa of Salicaceae strongly supported two monophyletic genera: Populus and Salix. Chosenia was nested within the genus Salix, and five clades within Populus were divided. Clade I included the three taxa P. euphratica, P. pruinosa, and P. ilicifolia. Clade II contained thirteen taxa [P. adenopoda, P. alba, P. bolleana, P. davidiana, P. hopeiensis, P. nigra, P. qiongdaoensis, P. rotundifolia, P. rotundifolia var. duclouxiana, P. tremula, P. tremula × alba, P. tomentosa, and P. tomentosa (NC)]. Clade III included the ten taxa P. haoana, P. kangdingensis, P. lasiocarpa, P. pseudoglauca, P. qamdoensis, P. schneideri, P. simonii, P. szechuanica, P. szechuanica var. tibetica, and P. yunnanensis. Clade IV included P. cathayana, P. gonggaensis, P. koreana, P. laurifolia, P. trinervis, P. wilsonii, and P. xiangchengensis. The last clade comprised P. angustifolia, P. balsamifera, P. deltoides, P. deltoides × nigra, P. fremontii, P. mexicana, and P. trichocarpa. This phylogeny is also supported by morphological traits, including bark smoothness, bud size, petiole shape, leaf inflorescence, male anther length and male anther tip.
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Affiliation(s)
- Dan Zong
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Peihua Gan
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Anpei Zhou
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Yao Zhang
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Xinlian Zou
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Anan Duan
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Yu Song
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw, Myanmar
| | - Chengzhong He
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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Gao H, Tan W, Yang T, Tian X. The complete chloroplast genome of Rheum rhabarbarum. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1617088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Han Gao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wei Tan
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Tianying Yang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoxuan Tian
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Manish K, Pandit MK. Geophysical upheavals and evolutionary diversification of plant species in the Himalaya. PeerJ 2018; 6:e5919. [PMID: 30425898 PMCID: PMC6228543 DOI: 10.7717/peerj.5919] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/11/2018] [Indexed: 11/20/2022] Open
Abstract
The Himalaya is one of the youngest and the loftiest mountain chains of the world; it is also referred to as the water tower of Asia. The Himalayan region harbors nearly 10,000 plant species constituting approximately 2.5% of the global angiosperm diversity of which over 4,000 are endemics. The present-day Himalayan flora consists of an admixture of immigrant taxa and diversified species over the last 40 million years. The interesting questions about the Himalayan flora discussed here are: how did the Himalaya achieve high endemic plant diversity starting with immigrant taxa and what were the main drivers of this diversity? This contribution aims to answer these questions and raise some more. We review and analyze existing information from diverse areas of earth and climate sciences, palaeobiology and phytogeography to evolve a bio-chronological record of plant species divergence and evolution in the Himalaya. From the analysis we infer the effects of major environmental upheavals on plant diversity in the region. The understanding developed in the following discussion is based on the idea that Himalaya experienced at least five phases of major geophysical upheavals, namely: (i) mega-collision between India and Eurasian plates, (ii) tectonic uplift in phases and progressive landform elevation, (iii) onset of southwest (SW) Indian monsoon, (iv) spurring of arid conditions in Central Asia, and (v) cyclic phases of cooling and warming in the Quaternary. The geophysical upheavals that were potentially disrupting for the ecosystem stability had a key role in providing impetus for biological diversification. The upheavals produced new geophysical environments, new ecological niches, imposed physical and physiological isolation barriers, acted as natural selection sieves and led to the formation of new species. This contribution aims to develop a comprehensive understanding of the plant biodiversity profile of the Himalaya in the context of complex, interconnected and dynamic relationship between earth system processes, climate and plant diversity.
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Affiliation(s)
- Kumar Manish
- Department of Environmental Studies, University of Delhi, Delhi, India.,Department of Environmental Studies, Dr. Bhim Rao Ambedkar College, University of Delhi, Delhi, India.,Centre for Interdisciplinary Studies of Mountain and Hill Environment, University of Delhi, Delhi, India
| | - Maharaj K Pandit
- Department of Environmental Studies, University of Delhi, Delhi, India.,Centre for Interdisciplinary Studies of Mountain and Hill Environment, University of Delhi, Delhi, India
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Dagarova SS, Sitpayeva GT, Pak JH, Kim JS. The complete plastid genome sequence of Rheum wittrockii (Polygonaceae), endangered species of Kazakhstan. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:516-517. [PMID: 33490462 PMCID: PMC7801014 DOI: 10.1080/23802359.2017.1361359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The complete chloroplast (cp) genome sequence of Rheum wittrockii, an endangered and medicinal plant of Kazakhstan, was firstly determined in the present study. It was 159,051 bp and contained a large single copy region (84,750 bp) and a small single copy region (12,999 bp) which were separated by two inverted repeat regions (30,651 bp). In total, 131 genes were identified and they were consisted of 79 coding genes, 8 rRNA genes, and 36 tRNA genes. rpl23 was pseudogenes due to sequence substitution. Among 23 genes containing introns, rps12 and ycf3 contained two introns and the rest had just one intron. Comparing to Chinese R. palmatum chloroplast genome, rpl32 and rpoA gene were shortened due to 1bp and 7bp deletion at poly-T and poly-A, respectively.
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Affiliation(s)
- Shynar S Dagarova
- Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan.,RSE "Institute of Botany and Phytointroduction" CS MES of Republic, Almaty, Kazakhstan
| | - Gulnara T Sitpayeva
- RSE "Institute of Botany and Phytointroduction" CS MES of Republic, Almaty, Kazakhstan
| | - Jae-Hong Pak
- Research Institute for Dokdo and Ulleungdo Island, Kyungpook National University, Daegu, Republic of Korea.,Department of Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Jung Sung Kim
- Research Institute for Dokdo and Ulleungdo Island, Kyungpook National University, Daegu, Republic of Korea
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Zhao B, Li J, Yuan R, Mao S. Adaptive evolution of the rbcL gene in the genus Rheum (Polygonaceae). BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1288072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Bo Zhao
- Department of Plant Resources, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, PR China
| | - Jingjian Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
| | - Ruwen Yuan
- Chemistry and Pharmacy School, Zhuhai College of Jilin University, Zhuhai, PR China
| | - Shizhong Mao
- Guangxi Institute of Botany, The Chinese Academy of Sciences, Guilin, PR China
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Wang A, Li W. Genetic diversity of Rheum tanguticum (Polygonaceae), an endangered species on Qinghai-Tibetan Plateau. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Huang Y, Jia L, Wang Q, Mosbrugger V, Utescher T, Su T, Zhou Z. Cenozoic plant diversity of Yunnan: A review. PLANT DIVERSITY 2016; 38:271-282. [PMID: 30159478 PMCID: PMC6112251 DOI: 10.1016/j.pld.2016.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 05/22/2023]
Abstract
Yunnan in southwestern China is renowned for its high plant diversity. To understand how this modern botanical richness formed, it is critical to investigate the past biodiversity throughout the geological time. In this review, we present a summary on plant diversity, floristics and climates in the Cenozoic of Yunnan and document their changes, by compiling published palaeobotanical sources. Our review demonstrates that thus far a total of 386 fossil species of ferns, gymnosperms and angiosperms belonging to 170 genera within 66 families have been reported from the Cenozoic, particularly the Neogene, of Yunnan. Angiosperms display the highest richness represented by 353 species grouped into 155 genera within 60 families, with Fagaceae, Fabaceae, Lauraceae and Juglandaceae being the most diversified. Most of the families and genera recorded as fossils still occur in Yunnan, but seven genera have disappeared, including Berryophyllum, Cedrelospermum, Cedrus, Palaeocarya, Podocarpium, Sequoia and Wataria. The regional extinction of these genera is commonly referred to an aridification of the dry season associated with Asian monsoon development. Floristic analyses indicate that in the late Miocene, Yunnan had three floristic regions: a northern subtropical floristic region in the northeast, a subtropical floristic region in the east, and a tropical floristic region in the southwest. In the late Pliocene, Yunnan saw two kinds of floristic regions: a subalpine floristic region in the northwest, and two subtropical floristic regions separately in the southwest and the eastern center. These floristic concepts are verified by results from our areal type analyses which suggest that in the Miocene southwestern Yunnan supported the most Pantropic elements, while in the Pliocene southwestern Yunnan had abundant Tropical Asia (Indo-Malaysia) type and East Asia and North America disjunct type that were absent from northwestern Yunnan. From the late Miocene to late Pliocene through to the present, floristic composition and vegetation types changed markedly, presumably in response to altitude changes and coeval global cooling. An integration of palaeoclimate data suggests that during the Neogene Yunnan was warmer and wetter than today. Moreover, northern Yunnan witnessed a pronounced temperature decline, while southern Yunnan experienced only moderate temperature changes. Summer precipitation was consistently higher than winter precipitation, suggesting a rainfall seasonality. This summary on palaeoclimates helps us to understand under what conditions plant diversity occurred and evolved in Yunnan throughout the Cenozoic.
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Affiliation(s)
- Yongjiang Huang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- State Key Laboratory of Paleobiology and Stratigraphy, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Linbo Jia
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qiong Wang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Volker Mosbrugger
- Senckenberg Research Institute/BiK F (Loewe), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Torsten Utescher
- Senckenberg Research Institute/BiK F (Loewe), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Steinmann Institute, University of Bonn, Nussallee 8, 53115 Bonn, Germany
| | - Tao Su
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
- State Key Laboratory of Paleobiology and Stratigraphy, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhekun Zhou
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
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Huang YJ, Su T, Zhou ZK. Late Pliocene diversity and distribution of Drynaria (Polypodiaceae) in western Yunnan explained by forest vegetation and humid climates. PLANT DIVERSITY 2016; 38:194-200. [PMID: 30159465 PMCID: PMC6112196 DOI: 10.1016/j.pld.2016.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 05/12/2023]
Abstract
The palaeodiversity of flowering plants in Yunnan has been extensively interpreted from both a molecular and fossil perspective. However, for cryptogamic plants such as ferns, the palaeodiversity remains poorly known. In this study, we describe a new ferny fossil taxon, Drynaria lanpingensis sp. nov. Huang, Su et Zhou (Polypodiaceae), from the late Pliocene of northwestern Yunnan based on fragmentary frond and pinna with in situ spores. The frond is pinnatifid and the pinnae are entirely margined. The sori are arranged in one row on each side of the primary vein. The spores have a semicircular to bean-shaped equatorial view and a tuberculate surface. Taken together with previously described fossils, there are now representatives of three known fossil taxa of Drynaria from the late Pliocene of western Yunnan. These finds suggest that Drynaria diversity was considerable in the region at that time. As Drynaria is a shade-tolerant plant, growing preferably in wet conditions in the understory of forests, its extensive existence may indicate forest vegetation and humid climates in western Yunnan during the late Pliocene. This is in line with results from floristic investigations and palaeoclimatic reconstructions based on fossil floras.
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Affiliation(s)
- Yong-Jiang Huang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Tao Su
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Zhe-Kun Zhou
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
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Gao YD, Harris AJ, He XJ. Morphological and ecological divergence of Lilium and Nomocharis within the Hengduan Mountains and Qinghai-Tibetan Plateau may result from habitat specialization and hybridization. BMC Evol Biol 2015; 15:147. [PMID: 26219287 PMCID: PMC4518642 DOI: 10.1186/s12862-015-0405-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/02/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several previous studies have shown that some morphologically distinctive, small genera of vascular plants that are endemic to the Qinghai-Tibetan Plateau and adjacent Hengduan Mountains appear to have unexpected and complex phylogenetic relationships with their putative sisters, which are typically more widespread and more species rich. In particular, the endemic genera may form one or more poorly resolved paraphyletic clades within the sister group despite distinctive morphology. Plausible explanations for this evolutionary and biogeographic pattern include extreme habitat specialization and hybridization. One genus consistent with this pattern is Nomocharis Franchet. Nomocharis comprises 7-15 species bearing showy-flowers that are endemic to the H-D Mountains. Nomocharis has long been treated as sister to Lilium L., which is comprised of more than 120 species distributed throughout the temperate Northern Hemisphere. Although Nomocharis appears morphologically distinctive, recent molecular studies have shown that it is nested within Lilium, from which is exhibits very little sequence divergence. In this study, we have used a dated molecular phylogenetic framework to gain insight into the timing of morphological and ecological divergence in Lilium-Nomocharis and to preliminarily explore possible hybridization events. We accomplished our objectives using dated phylogenies reconstructed from nuclear internal transcribed spacers (ITS) and six chloroplast markers. RESULTS Our phylogenetic reconstruction revealed several Lilium species nested within a clade of Nomocharis, which evolved ca. 12 million years ago and is itself nested within the rest of Lilium. Flat/open and horizon oriented flowers are ancestral in Nomocharis. Species of Lilium nested within Nomocharis diverged from Nomocharis ca. 6.5 million years ago. These Lilium evolved recurved and campanifolium flowers as well as the nodding habit by at least 3.5 million years ago. Nomocharis and the nested Lilium species had relatively low elevation ancestors (<1000 m) and underwent diversification into new, higher elevational habitats 3.5 and 5.5 million years ago, respectively. Our phylogeny reveals signatures of hybridization including incongruence between the plastid and nuclear gene trees, geographic clustering of the maternal (i.e., plastid) lineages, and divergence ages of the nuclear gene trees consistent with speciation and secondary contact, respectively. CONCLUSIONS The timing of speciation and ecological and morphological evolutionary events in Nomocharis are temporally consistent with uplift in the Qinghai-Tibetan Plateau and of the Hengduan Mountains 7 and 3-4 million years ago, respectively. Thus, we speculate that the mountain building may have provided new habitats that led to specialization of morphological and ecological features in Nomocharis and the nested Lilium along ecological gradients. Additionally, we suspect that the mountain building may have led to secondary contact events that enabled hybridization in Lilium-Nomocharis. Both the habitat specialization and hybridization have probably played a role in generating the striking morphological differences between Lilium and Nomocharis.
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Affiliation(s)
- Yun-Dong Gao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, China.
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - A J Harris
- Department of Botany, Oklahoma State University, 301 Physical Sciences, Stillwater, OK, 74078-3013, USA.
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, China.
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Zhang ML, Wen ZB, Fritsch PW, Sanderson SC. Spatiotemporal evolution of Calophaca (fabaceae) reveals multiple dispersals in central Asian mountains. PLoS One 2015; 10:e0123228. [PMID: 25849146 PMCID: PMC4388477 DOI: 10.1371/journal.pone.0123228] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/17/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The Central Asian flora plays a significant role in Eurasia and the Northern Hemisphere. Calophaca, a member of this flora, includes eight currently recognized species, and is centered in Central Asia, with some taxa extending into adjacent areas. A phylogenetic analysis of the genus utilizing nuclear ribosomal ITS and plastid trnS-trnG and rbcL sequences was carried out in order to confirm its taxonomic status and reconstruct its evolutionary history. METHODOLOGY/PRINCIPAL FINDING We employed BEAST Bayesian inference for dating, and S-DIVA and BBM for ancestral area reconstruction, to study its spatiotemporal evolution. Our results show that Calophacais monophyletic and nested within Caragana. The divergence time of Calophaca is estimated at ca. 8.0 Ma, most likely driven by global cooling and aridification, influenced by rapid uplift of the Qinghai Tibet Plateau margins. CONCLUSIONS/SIGNIFICANCE According to ancestral area reconstructions, the genus most likely originated in the Pamir Mountains, a global biodiversity hotspot and hypothesized Tertiary refugium of many Central Asian plant lineages. Dispersals from this location are inferred to the western Tianshan Mountains, then northward to the Tarbagatai Range, eastward to East Asia, and westward to the Caucasus, Russia, and Europe. The spatiotemporal evolution of Calophaca provides a case contributing to an understanding of the flora and biodiversity of the Central Asian mountains and adjacent regions.
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Affiliation(s)
- Ming-Li Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Bin Wen
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Peter W. Fritsch
- Department of Botany, California Academy of Sciences, Golden Gate Park, San Francisco, California, United States of America
| | - Stewart C. Sanderson
- Shrub Sciences Laboratory, Intermountain Research Station, Forest Service, U.S. Department of Agriculture, Provo, Utah, United States of America
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Wang XM, Hou XQ, Zhang YQ, Li Y. Morphological variation in leaf dissection of Rheum palmatum complex (Polygonaceae). PLoS One 2014; 9:e110760. [PMID: 25349989 PMCID: PMC4211699 DOI: 10.1371/journal.pone.0110760] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/16/2014] [Indexed: 11/21/2022] Open
Abstract
Aims Rheum palmatum complex comprises all taxa within section Palmata in the genus Rheum, including R. officinale, R. palmatum, R. tanguticum, R. tanguticum var. liupanshanense and R. laciniatum. The identification of the taxa in section Palmata is based primarily on the degree of leaf blade dissection and the shape of the lobes; however, difficulties in species identification may arise from their significant variation. The aim of this study is to analyze the patterns of variation in leaf blade characteristics within and among populations through population-based sampling covering the entire distribution range of R. palmatum complex. Methods Samples were taken from 2340 leaves from 780 individuals and 44 populations representing the four species, and the degree of leaf blade dissection and the shape of the lobe were measured to yield a set of quantitative data. Furthermore, those data were statistically analyzed. Important Findings The statistical analysis showed that the degree of leaf blade dissection is continuous from lobed to parted, and the shape of the lobe is also continuous from broadly triangular to lanceolate both within and between populations. We suggested that taxa in section Palmata should be considered as one species. Based on the research on the R. palmatum complex, we considered that the quantitative characteristics were greatly influenced by the environment. Therefore, it is not reliable to delimitate the species according to the continuously quantitative vegetative characteristics.
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Affiliation(s)
- Xu-Mei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
- * E-mail:
| | - Xiao-Qi Hou
- Guiyang Museum of Medical Resources, Guiyang Botanical Garden of Medicinal Plants, Guiyang, China
| | - Yu-Qu Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yan Li
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
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Wang L, Zhou H, Han J, Milne RI, Wang M, Liu B. Genome-scale transcriptome analysis of the alpine "glasshouse" plant Rheum nobile (Polygonaceae) with special translucent bracts. PLoS One 2014; 9:e110712. [PMID: 25343261 PMCID: PMC4208811 DOI: 10.1371/journal.pone.0110712] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 09/16/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Rheum nobile is an alpine plant with translucent bracts concealing the inflorescence which produce a "glasshouse" effect promoting the development of fertile pollen grains in such conditions. The current understanding of the adaptation of such bracts to alpine environments mainly focuses on the phenotypic and physiological changes while the genetic basis is very limited. By sequencing the upper bract and the lower rosulate leaf from the same R. nobile stem, we identified candidate genes that may be involved in alpine adaption of the translucent bract in "glasshouse" plants and illustrated the changes in gene expression underlying the adaptive and complex evolution of the bracts phenotype. RESULTS A total of 174.2 million paired-end reads from each transcriptome were assembled into 25,249 unigenes. By comparing the gene expression profiles, we identified 1,063 and 786 genes up-regulated respectively in the upper bract and the lower leaf. Functional enrichment analyses of these genes recovered a number of differential important pathways, including flavonoid biosynthesis, mismatch repair and photosynthesis related pathways. These pathways are mainly involved in three types of functions: 9 genes in the UV protective process, 9 mismatch repair related genes and 88 genes associated with photosynthesis. CONCLUSIONS This study provides the first comprehensive dataset characterizing Rheum nobile gene expression at the transcriptomic scale, and provides novel insights into the gene expression profiles associated with the adaptation of the "glasshouse" plant bracts. The dataset will be served as a public genetic resources for further functional and evolutionary studies of "glasshouse" plants.
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Affiliation(s)
- Lizhong Wang
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Science, Lanzhou University, Lanzhou, Gansu, China
| | - Haihong Zhou
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Jin Han
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Science, Lanzhou University, Lanzhou, Gansu, China
| | - Richard I. Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Mingyu Wang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
- * E-mail: (MW); (BL)
| | - Bingbing Liu
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Science, Lanzhou University, Lanzhou, Gansu, China
- * E-mail: (MW); (BL)
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Jeong YM, Chung WH, Mun JH, Kim N, Yu HJ. De novo assembly and characterization of the complete chloroplast genome of radish (Raphanus sativus L.). Gene 2014; 551:39-48. [PMID: 25151309 DOI: 10.1016/j.gene.2014.08.038] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 11/28/2022]
Abstract
Radish (Raphanus sativus L.) is an edible root vegetable crop that is cultivated worldwide and whose genome has been sequenced. Here we report the complete nucleotide sequence of the radish cultivar WK10039 chloroplast (cp) genome, along with a de novo assembly strategy using whole genome shotgun sequence reads obtained by next generation sequencing. The radish cp genome is 153,368 bp in length and has a typical quadripartite structure, composed of a pair of inverted repeat regions (26,217 bp each), a large single copy region (83,170 bp), and a small single copy region (17,764 bp). The radish cp genome contains 87 predicted protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Sequence analysis revealed the presence of 91 simple sequence repeats (SSRs) in the radish cp genome. Phylogenetic analysis of 62 protein-coding gene sequences from the 17 cp genomes of the Brassicaceae family suggested that the radish cp genome is most closely related to the cp genomes of Brassica rapa and Brassicanapus. Comparisons with the B. rapa and B. napus cp genomes revealed highly divergent intergenic sequences and introns that can potentially be developed as diagnostic cp markers. Synonymous and nonsynonymous substitutions of cp genes suggested that nucleotide substitutions have occurred at similar rates in most genes. The complete sequence of the radish cp genome would serve as a valuable resource for the development of new molecular markers and the study of the phylogenetic relationships of Raphanus species in the Brassicaceae family.
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Affiliation(s)
- Young-Min Jeong
- Department of Life Science, The Catholic University of Korea, Bucheon 420-743, Republic of Korea
| | - Won-Hyung Chung
- Korean Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Jeong-Hwan Mun
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 449-728, Republic of Korea
| | - Namshin Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea.
| | - Hee-Ju Yu
- Department of Life Science, The Catholic University of Korea, Bucheon 420-743, Republic of Korea.
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Favre A, Päckert M, Pauls SU, Jähnig SC, Uhl D, Michalak I, Muellner‐Riehl AN. The role of the uplift of the Qinghai‐Tibetan Plateau for the evolution of Tibetan biotas. Biol Rev Camb Philos Soc 2014; 90:236-53. [DOI: 10.1111/brv.12107] [Citation(s) in RCA: 422] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 03/15/2014] [Accepted: 03/19/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Adrien Favre
- Department of Molecular Evolution and Systematics of Plants Institute of Biology, University of Leipzig Johannisallee 21‐23 04103 Leipzig Germany
- Biodiversity and Climate Research Centre (BiK‐F) & Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25 60325 Frankfurt am Main Germany
| | - Martin Päckert
- Biodiversity and Climate Research Centre (BiK‐F) & Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25 60325 Frankfurt am Main Germany
- Senckenberg Natural History Collections, Museum für Tierkunde Koenigsbruecker Landstraße 159 01109 Dresden Germany
| | - Steffen U. Pauls
- Biodiversity and Climate Research Centre (BiK‐F) & Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25 60325 Frankfurt am Main Germany
| | - Sonja C. Jähnig
- Biodiversity and Climate Research Centre (BiK‐F) & Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25 60325 Frankfurt am Main Germany
- Department of Ecosystem Research Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Müggelseedamm 301 12587 Berlin Germany
| | - Dieter Uhl
- Section of Palaeoclimate and Palaeoenvironmental Research Senckenberg Research Institute and Natural History Museum Frankfurt Senckenberganlage 25 60325 Frankfurt am Main Germany
| | - Ingo Michalak
- Department of Molecular Evolution and Systematics of Plants Institute of Biology, University of Leipzig Johannisallee 21‐23 04103 Leipzig Germany
| | - Alexandra N. Muellner‐Riehl
- Department of Molecular Evolution and Systematics of Plants Institute of Biology, University of Leipzig Johannisallee 21‐23 04103 Leipzig Germany
- Biodiversity and Climate Research Centre (BiK‐F) & Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25 60325 Frankfurt am Main Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Deutscher Platz 5e 04103 Leipzig Germany
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Vasighzadeh A, Zafari D, Selçuk F, Hüseyin E, Kurşat M, Lutz M, Piątek M. Discovery of Thecaphora schwarzmaniana on Rheum ribes in Iran and Turkey: implications for the diversity and phylogeny of leaf smuts on rhubarbs. Mycol Prog 2014. [DOI: 10.1007/s11557-014-0972-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Salas-Leiva DE, Meerow AW, Francisco-Ortega J, Calonje M, Griffith MP, Stevenson DW, Nakamura K. Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads. Mol Ecol Resour 2014; 14:831-45. [PMID: 24444413 DOI: 10.1111/1755-0998.12228] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 01/09/2014] [Accepted: 01/13/2014] [Indexed: 01/28/2023]
Abstract
Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single-copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and (ii) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single-Copy genes (APVO SSC) against the EST Zamia databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginkgo biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single-copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Zamia pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.
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Affiliation(s)
- Dayana E Salas-Leiva
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA; USDA-ARS-SHRS, National Germplasm Repository, Miami, FL, 33158, USA; Montgomery Botanical Center, Miami, FL, 33156, USA
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Multiple ITS copies reveal extensive hybridization within Rheum (Polygonaceae), a genus that has undergone rapid radiation. PLoS One 2014; 9:e89769. [PMID: 24587023 PMCID: PMC3937351 DOI: 10.1371/journal.pone.0089769] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 01/25/2014] [Indexed: 11/24/2022] Open
Abstract
Background During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual. Methodology/Principal Findings In this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively. Conclusions These findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation.
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Wen J, Zhang JQ, Nie ZL, Zhong Y, Sun H. Evolutionary diversifications of plants on the Qinghai-Tibetan Plateau. Front Genet 2014; 5:4. [PMID: 24575120 PMCID: PMC3921583 DOI: 10.3389/fgene.2014.00004] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 01/06/2014] [Indexed: 11/13/2022] Open
Abstract
The Qinghai-Tibetan Plateau (QTP) is the highest and one of the most extensive plateaus in the world. Phylogenetic, phylogeographic, and ecological studies support plant diversifications on the QTP through multiple mechanisms such as allopatric speciation via geographic isolation, climatic oscillations and divergences, pollinator-mediated isolation, diploid hybridization and introgression, and allopolyploidy. These mechanisms have driven spectacular radiations and/or species diversifications in various groups of plants such as Pedicularis L., Saussurea DC., Rhododendron L., Primula L., Meconopsis Vig., Rhodiola L., and many lineages of gymnosperms. Nevertheless, much work is needed toward understanding the evolutionary mechanisms of plant diversifications on the QTP. Well-sampled biogeographic analyses of the QTP plants in the broad framework of the Northern Hemisphere as well as the Southern Hemisphere are still relatively few and should be encouraged in the next decade. This paper reviews recent evidence from phylogenetic and biogeographic studies in plants, in the context of rapid radiations, mechanisms of species diversifications on the QTP, and the biogeographic significance of the QTP in the broader context of both the Northern and Southern Hemisphere biogeography. Integrative multidimensional analyses of phylogeny, morphological innovations, geography, ecology, development, species interactions and diversifications, and geology are needed and should shed insights into the patterns of evolutionary assembly and radiations in this fascinating region.
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Affiliation(s)
- Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution Washington, DC, USA
| | | | - Ze-Long Nie
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China
| | - Yang Zhong
- Institute of Biodiversity Science and Geobiology, Tibet University Lhasa, China ; School of Life Sciences, Fudan University Shanghai, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China
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Abstract
Taxonomy is the science that explores, describes, names, and classifies all organisms. In this introductory chapter, we highlight the major historical steps in the elaboration of this science that provides baseline data for all fields of biology and plays a vital role for society but is also an independent, complex, and sound hypothesis-driven scientific discipline.In a first part, we underline that plant taxonomy is one of the earliest scientific disciplines that emerged thousands of years ago, even before the important contributions of Greeks and Romans (e.g., Theophrastus, Pliny the Elder, and Dioscorides). In the fifteenth to sixteenth centuries, plant taxonomy benefited from the Great Navigations, the invention of the printing press, the creation of botanic gardens, and the use of the drying technique to preserve plant specimens. In parallel with the growing body of morpho-anatomical data, subsequent major steps in the history of plant taxonomy include the emergence of the concept of natural classification, the adoption of the binomial naming system (with the major role of Linnaeus) and other universal rules for the naming of plants, the formulation of the principle of subordination of characters, and the advent of the evolutionary thought. More recently, the cladistic theory (initiated by Hennig) and the rapid advances in DNA technologies allowed to infer phylogenies and to propose true natural, genealogy-based classifications.In a second part, we put the emphasis on the challenges that plant taxonomy faces nowadays. The still very incomplete taxonomic knowledge of the worldwide flora (the so-called taxonomic impediment) is seriously hampering conservation efforts that are especially crucial as biodiversity enters its sixth extinction crisis. It appears mainly due to insufficient funding, lack of taxonomic expertise, and lack of communication and coordination. We then review recent initiatives to overcome these limitations and to anticipate how taxonomy should and could evolve. In particular, the use of molecular data has been era-splitting for taxonomy and may allow an accelerated pace of species discovery. We examine both strengths and limitations of such techniques in comparison to morphology-based investigations, we give broad recommendations on the use of molecular tools for plant taxonomy, and we highlight the need for an integrative taxonomy based on evidence from multiple sources.
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Phylogenetic and biogeographic analyses of the Sino-Himalayan endemic genus Cyananthus (Campanulaceae) and implications for the evolution of its sexual system. Mol Phylogenet Evol 2013; 68:482-97. [DOI: 10.1016/j.ympev.2013.04.027] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 04/14/2013] [Accepted: 04/22/2013] [Indexed: 11/21/2022]
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Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q-T plateau and the Hengduan Mountains. Mol Phylogenet Evol 2013; 68:443-60. [PMID: 23665039 DOI: 10.1016/j.ympev.2013.04.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 04/24/2013] [Accepted: 04/26/2013] [Indexed: 11/21/2022]
Abstract
The Hengduan Mountains (H-D Mountains) in China flank the eastern edge of the Qinghai-Tibet Plateau (Q-T Plateau) and are a center of great temperate plant diversity. The geological history and complex topography of these mountains may have prompted the in situ evolution of many diverse and narrowly endemic species. Despite the importance of the H-D Mountains to biodiversity, many uncertainties remain regarding the timing and tempo of their uplift. One hypothesis is that the Q-T Plateau underwent a final, rapid phase of uplift 8-7 million years ago (Mya) and that the H-D Mountains orogeny was a separate event occurring 4-3 Mya. To evaluate this hypothesis, we performed phylogenetic, biogeographic, divergence time dating, and diversification rate analyses of the horticulturally important genus Lilium, including Nomocharis. The Lilium-Nomocharis complex is distributed throughout the temperate Northern Hemisphere but is most diverse within the H-D Mountains and Q-T Plateau. Our matK and ITS phylogenies support previous studies showing that Nomocharis is nested within Lilium. However, we detected incongruence between the two gene trees which may result from hybridization. Dating analyses performed using the ITS dataset showed that the evolution of major lineages within Lilium-Nomocharis may be temporally coincident with Q-T Plateau uplift occurring 8-7 Mya and H-D Mountains uplift approximately 4-3 Mya. Our analyses of diversification times and rates among Lilium-Nomocharis clades are less conclusive. However, these do suggest high extinction rates among H-D Mountains lineages.
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Wang X, Yang R, Feng S, Hou X, Zhang Y, Li Y, Ren Y. Genetic variation in Rheum palmatum and Rheum tanguticum (Polygonaceae), two medicinally and endemic species in China using ISSR markers. PLoS One 2012; 7:e51667. [PMID: 23289054 PMCID: PMC3527122 DOI: 10.1371/journal.pone.0051667] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 11/06/2012] [Indexed: 12/04/2022] Open
Abstract
Aims Both Rheum palmatum and R. tanguticum are important but endangered medicinal plants endemic to China. In this study, we aimed to (i) investigate the level and pattern of genetic variability within/among populations of those species; (ii) evaluate genetic differentiation between both species and its relationships and ascertain whether both species are consistent with their current taxonomical treatment as separate species; and (iii) discuss the implications for the effective conservation of two species. Methods Total 574 individuals from 30 populations of R. palmatum and R. tanguticum were collected, covering the entire distribution range of two species in China. The genetic variation within and among 30 populations was evaluated using inter-simple sequence repeat (ISSR) markers. Important Findings Twelve selected ISSR primers generated a total of 175 fragments, 173 (98.86%) of which were polymorphic. The Nei's gene diversity (H) and Shannon's index (I) of both species were high at species level (H = 0.3107, I = 0.4677 for R. palmatum; H = 0.2848, I = 0.4333 for R. tanguticum). But for both species, the genetic diversity was low at population level, and average within-population diversity of R. palmatum was H = 0.1438, I = 0.2151, and that of R. tanguticum was H = 0.1415, I = 0.2126. The hierarchical AMOVA revealed high levels of among-population genetic differentiation in both species, in line with the gene differentiation coefficient and the limited among-population gene flow (R. palmatum: Φst = 0.592, Gst = 0.537, Nm = 0.432; R. tanguticum: Φst = 0.567, Gst = 0.497, Nm = 0.507). By contrast, only 6.52% of the total genetic variance was partitioned between R. palmatum and R. tanguticum. Bayesian analysis, UPGMA cluster analysis, and PCoA analysis all demonstrated the similar results. A significant isolation-by-distance pattern was revealed in R. palmatum (r = 0.547, P = 0.010), but not in R. tanguticum (r = 0.241, P = 0.100). Based on these results, effective conservation strategies were proposed for these two species. The small molecular variance between R. palmatum and R. tanguticum revealed that they had a common ancestor, and we considered that these two species might not be good species.
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Affiliation(s)
- Xumei Wang
- College of Medicine, Xi'an Jiaotong University, Xi'an, China.
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Takeoka GR, Dao L, Harden L, Pantoja A, Kuhl JC. Antioxidant activity, phenolic and anthocyanin contents of various rhubarb (Rheumspp.) varieties. Int J Food Sci Technol 2012. [DOI: 10.1111/j.1365-2621.2012.03174.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Gary R. Takeoka
- Western Regional Research Service; Agricultural Research Service; United States Department of Agriculture; 800 Buchanan Street; Albany; CA; 94710; USA
| | - Lan Dao
- Western Regional Research Service; Agricultural Research Service; United States Department of Agriculture; 800 Buchanan Street; Albany; CA; 94710; USA
| | - Leslie Harden
- Western Regional Research Service; Agricultural Research Service; United States Department of Agriculture; 800 Buchanan Street; Albany; CA; 94710; USA
| | - Alberto Pantoja
- Agricultural Research Service; United States Department of Agriculture; 362 O'Neill Building; UAF 905 Koyukuk Drive; PO Box 757200; Fairbanks; AK; 99775; USA
| | - Joseph C. Kuhl
- Agricultural Research Service; United States Department of Agriculture; 533 East Fireweed Ave; Palmer; AK; 88645; USA
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Garrido JL, Fenu G, Mattana E, Bacchetta G. Spatial genetic structure of Aquilegia taxa endemic to the island of Sardinia. ANNALS OF BOTANY 2012; 109:953-64. [PMID: 22351486 PMCID: PMC3310493 DOI: 10.1093/aob/mcs011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS The Mediterranean Basin is one of the most important regions for the Earth's plant biodiversity; however, the scarcity of studies on fine scale patterns of genetic variation in this region is striking. Here, an assessment is made of the spatial genetic structure of all known locations of the three Sardinian endemic species of Aquilegia in order to determine the relative roles of gene flow and genetic drift as underlying evolutionary forces canalizing the divergence of Sardinian Aquilegia taxa, and to see if the spatial genetic structure found fits the current taxonomic differentiation of these taxa. METHODS DNA from 89 individuals from all known locations of Aquilegia across Sardinia was analysed by means of amplified fragment length polymorphism (AFLP) markers. Both principal co-ordinates analysis (PCoA) and Bayesian clustering analyses were used to determine the spatial genetic structure irrespective of any taxonomic affiliation. Historical effects of gene flow and genetic drift were assessed by checking for the existence of isolation-by-distance patterns. KEY RESULTS STRUCTURE and PCoA analyses revealed a pattern of genetic variation geographically structured into four spatial genetic groups. No migration-drift equilibrium was detected for Aquilegia in Sardinia, when analysed either as a whole or in individual groups. The scenario approached a Case III pattern sensu Hutchinson and Templeton, which is associated with extreme isolation conditions where genetic drift has historically played a dominant role over gene flow. CONCLUSIONS The pattern of genetic variation of Sardinian taxa of Aquilegia indicates that genetic drift has been historically more influential than gene flow on population structure of Sardinian species of Aquilegia. Limited seed dispersal and divergent selection imposed by habitat conditions have been probably the main causes reinforcing post-Pleistocene geographical isolation of Aquilegia populations. The spatial genetic structure found here is not fully compatible with current taxonomic affiliations of Sardinian Aquilegia taxa. This is probably a consequence of the uncoupling between morphological and genetic patterns of differentiation frequently found in recently radiated taxa.
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Affiliation(s)
- J L Garrido
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio s/n, Seville, Spain.
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Sun Y, Wang A, Wan D, Wang Q, Liu J. Rapid radiation of Rheum (Polygonaceae) and parallel evolution of morphological traits. Mol Phylogenet Evol 2012; 63:150-8. [PMID: 22266181 DOI: 10.1016/j.ympev.2012.01.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 12/30/2011] [Accepted: 01/03/2012] [Indexed: 10/14/2022]
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Qi D, Chao Y, Guo S, Zhao L, Li T, Wei F, Zhao X. Convergent, parallel and correlated evolution of trophic morphologies in the subfamily schizothoracinae from the Qinghai-Tibetan plateau. PLoS One 2012; 7:e34070. [PMID: 22470515 PMCID: PMC3314705 DOI: 10.1371/journal.pone.0034070] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 02/21/2012] [Indexed: 11/25/2022] Open
Abstract
Schizothoracine fishes distributed in the water system of the Qinghai-Tibetan plateau (QTP) and adjacent areas are characterized by being highly adaptive to the cold and hypoxic environment of the plateau, as well as by a high degree of diversity in trophic morphology due to resource polymorphisms. Although convergent and parallel evolution are prevalent in the organisms of the QTP, it remains unknown whether similar evolutionary patterns have occurred in the schizothoracine fishes. Here, we constructed for the first time a tentative molecular phylogeny of the schizothoracine fishes based on the complete sequences of the cytochrome b gene. We employed this molecular phylogenetic framework to examine the evolution of trophic morphologies. We used Pagel's maximum likelihood method to estimate the evolutionary associations of trophic morphologies and food resource use. Our results showed that the molecular and published morphological phylogenies of Schizothoracinae are partially incongruent with respect to some intergeneric relationships. The phylogenetic results revealed that four character states of five trophic morphologies and of food resource use evolved at least twice during the diversification of the subfamily. State transitions are the result of evolutionary patterns including either convergence or parallelism or both. Furthermore, our analyses indicate that some characters of trophic morphologies in the Schizothoracinae have undergone correlated evolution, which are somewhat correlated with different food resource uses. Collectively, our results reveal new examples of convergent and parallel evolution in the organisms of the QTP. The adaptation to different trophic niches through the modification of trophic morphologies and feeding behaviour as found in the schizothoracine fishes may account for the formation and maintenance of the high degree of diversity and radiations in fish communities endemic to QTP.
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Affiliation(s)
- Delin Qi
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, Qinghai, China
- * E-mail: (DLQ); (XQZ)
| | - Yan Chao
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, Qinghai, China
| | - Songchang Guo
- Key Laboratory of Qinghai-Tibetan Plateau Biological Evolution and Adaptation, Northwest Plateau Institute of Biology, The Chinese Academy of Sciences, Xining, Qinghai, China
| | - Lanying Zhao
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, Qinghai, China
| | - Taiping Li
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, Qinghai, China
| | - Fulei Wei
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, Qinghai, China
| | - Xinquan Zhao
- Key Laboratory of Qinghai-Tibetan Plateau Biological Evolution and Adaptation, Northwest Plateau Institute of Biology, The Chinese Academy of Sciences, Xining, Qinghai, China
- * E-mail: (DLQ); (XQZ)
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Wang XM, Hou XQ, Zhang YQ, Yang R, Feng SF, Li Y, Ren Y. Genetic diversity of the endemic and medicinally important plant Rheum officinale as revealed by Inter-Simpe Sequence Repeat (ISSR) Markers. Int J Mol Sci 2012; 13:3900-3915. [PMID: 22489188 PMCID: PMC3317748 DOI: 10.3390/ijms13033900] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 03/08/2012] [Accepted: 03/13/2012] [Indexed: 11/19/2022] Open
Abstract
Rheum officinale Baill., an important but endangered medicinal herb, is endemic to China. Inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and differentiation of 12 populations of R. officinale. Thirteen selected primers yielded 189 bright and discernible bands, with an average of 14.54 per primer. The genetic diversity was low at the population level, but pretty high at the species level (H = 0.1008, I = 0.1505, PPB = 28.95% vs. H = 0.3341, I = 0.5000, PPB = 95.24%, respectively) by POPGENE analysis. Analysis of molecular variance (AMOVA) showed that the genetic variation was found mainly among populations (74.38%), in line with the limited gene flow (N(m) = 0.2766) among populations. Mantel test revealed a significant correlation between genetic and geographic distances (r = 0.5381, P = 0.002), indicating the role of geographic isolation in shaping the present population genetic structure. Both Bayesian analysis and UPGMA cluster analysis demonstrated the similar results. Our results imply that the conservation efforts should aim to preserve all the extant populations of this endangered species, and cultivation is proposed in this study.
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Affiliation(s)
- Xu-Mei Wang
- College of Medicine, Xi’an Jiaotong University, Xi’an 710061, China; E-Mails: (R.Y.); (Y.L.)
| | - Xiao-Qi Hou
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, China; E-Mails: (X.-Q.H.); (Y.-Q.Z); (S.-F.F); (Y.R.)
| | - Yu-Qu Zhang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, China; E-Mails: (X.-Q.H.); (Y.-Q.Z); (S.-F.F); (Y.R.)
| | - Rui Yang
- College of Medicine, Xi’an Jiaotong University, Xi’an 710061, China; E-Mails: (R.Y.); (Y.L.)
| | - Shi-Fang Feng
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, China; E-Mails: (X.-Q.H.); (Y.-Q.Z); (S.-F.F); (Y.R.)
| | - Yan Li
- College of Medicine, Xi’an Jiaotong University, Xi’an 710061, China; E-Mails: (R.Y.); (Y.L.)
| | - Yi Ren
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, China; E-Mails: (X.-Q.H.); (Y.-Q.Z); (S.-F.F); (Y.R.)
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Gene duplication and adaptive evolution of the CHS-like genes within the genus Rheum (Polygonaceae). BIOCHEM SYST ECOL 2011. [DOI: 10.1016/j.bse.2011.05.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Tian X, Luo J, Wang A, Mao K, Liu J. On the origin of the woody buckwheat Fagopyrum tibeticum (=Parapteropyrum tibeticum) in the Qinghai-Tibetan Plateau. Mol Phylogenet Evol 2011; 61:515-20. [PMID: 21798359 DOI: 10.1016/j.ympev.2011.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 06/20/2011] [Accepted: 07/05/2011] [Indexed: 10/17/2022]
Abstract
Here we tested whether 'insular woodiness', a striking evolutionary pattern that commonly occurs on islands, has also appeared in QTP continental endemics. Parapteropyrum, a monotypic shrubby genus occurring in the central QTP, has been previously placed in the tribe Atraphaxideae of the family Polygonaceae, while all the other woody species of this tribe mainly occur in western and central Asia. We studied sequence variations of nuclear ITS (internal transcribed spacer) and cp (chloroplast) DNA (rbcL and accD) of this genus and the other ten genera. The constructed phylogenies based on ITS, cpDNA or a combination of both datasets, suggest that the woody Parapteropyrum is nested within and most likely evolved from the herbaceous Fagopyrum. We propose that the large-scale uplift of the QTP not only promoted continental species radiation, but also the secondary feature of woodiness in a few herbaceous lineages in response to strong selection pressures, similar to those acting on island flora. In addition, the confirmation of Parapteropyrum within Fagopyrum highlights its potential use as a new, perennial source of buckwheat.
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Affiliation(s)
- Xinmin Tian
- Molecular Ecology Group, Key Laboratory of Arid and Grassland Ecology, Lanzhou University, Lanzhou 730000, Gansu, PR China
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Sharma SK, Kumar S, Rawat D, Kumaria S, Kumar A, Rao SR. Genetic diversity and gene flow estimation in Prosopis cineraria (L.) Druce: A key stone tree species of Indian Thar Desert. BIOCHEM SYST ECOL 2011. [DOI: 10.1016/j.bse.2010.12.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Antimicrobial activity and total content of polyphenols of Rheum L. species growing in Poland. Open Life Sci 2010. [DOI: 10.2478/s11535-010-0067-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AbstractIn the crude ethanol extracts obtained from the rhizome and roots of Rheum palmatum L., Rheum undulatum L. and Rheum rhaponticum L. growing in Poland concentration of polyphenols ranged from 46.11 to 76.45 mg/g. Concentration of tannins ranged from 7.07% to 8.67%, while anthracene derivatives and anthraquinones varied by species - R. palmatum measured 36.3 and 34 mg/g, while R. undulatum or R. rhaponticum did not exceed 20.4 and 18.1 or 19.8 mg/g and 16.6 mg/g, respectively. Using a broth microdilution method it was found that all of the Rheum spp. extracts were more active against reference strains of Gram-positive bacteria (Staphylococcus spp.) than against those of Gram-negative bacteria (Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis). The strongest inhibitory effect against Staphylococcus spp. was exerted by R. undulatum extract with MIC = 125–250 μg/mL. The moderate in vitro antibacterial activity of R. undulatum suggests that this plant, often used in the European cuisine to improve flavour, may be also important and useful as an alternative or auxiliary medicine remedy in the treatment of uncomplicated superficial infections caused especially by clinically important staphylococci, potentially pathogenic S. aureus or opportunistic S. epidermidis.
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Zhang YH, Volis S, Sun H. Chloroplast phylogeny and phylogeography of Stellera chamaejasme on the Qinghai-Tibet Plateau and in adjacent regions. Mol Phylogenet Evol 2010; 57:1162-72. [PMID: 20828627 DOI: 10.1016/j.ympev.2010.08.033] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 08/27/2010] [Accepted: 08/31/2010] [Indexed: 11/30/2022]
Abstract
Historic events such as the uplift of Qinghai-Tibet Plateau (Q-T Plateau) and climatic oscillations in the Quaternary period greatly affected the evolution and modern distribution of Sino-Tibetan flora. Stellera chamaejasme, a perennial herb with flower color polymorphism that is distributed from the mountainous southeastern Q-T Plateau (Hengduan Mountains, H-D Mountains) to the vast platform of the Q-T Plateau and the adjacent plain of northern China, provides an excellent model to explore the effects of historic events on the origination and variation of species. In this study, we conducted a phylogenetic and phylogeographical study using three chloroplast sequences (trnT-L, trnL-F and rpL16) in 26 populations of S. chamaejasme and 12 outgroups from the Thymeleaceae. Phylogenetic analysis and molecular clock estimation revealed that the monophyletic origin of S. chamaejasme occurred ca. 6.5892 Ma, which is consistent with the radical environment changes caused by the rapid uplift of the Q-T Plateau ca. 7 Ma. Intra-specific differentiation of S. chamaejasme is estimated to have occurred after ca. 2.1 Ma. Twelve haplotypes were revealed from combined trnL-F and rpL16 sequences. High genetic diversity (h(T)=0.834) and population differentiation (N(ST)=0.997 and G(ST)=0.982) imply restricted gene flow among populations and significant geographical or environmental isolation. All populations from the vast plain of northern China were dominated by one haplotype (H1), and the same haplotype was fixed in most populations from the high elevation platform of the western and northern Q-T Plateau. In contrast, the majority of the haplotypes were found in the relatively narrow area of the H-D Mountains, in the southeastern distribution of S. chamaejasme. The contrasting haplotype distribution patterns suggested that the H-D Mountains were either a refugium for S. chamaejasme during the Quaternary climatic oscillations or a diversification center of this species. The present wide distribution of this species on the Q-T Plateau platform and in northern China is likely to have resulted from a rapid post-glacial population expansion from the southeastern refugium involving founder effects, facilitated by the adjacent geographic range with a similar grassland habitat.
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Affiliation(s)
- Yong-Hong Zhang
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, People's Republic of China
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Abstract
Leontopodium is a genus of approximately 30 species with a conspicuous Asian–European disjunct distribution. In this study samples from the Himalayan/Tibetan centre of diversity of the genus, as well as from Europe, were analysed to infer a phylogeny of the genus using sequences of nuclear ribosomal (ITS and ETS) and plastid (matK and trnL/F) DNA. The Southeast Tibetan monotypic Sinoleontopodium [Leontopodium lingianum (Y.L.Chen) Dickoré, comb. nov.] falls into Leontopodium. Monophyly of Leontopodium, including Sinoleontopodium, is supported. Due to low rates of sequence divergence, intrageneric relationships in general are weakly supported, a pattern frequently observed in plant groups centred in the Tibetan Plateau. Three phylogenetic groups can be identified, however, and these are also supported by morphology. The low levels of nucleotide divergence suggest a young age for the group, which has been influenced by the turbulent geological history of the Tibetan Plateau. Leontopodium is a characteristic Sino-Himalayan element that appears to have found its way into the mountains of Europe in geologically recent times. The two European taxa, Leontopodium alpinum and L. nivale, form a genetically distinct group, which, considering the wide geographic disjunction, shows surprisingly little divergence from its Asian relatives.
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Genetic diversity and population structure of the endangered and medically important Rheum tanguticum (Polygonaceae) revealed by SSR Markers. BIOCHEM SYST ECOL 2009. [DOI: 10.1016/j.bse.2009.08.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Fan X, Sha LN, Yang RW, Zhang HQ, Kang HY, Ding CB, Zhang L, Zheng YL, Zhou YH. Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae) based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase. BMC Evol Biol 2009; 9:247. [PMID: 19814813 PMCID: PMC2770499 DOI: 10.1186/1471-2148-9-247] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 10/08/2009] [Indexed: 11/28/2022] Open
Abstract
Background Single- and low- copy genes are less likely subject to concerted evolution, thus making themselves ideal tools for studying the origin and evolution of polyploid taxa. Leymus is a polyploid genus with a diverse array of morphology, ecology and distribution in Triticeae. The genomic constitution of Leymus was assigned as NsXm, where Ns was presumed to be originated from Psathyrostachys, while Xm represented a genome of unknown origin. In addition, little is known about the evolutionary history of Leymus. Here, we investigate the phylogenetic relationship, genome donor, and evolutionary history of Leymus based on a single-copy nuclear Acc1 gene. Results Two homoeologues of the Acc1 gene were isolated from nearly all the sampled Leymus species using allele-specific primer and were analyzed with those from 35 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1) Leymus is closely related to Psathyrostachys, Agropyron, and Eremopyrum; (2) Psathyrostachys juncea is an ancestral Ns-genome donor of Leymus species; (3) the Xm genome in Leymus may be originated from an ancestral lineage of Agropyron and Eremopyrum triticeum; (4) the Acc1 sequences of Leymus species from the Qinghai-Tibetan plateau are evolutionarily distinct; (5) North America Leymus species might originate from colonization via the Bering land bridge; (6) Leymus originated about 11-12MYA in Eurasia, and adaptive radiation might have occurred in Leymus during the period of 3.7-4.3 MYA and 1.7-2.1 MYA. Conclusion Leymus species have allopolyploid origin. It is hypothesized that the adaptive radiation of Leymus species might have been triggered by the recent upliftings of the Qinghai-Tibetan plateau and subsequent climatic oscillations. Adaptive radiation may have promoted the rapid speciation, as well as the fixation of unique morphological characters in Leymus. Our results shed new light on our understanding of the origin of Xm genome, the polyploidization events and evolutionary history of Leymus that could account for the rich diversity and ecological adaptation of Leymus species.
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Affiliation(s)
- Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, PR China.
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WANG YUJIN, SUSANNA ALFONSO, VON RAAB-STRAUBE ECKHARD, MILNE RICHARD, LIU JIANQUAN. Island-like radiation of Saussurea (Asteraceae: Cardueae) triggered by uplifts of the Qinghai-Tibetan Plateau. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01225.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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LIU YIFEI, WANG YONG, HUANG HONGWEN. Species-level phylogeographical history ofMyricariaplants in the mountain ranges of western China and the origin ofM. laxiflorain the Three Gorges mountain region. Mol Ecol 2009; 18:2700-12. [DOI: 10.1111/j.1365-294x.2009.04214.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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