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Zhang Q, Yang Y, Liu B, Lu L, Sauquet H, Li D, Chen Z. Meta-analysis provides insights into the origin and evolution of East Asian evergreen broad-leaved forests. THE NEW PHYTOLOGIST 2024; 242:2369-2379. [PMID: 38186378 DOI: 10.1111/nph.19524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024]
Abstract
Evergreen broad-leaved forests (EBLFs) are dominated by a monsoon climate and form a distinct biome in East Asia with notably high biodiversity. However, the origin and evolution of East Asian EBLFs (EAEBLFs) remain elusive despite the estimation of divergence times for various representative lineages. Using 72 selected generic-level characteristic lineages, we constructed an integrated lineage accumulation rate (LAR) curve based on their crown ages. According to the crown-based LAR, the EAEBLF origin was identified at least as the early Oligocene (c. 31.8 million years ago (Ma)). The accumulation rate of the characteristic genera peaked at 25.2 and 6.4 Ma, coinciding with the two intensification periods of the Asian monsoon at the Oligocene - Miocene and the Miocene - Pliocene boundaries, respectively. Moreover, the LAR was highly correlated with precipitation in the EAEBLF region and negatively to global temperature, as revealed through time-lag cross-correlation analyses. An early Oligocene origin is suggested for EAEBLFs, bridging the gap between paleobotanical and molecular dating studies and solving conflicts among previous estimates based on individual representative lineages. The strong correlation between the crown-based LAR and the precipitation brought about by the Asian monsoon emphasizes its irreplaceable role in the origin and development of EAEBLFs.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yuchang Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Limin Lu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Hervé Sauquet
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, NSW, 2000, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Dezhu Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhiduan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
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Wei YF, Jiang XH, Song R, She CW. Molecular cytogenetic characterization of 9 populations of four species in the genus Polygonatum (Asparagaceae). COMPARATIVE CYTOGENETICS 2024; 18:73-95. [PMID: 38798789 PMCID: PMC11116888 DOI: 10.3897/compcytogen.18.122399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/21/2024] [Indexed: 05/29/2024]
Abstract
To characterize the chromosomes of the four species of Polygonatum Miller, 1754, used in traditional Chinese medicine, P.cyrtonema Hua, 1892, P.kingianum Collett et Hemsley, 1890, P.odoratum (Miller, 1768) Druce, 1906, and P.sibiricum Redouté, 1811, and have an insight into the karyotype variation of the genus Polygonatum, fluorescence in situ hybridization (FISH) with 5S and 45S rDNA oligonucleotide probes was applied to analyze the karyotypes of 9 populations of the four species. Detailed molecular cytogenetic karyotypes of the 9 populations were established for the first time using the dataset of chromosome measurements and FISH signals of 5S and 45S rDNA. Four karyotype asymmetry indices, CVCI, CVCL, MCA and Stebbins' category, were measured to elucidate the asymmetry of the karyotypes and karyological relationships among species. Comparison of their karyotypes revealed distinct variations in the karyotypic parameters and rDNA patterns among and within species. The basic chromosome numbers detected were x = 9, 11 and 13 for P.cyrtonema, x = 15 for P.kingianum, x = 10 and 11 for P.odoratum, and x = 12 for P.sibiricum. The original basic chromosome numbers of the four species were inferred on the basis of the data of this study and previous reports. All the 9 karyotypes were of moderate asymmetry and composed of metacentric, submetacentric and subtelocentric chromosomes or consisted of two of these types of chromosomes. Seven populations have one locus of 5S rDNA and two loci of 45S rDNA, and two populations added one 5S or 45S locus. The karyological relationships among the four species revealed by comparison of rDNA patterns and PCoA based on x, 2n, TCL, CVCI, MCA and CVCL were basically accordant with the phylogenetic relationships revealed by molecular phylogenetic studies. The mechanisms of both intra- and inter-specific dysploidy in Polygonatum were discussed based on the data of this study and literature.
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Affiliation(s)
- Yan-Fang Wei
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, Hunan, 412007, ChinaHunan University of TechnologyZhuzhouChina
| | - Xiang-Hui Jiang
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, Huaihua University, Huaihua, Hunan, 418008, ChinaHuaihua UniversityHuaihuaChina
| | - Rong Song
- Institute of Agricultural Environment and Ecology, Hunan Academy of Agricultural Sciences, Changsha, Hunan, 410125, ChinaInstitute of Agricultural Environment and Ecology, Hunan Academy of Agricultural SciencesChangshaChina
| | - Chao-Wen She
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, Hunan, 412007, ChinaHunan University of TechnologyZhuzhouChina
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Qin YQ, Zhang MH, Yang CY, Nie ZL, Wen J, Meng Y. Phylogenomics and divergence pattern of Polygonatum (Asparagaceae: Polygonateae) in the north temperate region. Mol Phylogenet Evol 2024; 190:107962. [PMID: 37926394 DOI: 10.1016/j.ympev.2023.107962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Polygonatum is the largest genus of tribe Polygonateae (Asparagaceae) and is widely distributed in the temperate Northern Hemisphere, especially well diversified in southwestern China to northeastern Asia. Phylogenetic relationships of many species are still controversial. Hence it is necessary to clarify their phylogenetic relationships and infer possible reticulate relationships for the genus. In this study, genome-wide data of 43 species from Polygonatum and its closely related taxa were obtained by Hyb-Seq sequencing. The phylogenetic trees constructed from genome-wide nuclear and chloroplast sequences strongly supported the monophyly of Polygonatum with division into three major clades. A high level of incongruence was detected between nuclear and chloroplast trees as well as among gene trees within the genus, but all occurred within each major clade. However, introgression tests and reticulate evolution analyses revealed low level of gene flow and weak introgression events in the genus, suggesting hybridization and introgression were not dominant during the evolutionary diversification of Polygonatum in the Northern Hemisphere. This study provides important insights into reconstructing evolutionary relationships and speciation pattern of taxa from the north temperate flora.
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Affiliation(s)
- Yu-Qian Qin
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Meng-Hua Zhang
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Chu-Yun Yang
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Ze-Long Nie
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Ying Meng
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China.
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Phylogenomics of Aralia sect. Aralia (Araliaceae): Signals of hybridization and insights into its species delimitations and intercontinental biogeography. Mol Phylogenet Evol 2023; 181:107727. [PMID: 36754338 DOI: 10.1016/j.ympev.2023.107727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
Genome-scale data have significantly increased the number of informative characters for phylogenetic analyses and recent studies have also revealed widespread phylogenomic discordance in many plant lineages. Aralia sect. Aralia is a small plant lineage (14 spp.) of the ginseng family Araliaceae with a disjunct distribution between eastern Asia (11 spp.) and North America (3 spp.). We herein employ sequences of hundreds of nuclear loci and the complete plastomes using targeted sequence capture and genome skimming to reconstruct the phylogenetic and biogeographic history of this section. We detected substantial conflicts among nuclear genes, yet different analytical strategies generated largely congruent topologies from the nuclear data. Significant cytonuclear discordance was detected, especially concerning the positions of the three North American species. The phylogenomic results support two intercontinental disjunctions: (1) Aralia californica of western North America is sister to the eastern Asian clade consisting of A. cordata and A. continentalis in the nuclear tree, and (2) the eastern North American A. racemosa forms a clade with A. bicrenata from southwestern North America, and the North American A. racemosa - A. bicrenata clade is then sister to the eastern Asian clade consisting of A. glabra (Japan), A. fargesii (C China), and A. apioides and A. atropurpurea (the Hengduan Mountains). Aralia cordata is supported to be disjunctly distributed in Japan, Taiwan, the Ulleung island of Korea, and in Central, Southwest and South China, and Aralia continentalis is redefined with a narrower distribution in Northeast China, eastern Russia and peninsular Korea.
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Hu Y, Liu Y, Ali M, Wu W, Li X, Chen L, Shao J. Polygonatumpraecox (Asparagaceae), a new species from mid-eastern China revealed by morphological and molecular evidence. PHYTOKEYS 2022; 211:125-138. [PMID: 36760726 PMCID: PMC9878575 DOI: 10.3897/phytokeys.211.90456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 10/05/2022] [Indexed: 06/18/2023]
Abstract
A new species, Polygonatumpraecox Y.F.Hu & J.W.Shao (Asparagaceae), is described and illustrated. This species is similar to P.cyrtonema, P.odoratum and P.caulialatum, but can be distinguished from P.cyrtonema by its racemose inflorescence, cylindrical hairless filaments and apex without a retrorse spur; from P.odoratum by its stout moniliform rhizome, straight stem and longer (1.7-2.2 cm long) floral tube; and from P.caulialatum by its upper part straight stem, yellowish-green corolla, lobes excurved and earlier flowering. The complete chloroplast genome of this new species is 155,115-155,256 bp in length. Phylogenetic analysis revealed that P.praecox is not genetically related to the above three morphological similar species, but is closely related to the two European species (P.multiforum and P.latifolium). This species is relatively common in mid-eastern China and has previously been confused with P.cyrtonema. As its wild resources have decreased in recent years due to over-exploitation for medicinal or edible purposes, we classify it as Near Threatened (NT) according to the IUCN Red List Criteria.
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Affiliation(s)
- Yingfeng Hu
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, ChinaAnhui Normal UniversityWuhuChina
| | - Yujun Liu
- Anhui Academy of Science and Technology, Hefei 230000, ChinaAnhui Academy of Science and TechnologyHefeiChina
| | - Maroof Ali
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, ChinaAnhui Normal UniversityWuhuChina
| | - Wei Wu
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, ChinaAnhui Normal UniversityWuhuChina
| | - Xiaohong Li
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, ChinaAnhui Normal UniversityWuhuChina
| | - Longsheng Chen
- Anhui Academy of Science and Technology, Hefei 230000, ChinaAnhui Academy of Science and TechnologyHefeiChina
| | - Jianwen Shao
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, ChinaAnhui Normal UniversityWuhuChina
- Provincial Key Laboratory of Conservation and Utilization of Biological Resources, Wuhu, Anhui 241000, ChinaProvincial Key Laboratory of Conservation and Utilization of Biological ResourcesWuhuChina
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Lu QX, Chang X, Gao J, Wu X, Wu J, Qi ZC, Wang RH, Yan XL, Li P. Evolutionary Comparison of the Complete Chloroplast Genomes in Convallaria Species and Phylogenetic Study of Asparagaceae. Genes (Basel) 2022; 13:genes13101724. [PMID: 36292609 PMCID: PMC9601677 DOI: 10.3390/genes13101724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/18/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
The genus Convallaria (Asparagaceae) comprises three herbaceous perennial species that are widely distributed in the understory of temperate deciduous forests in the Northern Hemisphere. Although Convallaria species have high medicinal and horticultural values, studies related to the phylogenetic analysis of this genus are few. In the present study, we assembled and reported five complete chloroplast (cp) sequences of three Convallaria species (two of C. keiskei Miq., two of C. majalis L., and one of C. montana Raf.) using Illumina paired-end sequencing data. The cp genomes were highly similar in overall size (161,365–162,972 bp), and all consisted of a pair of inverted repeats (IR) regions (29,140–29,486 bp) separated by a large single-copy (LSC) (85,183–85,521 bp) and a small single-copy (SSC) region (17,877–18,502 bp). Each cp genome contained the same 113 unique genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene content, gene order, AT content and IR/SC boundary structure were nearly identical among all of the Convallaria cp genomes. However, their lengths varied due to contraction/expansion at the IR/LSC borders. Simple sequence repeat (SSR) analyses indicated that the richest SSRs are A/T mononucleotides. Three highly variable regions (petA-psbJ, psbI-trnS and ccsA-ndhD) were identified as valuable molecular markers. Phylogenetic analysis of the family Asparagaceae using 48 cp genome sequences supported the monophyly of Convallaria, which formed a sister clade to the genus Rohdea. Our study provides a robust phylogeny of the Asparagaceae family. The complete cp genome sequences will contribute to further studies in the molecular identification, genetic diversity, and phylogeny of Convallaria.
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Affiliation(s)
- Qi-Xiang Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xiao Chang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jing Gao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xue Wu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jing Wu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhe-Chen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Shaoxing Academy of Biomedicine, Zhejiang Sci-Tech University, Shaoxing 312366, China
- Correspondence: (Z.-C.Q.); (R.-H.W.)
| | - Rui-Hong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Correspondence: (Z.-C.Q.); (R.-H.W.)
| | - Xiao-Ling Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Pan Li
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Liu BB, Ren C, Kwak M, Hodel RGJ, Xu C, He J, Zhou WB, Huang CH, Ma H, Qian GZ, Hong DY, Wen J. Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1020-1043. [PMID: 35274452 DOI: 10.1111/jipb.13246] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.
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Affiliation(s)
- Bin-Bin Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, 20013-7012, DC, USA
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Myounghai Kwak
- National Institute of Biological Resources, Incheon, 22689, South Korea
| | - Richard G J Hodel
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, 20013-7012, DC, USA
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Wen-Bin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, 27965, NC, USA
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, 510D Mueller Laboratory, University Park, Pennsylvania, 16802, USA
| | - Guan-Ze Qian
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, China
| | - De-Yuan Hong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, 20013-7012, DC, USA
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Chao CT, Tzeng HY, Tseng YH. Leaf epidermal morphology of Asparagaceae of Taiwan and its systematic significance. Microsc Res Tech 2022; 85:2162-2180. [PMID: 35238102 DOI: 10.1002/jemt.24074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 11/08/2022]
Abstract
The current study analyzed the epidermal morphology of Asparagaceae in detail and assessed its systematic importance. At the familial level, no consistent characteristics were found, but anticlinal wall and stomata morphology provided systematic information of different tribes, especially Ophiopogoneae and Polygonateae. In Ophiopogoneae, Liriope and Ophiopogon had similar epidermis, which implying a close relationship between them, and was also supported by related studies. The leaves of Polygonateae exhibited rounded and undulate anticlinal wall. Polygonatum arisanense var. formosanum had a rounded anticlinal wall, whereas other species exhibited undulate anticlinal walls. Different epidemis of Po. arisanense var. formosanum supported the variety treatment of Po. arisanense. The intergeneric relationship was also interpreted based on the anticlinal wall and stomata. Therefore, the epidermis could provide the systematic value of Asparagaceae. The present study also revealed the linkage of stomata and habitat types, though the adaptative significance of epidermal traits needs further study.
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Affiliation(s)
- Chien-Ti Chao
- School of Life Science, National Taiwan Normal University, No. 88, Tingchou Rd. 4th Section, Wenshan District, Taipei City, 116, Taiwan
| | - Hsy-Yu Tzeng
- Department of Forestry, National Chung Hsing University, No. 145, Xinda Rd., Taichung City, 402, Taiwan
| | - Yen-Hsueh Tseng
- Department of Forestry, National Chung Hsing University, No. 145, Xinda Rd., Taichung City, 402, Taiwan.,Director General, Taiwan Forestry Research Institute, Council of Agriculture, Executive Yuan, R. O. C. (Taiwan), No. 53, Nanhai Rd., Zhongzheng Dist., Taipei City, 100, Taiwan
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Wang J, Qian J, Jiang Y, Chen X, Zheng B, Chen S, Yang F, Xu Z, Duan B. Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe Polygonateae. FRONTIERS IN PLANT SCIENCE 2022; 13:882189. [PMID: 35812916 PMCID: PMC9263837 DOI: 10.3389/fpls.2022.882189] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/03/2022] [Indexed: 05/22/2023]
Abstract
Members of Polygonatum are perennial herbs that have been widely used in traditional Chinese medicine to invigorate Qi, moisten the lung, and benefit the kidney and spleen among patients. However, the phylogenetic relationships and intrageneric taxonomy within Polygonatum have long been controversial because of the complexity of their morphological variations and lack of high-resolution molecular markers. The chloroplast (cp) genome is an optimal model for deciphering phylogenetic relationships in related families. In the present study, the complete cp genome of 26 species of Trib. Polygonateae were de novo assembled and characterized; all species exhibited a conserved quadripartite structure, that is, two inverted repeats (IR) containing most of the ribosomal RNA genes, and two unique regions, large single sequence (LSC) and small single sequence (SSC). A total of 8 highly variable regions (rps16-trnQ-UUG, trnS-GCU-trnG-UCC, rpl32-trnL-UAG, matK-rps16, petA-psbJ, trnT-UGU-trnL-UAA, accD-psaI, and trnC-GCA-petN) that might be useful as potential molecular markers for identifying Polygonatum species were identified. The molecular clock analysis results showed that the divergence time of Polygonatum might occur at ∼14.71 Ma, and the verticillate leaf might be the ancestral state of this genus. Moreover, phylogenetic analysis based on 88 cp genomes strongly supported the monophyly of Polygonatum. The phylogenetic analysis also suggested that Heteropolygonatum may be the sister group of the Polygonatum, but the Disporopsis, Maianthemum, and Disporum may have diverged earlier. This study provides valuable information for further species identification, evolution, and phylogenetic research of Polygonatum.
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Affiliation(s)
- Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, China
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, College of Life Science, Northeast Forestry University, Harbin, China
| | - Jun Qian
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Yuan Jiang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Xiaochen Chen
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, College of Life Science, Northeast Forestry University, Harbin, China
| | - Baojiang Zheng
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, College of Life Science, Northeast Forestry University, Harbin, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fajian Yang
- Baoshan College of Traditional Chinese Medicine, Baoshan, China
| | - Zhichao Xu
- College of Pharmaceutical Science, Dali University, Dali, China
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, College of Life Science, Northeast Forestry University, Harbin, China
- *Correspondence: Zhichao Xu,
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, China
- Baozhong Duan,
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Xia M, Liu Y, Liu J, Chen D, Shi Y, Bai Z, Xiao Y, Peng C, Si J, Li P, Qiu Y. A new synonym of Polygonatum in China, based on morphological and molecular evidence. PHYTOKEYS 2021; 175:137-149. [PMID: 34475796 PMCID: PMC8390792 DOI: 10.3897/phytokeys.175.63383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/22/2021] [Indexed: 06/13/2023]
Abstract
PolygonatumkingianumCollett et Hemsl.var.grandifolium D.M. Liu & W.Z. Zeng (1981), which sprouts twice a year, once in spring and once in autumn, differs from Polygonatumkingianum in leaves, bracts, perianth and filaments. Morphological comparison and molecular phylogeny indicate that it is identical to the newly-published Polygonatumhunanense H.H. Liu & B.Z. Wang (2021). Hence, we propose that P.kingianumvar.grandifolium should be recognised as a new synonym of P.hunanense. In addition, phylogenetic analyses confirmed that P.hunanense is sister to Polygonatumsect.Polygonatum, rather than P.kingianum of Polygonatumsect.Verticillata.
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Affiliation(s)
- Maoqin Xia
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, ChinaZhejiang UniversityHangzhouChina
| | - Ying Liu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, ChinaZhejiang UniversityHangzhouChina
| | - Jingjing Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou 311300, ChinaZhejiang A&F UniversityHangzhouChina
| | - Donghong Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou 311300, ChinaZhejiang A&F UniversityHangzhouChina
| | - Yan Shi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou 311300, ChinaZhejiang A&F UniversityHangzhouChina
| | - Zhicong Bai
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, ChinaZhejiang UniversityHangzhouChina
| | - Yu Xiao
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, ChinaZhejiang UniversityHangzhouChina
| | - Chen Peng
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, ChinaZhejiang UniversityHangzhouChina
| | - Jinping Si
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou 311300, ChinaZhejiang A&F UniversityHangzhouChina
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, ChinaZhejiang UniversityHangzhouChina
| | - Yingxiong Qiu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, ChinaZhejiang UniversityHangzhouChina
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Meng R, Meng Y, Yang YP, Nie ZL. Phylogeny and biogeography of Maianthemum (Asparagaceae: Nolinoideae) revisited with emphasis on its divergence pattern in SW China. PLANT DIVERSITY 2021; 43:93-101. [PMID: 33997541 PMCID: PMC8103418 DOI: 10.1016/j.pld.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 01/21/2021] [Accepted: 02/01/2021] [Indexed: 05/30/2023]
Abstract
Maianthemum is a genus with more than 35 species from the tribe Polygonateae (Asparagaceae), widely distributed between North to Central Americas and eastern Asia with high diversity in the eastern Himalayas to the Hengduan Mountains of SW China. Although most species from SW China form a well-supported clade, phylogenetic relationships within this clade remain unclear. With a broad level of taxon sampling and an extensive character sampling from eight DNA regions, this study intends to revisit the phylogeny and biogeography of the genus to better understand the divergence patterns of species from SW China. Phylogenetic results suggested the monophyly of Maianthemum with recognition of nine strongly supported clades, but backbone relationships among these clades remained largely uncertain. For the SW China clade, individuals from the same species are grouped into different lineages. Our results revealed that the fast radiation of the SW China clade was occurred in the eastern Himalayas, followed by subsequent radiation in the Hengduan Mountains in the Pliocene. Intercontinental disjunctions of Maianthemum in the Northern Hemisphere appear to have occurred multiple times during the late Miocene to the Pliocene, likely resulted by a combination of both vicariance and long-distance dispersal events.
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Affiliation(s)
- Ran Meng
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou 416000, Hunan, China
| | - Ying Meng
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou 416000, Hunan, China
| | - Yong-Ping Yang
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou 416000, Hunan, China
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12
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Meng R, Luo LY, Zhang JY, Zhang DG, Nie ZL, Meng Y. The Deep Evolutionary Relationships of the Morphologically Heterogeneous Nolinoideae (Asparagaceae) Revealed by Transcriptome Data. FRONTIERS IN PLANT SCIENCE 2021; 11:584981. [PMID: 33519845 PMCID: PMC7840527 DOI: 10.3389/fpls.2020.584981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
The subfamily Nolinoideae of Asparagaceae is an extremely morphologically heterogeneous group, which is comprised of seven lineages, formerly known as Eriospermaceae, Polygonateae, Ophiopogoneae, Convallarieae, Ruscaceae s.s., Dracaenaceae, and Nolinaceae from different families or even orders. Their drastically divergent morphologies and low level of molecular resolution have hindered our understanding on their evolutionary history. To resolve reliable and clear phylogenetic relationships of the Nolinoideae, a phylogenetic study was conducted based on transcriptomic sequencing of 15 species representing all the seven lineages. A dataset containing up to 2,850,331 sites across 2,126 genes was analyzed using both concatenated and coalescent methods. Except for Eriospermum as outgroup, the transcriptomic data strongly resolved the remaining six lineages into two groups, one is a paraphyletic grade including the woody lineages of dracaenoids, ruscoids, and nolinoids and a monophyletic herbaceous clade. Within the herbaceous group, the Ophiopogoneae + Theropogon is sister to a clade that is composed of Convallarieae and the monophyletic Polygonateae. Our work provides a first robust deep relationship of the highly heterogeneous Nolinoideae and paves the way for further investigations of its complex evolution.
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Using phylogenomics to reconstruct phylogenetic relationships within tribe Polygonateae (Asparagaceae), with a special focus on Polygonatum. Mol Phylogenet Evol 2018; 129:202-213. [DOI: 10.1016/j.ympev.2018.08.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/22/2018] [Accepted: 08/27/2018] [Indexed: 01/08/2023]
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14
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Wei X, Qi Y, Zhang X, Luo L, Shang H, Wei R, Liu H, Zhang B. Phylogeny, historical biogeography and characters evolution of the drought resistant fern Pyrrosia Mirbel (Polypodiaceae) inferred from plastid and nuclear markers. Sci Rep 2017; 7:12757. [PMID: 28986552 PMCID: PMC5630607 DOI: 10.1038/s41598-017-12839-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/14/2017] [Indexed: 11/09/2022] Open
Abstract
Pyrrosia s.l. comprises ca. 60 species with a disjunct Africa/Asia and Australia distribution. The infrageneric classification of Pyrrosia s.l. is controversial based on the phylogenetic analyses of chloroplast markers and morphology. Based on the expanded taxon sampling of Pyrrosia s.l. (51 species), we investigated its phylogeny, biogeography, character evolution and environmental adaptation by employing five chloroplastid markers (rbcL, matK, psbA-trnH, and rps4 + rps4-trnS) and one single (low)-copy nuclear gene, LEAFY. Pyrrosia s.l. was divided into six major clades and eight subclades. Reticulate evolution was revealed both among clades and among species in Pyrrosia s.l. Ancestral character state optimization revealed high levels of homoplastic evolution of the diagnostic characters in Pyrrosia s.l., while the crassulacean acid metabolism pathway seems to have an independent origin. Molecular dating and biogeographic diversification analyses suggested that Pyrrosia s.l. originated no later than the Oligocene and the main clades diversified during the Oligocene and Miocene, with southern Asia, the Indo-China Peninsula and southwestern and southern China as the most likely ancestral areas. Transoceanic long-distance dispersal, rather than vicariance, contributed to the intercontinental disjunction. Diversification scenarios of Pyrrosia s.l. under geological movements and climate fluctuation are also discussed.
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Affiliation(s)
- Xueping Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yaodong Qi
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xianchun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Luo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hui Shang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences; Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Haitao Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Bengang Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
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