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Ling YY, Xiang KL, Peng HW, Erst AS, Lian L, Zhao L, Jabbour F, Wang W. Biogeographic diversification of Actaea (Ranunculaceae): Insights into the historical assembly of deciduous broad-leaved forests in the Northern Hemisphere. Mol Phylogenet Evol 2023:107870. [PMID: 37406952 DOI: 10.1016/j.ympev.2023.107870] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/28/2023] [Accepted: 07/02/2023] [Indexed: 07/07/2023]
Abstract
The deciduous broad-leaved forests (DBLFs) cover large temperate and subtropical high-altitude regions in the Northern Hemisphere. They are home to rich biodiversity, especially to numerous endemic and relict species. However, we know little about how this vegetation in the Northern Hemisphere has developed through time. Here, we used Actaea (Ranunculaceae), an herbaceous genus almost exclusively growing in the understory of the Northern Hemisphere DBLFs, to shed light on the historical assembly of this biome in the Northern Hemisphere. We present a complete species-level phylogenetic analysis of Actaea based on five plastid and nuclear loci. Using the phylogenetic framework, we estimated divergence times, ancestral ranges, and diversification rates. Phylogenetic analyses strongly support Actaea as monophyletic. Sections Podocarpae and Oligocarpae compose a clade, sister to all other Actaea. The sister relationship between sections Chloranthae and Souliea is strongly supported. Section Dichanthera is not monophyletic unless section Cimicifuga is included. Actaea originated in East Asia, likely the Qinghai-Tibet Plateau, in the late Paleocene (c. 57 Ma), and subsequently dispersed into North America in the middle Eocene (c. 43 Ma) via the Thulean bridge. Actaea reached Europe twice, Japan twice, and Taiwan once, and all these five colonization events occurred in the late Miocene-early Pliocene, a period when sea level dropped. Actaea began to diversify at c. 43 Ma. The section-level diversification took place at c. 27-37 Ma and the species-level diversification experienced accelerations twice, which occurred at c. 15 Ma and c. 5 Ma, respectively. Our findings suggest that the Northern Hemisphere DBLFs might have risen in the middle Eocene and further diversified in the late Eocene-Oligocene, middle Miocene and early Pliocene, in association with climatic deterioration during these four periods.
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Affiliation(s)
- Yuan-Yuan Ling
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun-Li Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Huan-Wen Peng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Andrey S Erst
- Central Siberian Botanical Garden, Russian Academy of Sciences, Zolotodolinskaya str. 101, Novosibirsk 630090, Russia
| | - Lian Lian
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris 75005, France
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Zhang DQ, Ren Y, Zhang JQ. Nonadaptive molecular evolution of plastome during the speciation of Actaea purpurea and its relatives. Ecol Evol 2022; 12:e9321. [PMID: 36177132 PMCID: PMC9482002 DOI: 10.1002/ece3.9321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/02/2022] [Accepted: 08/30/2022] [Indexed: 11/09/2022] Open
Abstract
We have seen an explosive increase of plant plastid genome (plastome) sequences in the last decade, and the view that sequence variation in plastomes is maintained by the mutation-drift balance has been challenged by new evidence. Although comparative genomic and population-level studies provided us with evidence for positive evolution of plastid genes at both the macro- and micro-evolution levels, less studies have systematically investigated how plastomes have evolved during the speciation process. We here sequenced 13 plastomes of Actaea purpurea (P.K. Hsiao) J. Compton, and its closest relatives, and conducted a systematic survey of positive selection in their plastid genes using the McDonald-Kreitman test and codon-based methods using maximum likelihood to estimate the ratio of nonsynonymous to synonymous substitutions (ω) across a phylogeny. We found that during the speciation of A. purpurea and its relatives, all plastid genes evolved neutrally or were under purifying selection. Genome size, gene order, and number were highly conserved. Comparing to A. purpurea, plastomes of Actaea japonica and Actaea biternata had low genetic diversity, consistent with previous studies. Our work not only sheds important light on the evolutionary history of A. purpurea and its kin, but also on the evolution of plastomes during plant speciation.
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Affiliation(s)
- Dan-Qing Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China College of Life Sciences, Shaanxi Normal University Xi'an China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education Shaanxi Normal University Xi'an China
| | - Yi Ren
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China College of Life Sciences, Shaanxi Normal University Xi'an China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education Shaanxi Normal University Xi'an China
| | - Jian-Qiang Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China College of Life Sciences, Shaanxi Normal University Xi'an China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education Shaanxi Normal University Xi'an China
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Park I, Song JH, Yang S, Moon BC. Comparative Analysis of Actaea Chloroplast Genomes and Molecular Marker Development for the Identification of Authentic Cimicifugae Rhizoma. Plants (Basel) 2020; 9:E157. [PMID: 32012666 PMCID: PMC7076663 DOI: 10.3390/plants9020157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/11/2022]
Abstract
Actaea (Ranunculaceae; syn. Cimicifuga) is a controversial and complex genus. Dried rhizomes of Actaea species are used as Korean traditional herbal medicine. Although Actaea species are valuable, given their taxonomic classification and medicinal properties, sequence information of Actaea species is limited. In this study, we determined the complete chloroplast (cp) genome sequences of three Actaea species, including A. simplex, A. dahurica, and A. biternata. The cp genomes of these species varied in length from 159,523 to 159,789 bp and contained 112 unique functional genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene order, orientation, and content were well conserved in the three cp genomes. Comparative sequence analysis revealed the presence of hotspots, including ndhC-trnV-UAC, in Actaea cp genomes. High-resolution phylogenetic relationships were established among Actaea species based on cp genome sequences. Actaea species were clustered into each Actaea section, consistent with the Angiosperm Phylogeny Group (APG) IV system of classification. We also developed a novel indel marker, based on copy number variation of tandem repeats, to facilitate the authentication of the herbal medicine Cimicifugae Rhizoma. The availability Actaea cp genomes will provide abundant information for the taxonomic and phylogenetic analyses of Actaea species, and the Actaea (ACT) indel marker will be useful for the authentication of the herbal medicine.
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Affiliation(s)
| | | | | | - Byeong Cheol Moon
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Korea; (I.P.); (J.-H.S.); (S.Y.)
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Xia HM, Dai YP, Sun LL. [Research progress on cycloartane triterpenoids of Actaea]. Zhongguo Zhong Yao Za Zhi 2018; 43:4000-4010. [PMID: 30486523 DOI: 10.19540/j.cnki.cjcmm.20180703.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Indexed: 11/18/2022]
Abstract
The genus Actaea plants are widely distributed in China, and the cycloartane triterpenoids are the characteristic constituents of this genus. They are divided into types of cimigenol, hydroshengmanol, shengmanol, cimiacerogenin, acteol, 16, 23-diketo, foetidonol, dahurinol, etc. Cycloartane triterpenoids show many biological activities, such as cytotoxicity, anti-osteoporosis, antiviral, anti-inflammatory, anti-nucleoside transport, neuroprotective, anti-oxidant, antibacterial activities. The present paper reviewed the distribution of the plant resources of Actaea, chemical structures and biological activities of cycloartane triterpenoids, aiming to provide a reference for the further research in the future.
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Affiliation(s)
- Hong-Min Xia
- Taishan Scholar-Distinguished Experts Position, Key Disciplines on Analysis of Traditional Chinese Medicine, the Key Unit for Research of Technique and Principle of Honey-processing and Carbonizing of SATCM, Shandong Key Laboratory of Chinese Medicine Quality Standard Research, Shandong Academy of Chinese Medicine, Ji'nan 250014, China
| | - Yan-Peng Dai
- Taishan Scholar-Distinguished Experts Position, Key Disciplines on Analysis of Traditional Chinese Medicine, the Key Unit for Research of Technique and Principle of Honey-processing and Carbonizing of SATCM, Shandong Key Laboratory of Chinese Medicine Quality Standard Research, Shandong Academy of Chinese Medicine, Ji'nan 250014, China
| | - Li-Li Sun
- Taishan Scholar-Distinguished Experts Position, Key Disciplines on Analysis of Traditional Chinese Medicine, the Key Unit for Research of Technique and Principle of Honey-processing and Carbonizing of SATCM, Shandong Key Laboratory of Chinese Medicine Quality Standard Research, Shandong Academy of Chinese Medicine, Ji'nan 250014, China
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