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Xie DF, Li J, Sun JH, Cheng RY, Wang Y, Song BN, He XJ, Zhou SD. Peering through the hedge: Multiple datasets yield insights into the phylogenetic relationships and incongruences in the tribe Lilieae (Liliaceae). Mol Phylogenet Evol 2024; 200:108182. [PMID: 39222738 DOI: 10.1016/j.ympev.2024.108182] [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: 11/09/2023] [Revised: 08/06/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
The increasing use of genome-scale data has significantly facilitated phylogenetic analyses, contributing to the dissection of the underlying evolutionary mechanisms that shape phylogenetic incongruences, such as incomplete lineage sorting (ILS) and hybridization. Lilieae, a prominent member of the Liliaceae family, comprises four genera and approximately 260 species, representing 43% of all species within Liliaceae. They possess high ornamental, medicinal and edible values. Yet, no study has explored the validity of various genome-scale data in phylogenetic analyses within this tribe, nor have potential evolutionary mechanisms underlying its phylogenetic incongruences been investigated. Here, transcriptome, Angiosperms353, plastid and mitochondrial data, were collected from 50 to 93 samples of Lilieae, covering all four recognized genera. Multiple datasets were created and used for phylogenetic analyses based on concatenated and coalescent-based methods. Evolutionary rates of different datasets were calculated, and divergence times were estimated. Various approaches, including coalescence simulation, Quartet Sampling (QS), calculation of concordance factors (gCF and sCF), as well as MSCquartets and reticulate network inference, were carried out to infer the phylogenetic discordances and analyze their underlying mechanisms using a reduced 33-taxon dataset. Despite extensive phylogenetic discordances among gene trees, robust phylogenies were inferred from nuclear and plastid data compared to mitochondrial data, with lower synonymous substitution detected in mitochondrial genes than in nuclear and plastid genes. Significant ILS was detected across the phylogeny of Lilieae, with clear evidence of reticulate evolution identified. Divergence time estimation indicated that most of lineages in Lilieae diverged during a narrow time frame (ranging from 5.0 Ma to 10.0 Ma), consistent with the notion of rapid radiation evolution. Our results suggest that integrating transcriptomic and plastid data can serve as cost-effective and efficient tools for phylogenetic inference and evolutionary analysis within Lilieae, and Angiosperms353 data is also a favorable choice. Mitochondrial data are more suitable for phylogenetic analyses at higher taxonomic levels due to their stronger conservation and lower synonymous substitution rates. Significant phylogenetic incongruences detected in Lilieae were caused by both incomplete lineage sorting (ILS) and reticulate evolution, with hybridization and "ghost introgression" likely prevalent in the evolution of Lilieae species. Our findings provide new insights into the phylogeny of Lilieae, enhancing our understanding of the evolution of species in this tribe.
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Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, PR China.
| | - Juan Li
- Southwest Minzu University, Institute Of Qinghai-Tibetan Plateau, 610225 Chengdu, Sichuan, PR China
| | - Jia-Hui Sun
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, PR China
| | - Rui-Yu Cheng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, PR China
| | - Yuan Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, PR China
| | - Bo-Ni Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, PR China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, PR China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, PR China.
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Lan ZQ, Zheng W, Talavera A, Nie ZL, Liu J, Johnson G, Yin XM, Zhao WQ, Zhao ZY, Handy SM, Wen J. Comparative and phylogenetic analyses of plastid genomes of the medicinally important genus Alisma (Alismataceae). FRONTIERS IN PLANT SCIENCE 2024; 15:1415253. [PMID: 39233910 PMCID: PMC11372848 DOI: 10.3389/fpls.2024.1415253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
Alisma L. is a medicinally important genus of aquatic and wetland plants consisting of c. 10 recognized species. However, largely due to polyploidy and limited taxon and gene sampling, the phylogenomic relationships of Alisma remain challenging. In this study, we sequenced 34 accessions of Alismataceae, including eight of the ten species of Alisma, one species of Echinodorus and one species of Luronium, to perform comparative analyses of plastid genomes and phylogenetic analyses. Comparative analysis of plastid genomes revealed high sequence similarity among species within the genus. Our study analyzed structural changes and variations in the plastomes of Alisma, including IR expansion or contraction, and gene duplication or loss. Phylogenetic results suggest that Alisma is monophyletic, and constitutes four groups: (1) A. lanceolatum and A. canaliculatum; (2) the North American clade of A. subcordatum and A. triviale; (3) A. wahlenbergii and A. gramineum; and (4) A. plantago-aquatica from Eurasia and northern Africa with the eastern Asian A. orientale nested within it. Hence the results challenge the recognition of A. orientale as a distinct species and raise the possibility of treating it as a synonym of the widespread A. plantago-aquatica. The well-known Alismatis Rhizoma (Zexie) in Chinese medicine was likely derived from the morphologically variable Alisma plantago-aquatica throughout its long history of cultivation in Asia. The plastome phylogenetic results also support the tetraploid A. lanceolatum as the likely maternal parent of the hexaploid eastern Asian A. canaliculatum.
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Affiliation(s)
- Zhi-Qiong Lan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy/College of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Wen Zheng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy/College of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Alicia Talavera
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Málaga, Spain
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Jing Liu
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Xian-Mei Yin
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy/College of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wen-Qi Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy/College of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zong-Yi Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy/College of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, United States
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
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Herrera F, Carvalho MR, Stull GW, Jaramillo C, Manchester SR. Cenozoic seeds of Vitaceae reveal a deep history of extinction and dispersal in the Neotropics. NATURE PLANTS 2024; 10:1091-1099. [PMID: 38951689 DOI: 10.1038/s41477-024-01717-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 05/01/2024] [Indexed: 07/03/2024]
Abstract
The remarkably diverse plant communities of the Neotropics are the result of diversification driven by multiple biotic (for example, speciation, extinction and dispersal) and abiotic (for example, climatic and tectonic) processes. However, in the absence of a well-preserved, thoroughly sampled and critically assessed fossil record, the associated processes of dispersal and extinction are poorly understood. We report an exceptional case study documenting patterns of extinction in the grape family (Vitaceae Juss.) on the basis of fossil seeds discovered in four Neotropical palaeofloras dated between 60 and 19 Ma. These include a new species that provides the earliest evidence of Vitaceae in the Western Hemisphere. Eight additional species reveal the former presence of major clades of the family that are currently absent from the Neotropics and elucidate previously unknown dispersal events. Our results indicate that regional extinction and dispersal have substantially impacted the evolutionary history of Vitaceae in the Neotropics. They also suggest that while the Neotropics have been dynamic centres of diversification through the Cenozoic, extant Neotropical botanical diversity has also been shaped by extensive extinction over the past 66 million years.
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Affiliation(s)
- Fabiany Herrera
- Earth Sciences, Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA.
| | - Mónica R Carvalho
- Museum of Paleontology and Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Gregory W Stull
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- National Identification Services, USDA-APHIS-PPQ, Beltsville, MD, USA
| | - Carlos Jaramillo
- Smithsonian Tropical Research Institute, Ancón, Republic of Panama
| | - Steven R Manchester
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
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You Y, Yu J, Nie Z, Peng D, Barrett RL, Rabarijaona RN, Lai Y, Zhao Y, Dang VC, Chen Y, Chen Z, Wen J, Lu L. Transition of survival strategies under global climate shifts in the grape family. NATURE PLANTS 2024; 10:1100-1111. [PMID: 39009829 DOI: 10.1038/s41477-024-01726-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 05/09/2024] [Indexed: 07/17/2024]
Abstract
Faced with environmental changes, plants may either move to track their ancestral niches or evolve to adapt to new niches. Vitaceae, the grape family, has evolved diverse adaptive traits facilitating a global expansion in wide-ranging habitats, making it ideal for investigating transition between move and evolve strategies and exploring the underlying mechanisms. Here we inferred the patterns of biogeographic diversification and trait evolution in Vitaceae based on a robust phylogeny with dense sampling including 495 species (~52% of Vitaceae species). Vitaceae probably originated from Asia-the diversity centre of extant genera and the major source of dispersals. Boundaries of the Eocene, Oligocene and Miocene were identified as turning points in shifting strategies. A significant decrease in move strategy was identified during the Oligocene, followed by increases in move and evolve. After the Miocene, evolve began to dominate, during which increased niche opportunities and key trait innovations played important roles.
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Affiliation(s)
- Yichen You
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinren Yu
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zelong Nie
- Hunan Provincial Key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources and Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Danxiao Peng
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Russell L Barrett
- Botanic Gardens of Sydney, National Herbarium of New South Wales, Australian Botanic Garden, Sydney, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Romer Narindra Rabarijaona
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Yangjun Lai
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Yujie Zhao
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Viet-Cuong Dang
- University of Medicine and Pharmacy, Vietnam National University, Hanoi, Vietnam
| | - Youhua Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhiduan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- China National Botanical Garden, Beijing, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
| | - Limin Lu
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- China National Botanical Garden, Beijing, China.
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Morales-Saldaña S, Hipp AL, Valencia-Ávalos S, Hahn M, González-Elizondo MS, Gernandt DS, Pham KK, Oyama K, González-Rodríguez A. Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae). ANNALS OF BOTANY 2024; 133:1007-1024. [PMID: 38428030 PMCID: PMC11089265 DOI: 10.1093/aob/mcae030] [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: 11/07/2023] [Accepted: 02/28/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND AND AIMS Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico. METHODS Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages. KEY RESULTS The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages. CONCLUSIONS The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.
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Affiliation(s)
- Saddan Morales-Saldaña
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
| | - Andrew L Hipp
- The Morton Arboretum, Lisle, IL 60532-1293, USA
- The Field Museum, Chicago, IL 60605, USA
| | - Susana Valencia-Ávalos
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, México
| | | | | | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, México
| | - Kasey K Pham
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex‐Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
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Zhang L, Meng Y, Wang D, He GH, Zhang JM, Wen J, Nie ZL. Plastid genome data provide new insights into the dynamic evolution of the tribe Ampelopsideae (Vitaceae). BMC Genomics 2024; 25:247. [PMID: 38443830 PMCID: PMC10916268 DOI: 10.1186/s12864-024-10149-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Ampelopsideae J. Wen & Z.L. Nie is a small-sized tribe of Vitaceae Juss., including ca. 47 species from four genera showing a disjunct distribution worldwide across all the continents except Antarctica. There are numerous species from the tribe that are commonly used as medicinal plants with immune-modulating, antimicrobial, and anti-hypertensive properties. The tribe is usually recognized into three clades, i.e., Ampelopsis Michx., Nekemias Raf., and the Southern Hemisphere clade. However, the relationships of the three clades differ greatly between the nuclear and the plastid topologies. There has been limited exploration of the chloroplast phylogenetic relationships within Ampelopsideae, and studies on the chloroplast genome structure of this tribe are only available for a few individuals. In this study, we aimed to investigate the evolutionary characteristics of plastid genomes of the tribe, including their genome structure and evolutionary insights. RESULTS We sequenced, assembled, and annotated plastid genomes of 36 species from the tribe and related taxa in the family. Three main clades were recognized within Ampelopsideae, corresponding to Ampelopsis, Nekemias, and the Southern Hemisphere lineage, respectively, and all with 100% bootstrap supports. The genome sequences and content of the tribe are highly conserved. However, comparative analyses suggested that the plastomes of Nekemias demonstrate a contraction in the large single copy region and an expansion in the inverted repeat region, and possess a high number of forward and palindromic repeat sequences distinct from both Ampelopsis and the Southern Hemisphere taxa. CONCLUSIONS Our results highlighted plastome variations in genome length, expansion or contraction of the inverted repeat region, codon usage bias, and repeat sequences, are corresponding to the three lineages of the tribe, which probably faced with different environmental selection pressures and evolutionary history. This study provides valuable insights into understanding the evolutionary patterns of plastid genomes within the Ampelopsideae of Vitaceae.
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Affiliation(s)
- Lei Zhang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Ying Meng
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Da Wang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Guan-Hao He
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Jun-Ming Zhang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, 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
| | - Ze-Long Nie
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China.
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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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He GH, Zhang L, Meng Y, Wen J, Nie ZL. The complete chloroplast genome of Nekemias hypoglauca (Hance) J. Wen & Z. L. Nie 2014 (Family: Vitaceae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:272-276. [PMID: 38352189 PMCID: PMC10863506 DOI: 10.1080/23802359.2024.2316071] [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: 06/02/2023] [Accepted: 02/04/2024] [Indexed: 02/16/2024] Open
Abstract
Nekemias is a perennial woody vine with nine species that had been originally placed in Ampelopsis. These species of Nekemias are economically and medically important. Limited information is available on the genomic characteristics of the chloroplasts of this genus. Nekemias hypoglauca (Hance) J. Wen & Z. L. Nie 2014 contains 131 unique genes (86 protein-coding genes, 8 rRNAs, and 37 tRNAs). The complete chloroplast sequence contains 162,976 bp. The large single-copy region contains 89,291 bp; the small single-copy region contains 19,063 bp, and a pair of inverted repeat sequences is composed of 27,311 bp. There are 84 simple sequence repeat (SSR) loci in the complete chloroplast genome of N. hypoglauca, with mononucleotide, dinucleotide, trinucleotide, tetranucleotide and hexanucleotide SSRs of 58, 9, 6, 10 and 1, respectively. A total of 337 repeats were identified, including 172 forward repeats, three reverse repeats and 163 palindromic repeats. A phylogenetic analysis based on the complete genome data of the chloroplasts of 10 plant species indicated the monophyly of Nekemias and determined the phylogenetic relationships of N. hypoglauca in Nekemias. This study provides a reference for further studies on the taxonomy, identification, origin and evolution of N. hypoglauca and Nekemias.
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Affiliation(s)
- Guan-Hao He
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Lei Zhang
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ying Meng
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Ze-Long Nie
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
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Kohut L, Baldovska S, Mihal M, Belej L, Sirotkin AV, Roychoudhury S, Kolesarova A. The multiple actions of grape and its polyphenols on female reproductive processes with an emphasis on cell signalling. Front Endocrinol (Lausanne) 2024; 14:1245512. [PMID: 38239977 PMCID: PMC10794324 DOI: 10.3389/fendo.2023.1245512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
Grapes are an economically important fruit crop, and their polyphenols (mainly phenolic acids, flavanols, flavonols, anthocyanins, proanthocyanidins, and stilbenes) can exert a wide range of health benefits as an interesting and valuable dietary supplement for natural complementary therapy. However, their potential physiological and therapeutic actions on reproductive processes have not been sufficiently elucidated. This evidence-based study presents current knowledge of grape extracts and polyphenols, as well as their properties and therapeutical actions in relation to female reproduction in a nutshell. Grape extract, and its polyphenols such as resveratrol, proanthocyanidin B2 or delphinidin may influence female reproductive physiology and pathology, as well as regulate multiple signaling pathways related to reproductive hormones, steroid hormones receptors, intracellular regulators of oxidative stress and subsequent inflammation, apoptosis, and proliferation. Their role in the management of ovarian cancer, age-related reproductive insufficiency, ovarian ischemia, PCOS, or menopausal syndrome has been indicated. In particular, the potential involvement of grapeseed extracts and/or proanthocyanidin B2 and delphinidin on ovarian steroidogenesis, oocyte maturation, and developmental capacity has been implicated, albeit at different regulatory levels. Grape polyphenols exert a wide range of health benefits posing grape extract as an interesting and valuable dietary supplement for natural complementary therapy. This evidence-based study focuses on the actions of grapeseed extract and grape polyphenols on female reproductive processes at various regulatory levels and multiple signalling pathways by regulating reproductive hormones (GnRH, gonadotropins, prolactin, steroid hormones, IGFBP), steroid receptors, markers of proliferation and apoptosis. However, lack of knowledge of standardized dosages so far limits their clinical application despite the wide range of their biological and therapeutic potentials.
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Affiliation(s)
- Ladislav Kohut
- Institute of Applied Biology, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Simona Baldovska
- AgroBioTech Research Center, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Michal Mihal
- Institute of Applied Biology, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Lubomir Belej
- Institute of Food Sciences, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Alexander V. Sirotkin
- Department of Zoology and Anthropology, Constantine the Philosopher University, Nitra, Slovakia
| | | | - Adriana Kolesarova
- Institute of Applied Biology, Slovak University of Agriculture in Nitra, Nitra, Slovakia
- AgroBioTech Research Center, Slovak University of Agriculture in Nitra, Nitra, Slovakia
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10
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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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11
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Talavera A, Nie ZL, Ma ZY, Johnson G, Ickert-Bond SM, Zimmer EA, Wen J. Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis. Mol Phylogenet Evol 2023:107866. [PMID: 37354923 DOI: 10.1016/j.ympev.2023.107866] [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: 02/10/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
A set of newly designed Vitaceae baits targeting 1013 genes was employed to explore phylogenetic relationships among North American Vitis. Eurasian Vitis taxa including Vitis vinifera were found to be nested within North American Vitis subgenus Vitis. North American Vitis subgenus Vitis can be placed into nine main groups: the Monticola group, the Occidentales group, the Californica group, the Vinifera group (introduced from Eurasia), the Mustangensis group, the Palmata group, the Aestivalis group, the Labrusca group, and the Cinerea group. Strong cytonuclear discordances were detected in North American Vitis, with many species non-monophyletic in the plastid phylogeny, while monophyletic in the nuclear phylogeny. The phylogenomic analyses support recognizing four distinct species in the Vitis cinerea complex in North America: V. cinerea, V. baileyana, V. berlandieri, and V. simpsonii. Such treatment will better serve the conservation of wild Vitis diversity in North America. Yet the evolutionary history of Vitis is highly complex, with the concordance analyses indicating conflicting signals across the phylogeny. Cytonuclear discordances and Analyses using the Species Networks applying Quartets (SNaQ) method support extensive hybridizations in North American Vitis. The results further indicate that plastid genomes alone are insufficient for resolving the evolutionary history of plant groups that have undergone rampant hybridization, like the case in North American Vitis. Nuclear gene data are essential for species delimitation, identification and reconstructing evolutionary relationships; therefore, they are imperative for plant phylogenomic studies.
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Affiliation(s)
- Alicia Talavera
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA; Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, 29071, Málaga, Spain.
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou 416000, China
| | - Zhi-Yao Ma
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518000 China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Stefanie M Ickert-Bond
- UA Museum of the North Herbarium and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775-6960, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA.
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12
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Nie ZL, Hodel R, Ma ZY, Johnson G, Ren C, Meng Y, Ickert-Bond SM, Liu XQ, Zimmer E, Wen J. Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1183-1203. [PMID: 36772845 DOI: 10.1111/jipb.13466] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 02/08/2023] [Indexed: 05/13/2023]
Abstract
The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene.
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Affiliation(s)
- Ze-Long Nie
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China
| | - Richard Hodel
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Zhi-Yao Ma
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Ying Meng
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China
| | - Stefanie M Ickert-Bond
- Herbarium (ALA), University of Alaska Museum of the North, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Xiu-Qun Liu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Elizabeth Zimmer
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
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13
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Yu J, Niu Y, You Y, Cox CJ, Barrett RL, Trias-Blasi A, Guo J, Wen J, Lu L, Chen Z. Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan-Hengduan Mountains. THE NEW PHYTOLOGIST 2023; 238:888-903. [PMID: 36305244 DOI: 10.1111/nph.18580] [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: 08/09/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Hybridization caused by frequent environmental changes can lead both to species diversification (speciation) and to speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus, a genus with its trifoliolate lineage in the Himalayan-Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating speciation dynamics based on integrated evidence. We investigated phylogenetic discordance and reticulate evolution in Parthenocissus based on rigorous analyses of plastome and transcriptome data. We focused on reticulations in the trifoliolate lineage in the HHM region using a population-level genome resequencing dataset, incorporating evidence from morphology, distribution, and elevation. Comprehensive analyses confirmed multiple introgressions within Parthenocissus in a robust temporal-spatial framework. Around the HHM region, at least three hybridization hot spots were identified, one of which showed evidence of ongoing speciation reversal. We present a solid case study using an integrative methodological approach to investigate reticulate evolutionary history and its underlying mechanisms in plants. It demonstrates an example of speciation reversal through frequent hybridizations in the HHM region, which provides new perspectives on speciation dynamics in mountainous areas with strong topographic and environmental heterogeneity.
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Affiliation(s)
- Jinren Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanting Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yichen You
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-319, Portugal
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, 2567, NSW, Australia
| | | | - Jing Guo
- 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
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Limin Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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14
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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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15
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Talebi M, Esmaeeli H, İlgün S, Talebi M, Farkhondeh T, Mishra G, Samarghandian S. The Protective Role of Grape Seed in Obesity and Lipid Profile: An Updated Narrative Overview of Preclinical and Clinical Studies. Endocr Metab Immune Disord Drug Targets 2023; 23:46-62. [PMID: 35786197 DOI: 10.2174/1871530322666220630091859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 04/29/2022] [Accepted: 05/06/2022] [Indexed: 11/22/2022]
Abstract
Obesity and dyslipidemia are common disorders universally. According to the acquired outcomes of recent studies, dietary supplementations which have great content of phenolic compounds exert protective effects against obesity and dyslipidemia. Grape [Vitis vinifera] seeds are considered attractive sources of phenolic compounds with anti-oxidative stress and anti-inflammatory effects. There are also various experimental studies describing hepatoprotective, neuroprotective, anti-aging, cardioprotective, and anti-carcinogenic effects of polyphenols isolated from grape seed, highlighting the therapeutic and biological aspects of proanthocyanidins. The present review article first discusses pharmacological, botanical, toxicological, and phytochemical characteristics of Vitis vinifera seeds and afterward designates the protective properties which are attributed to the intake of grape seeds in obesity and hyperlipidemia. Overall valuable and updated findings of this study display that polyphenol of grape seeds has meaningful impacts on the regulation of lipid profile levels and management of obesity.
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Affiliation(s)
- Marjan Talebi
- Department of Pharmacognosy, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, 1991953381, Iran
| | - Hadi Esmaeeli
- Research and Development Unit, NIAK Pharmaceutical Company, Gorgan, Iran.,Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Selen İlgün
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Erciyes University, Kayseri, 38039, Turkey
| | - Mohsen Talebi
- Viatris Pharmaceuticals Inc., 3300 Research Plaza, San Antonio, Texas, United States.,Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX, 76019, United States
| | - Tahereh Farkhondeh
- Department of Toxicology and Pharmacology, School of Pharmacy, Birjand University of Medical Sciences, Birjand, Iran
| | - Gaurav Mishra
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Saeed Samarghandian
- Healthy Ageing Research Centre, Neyshabur University of Medical Sciences, Neyshabur, Iran
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16
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Brillouet JM, Romieu C, Bacilieri R, Nick P, Trias-Blasi A, Maul E, Solymosi K, Teszlák P, Jiang JF, Sun L, Ortolani D, Londo JP, Gutierrez B, Prins B, Reynders M, Van Caekenberghe F, Maghradze D, Marchal C, Sultan A, Thomas JF, Scherberich D, Fulcrand H, Roumeas L, Billerach G, Salimov V, Musayev M, Ejaz Ul Islam Dar M, Peltier JB, Grisoni M. Tannin phenotyping of the Vitaceae reveals a phylogenetic linkage of epigallocatechin in berries and leaves. ANNALS OF BOTANY 2022; 130:159-171. [PMID: 35700109 PMCID: PMC9445598 DOI: 10.1093/aob/mcac077] [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: 12/04/2021] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Condensed tannins, responsible for berry and wine astringency, may have been selected during grapevine domestication. This work examines the phylogenetic distribution of condensed tannins throughout the Vitaceae phylogenetic tree. METHODS Green berries and mature leaves of representative true-to-type members of the Vitaceae were collected before 'véraison', freeze-dried and pulverized, and condensed tannins were measured following depolymerization by nucleophilic addition of 2-mercaptoethanol to the C4 of the flavan-3-ol units in an organic acidic medium. Reaction products were separated and quantified by ultrahigh pressure liquid chromatography/diode array detection/mass spectrometry. KEY RESULTS AND CONCLUSIONS The original ability to incorporate epigallocatechin (EGC) into grapevine condensed tannins was lost independently in both the American and Eurasian/Asian branches of the Vitaceae, with exceptional cases of reversion to the ancestral EGC phenotype. This is particularly true in the genus Vitis, where we now find two radically distinct groups differing with respect to EGC content. While Vitis species from Asia are void of EGC, 50 % of the New World Vitis harbour EGC. Interestingly, the presence of EGC is tightly coupled with the degree of leaf margin serration. Noticeably, the rare Asian EGC-forming species are phylogenetically close to Vitis vinifera, the only remnant representative of Vitis in Eurasia. Both the wild ancestral V. vinifera subsp. sylvestris as well as the domesticated V. vinifera subsp. sativa can accumulate EGC and activate galloylation biosynthesis that compete for photoassimilates and reductive power.
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Affiliation(s)
| | | | - Roberto Bacilieri
- INRA, Equipe DAAV, UMR AGAP (Univ. Montpellier, CIRAD, INRAE, SupAgro), Montpellier, France
| | - Peter Nick
- Karlsruhe Institute of Technology, Botanical Institute, Molecular Cell Biology, Karlsruhe, Germany
| | | | - Erika Maul
- Julius Kühn-Institut (JKI), Institut für Rebenzüchtung Geilweilerhof, Siebeldingen, Germany
| | - Katalin Solymosi
- Department of Plant Anatomy, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Peter Teszlák
- Department of Viticulture and Technology Development, Research Institute of Viticulture and Oenology, University of Pécs, Pécs, Hungary
| | - Jiang-Fu Jiang
- Zhengzhou Fruit Research Institute, Zhengzhou, Henan, PR China
| | - Lei Sun
- Zhengzhou Fruit Research Institute, Zhengzhou, Henan, PR China
| | | | - Jason P Londo
- USDA, Grape Genetics Research Unit, Agricultural Research Service, Geneva, New York, NY, USA
| | - Ben Gutierrez
- USDA, Plant Genetic Resources Unit, Agricultural Research Service, Geneva, New York, NY, USA
| | - Bernard Prins
- USDA, Nat’l Clonal Germplasm Rep – Tree Fruit & Nut Crops & Grapes, University of California, Davis, California, USA
| | | | | | | | - Cecile Marchal
- INRA, Grapevine Biological Resources Center, Experimental Unit of Domaine de Vassal, Marseillan-plage, France
| | - Amir Sultan
- National Herbarium (Stewart Collection), National Agricultural Research Centre, Islamabad, Pakistan
| | | | | | | | | | | | - Vugar Salimov
- Azerbaijani Scientific Research Institute of Viticulture and Winemaking, Baku, Azerbaijan
| | - Mirza Musayev
- Genetic Resources Institute of the Azerbaijan National Academy of Sciences, Baku, Azerbaijan
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17
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Coca‐de‐la‐Iglesia M, Medina NG, Wen J, Valcárcel V. Evaluation of tropical-temperate transitions: An example of climatic characterization in the Asian Palmate group of Araliaceae. AMERICAN JOURNAL OF BOTANY 2022; 109:1488-1507. [PMID: 36039662 PMCID: PMC9826302 DOI: 10.1002/ajb2.16059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
PREMISE There has been a great increase in using climatic data in phylogenetic studies over the past decades. However, compiling the high-quality spatial data needed to perform accurate climatic reconstructions is time-consuming and can result in poor geographical coverage. Therefore, researchers often resort to qualitative approximations. Our aim was to evaluate the climatic characterization of the genera of the Asian Palmate Group (AsPG) of Araliaceae as an exemplar lineage of plants showing tropical-temperate transitions. METHODS We compiled a curated worldwide spatial database of the AsPG genera and created five raster layers representing bioclimatic regionalizations of the world. Then, we crossed the database with the layers to climatically characterize the AsPG genera. RESULTS We found large disagreement in the climatic characterization of genera among regionalizations and little support for the climatic nature of the tropical-temperate distribution of the AsPG. Both results are attributed to the complexity of delimiting tropical, subtropical, and temperate climates in the world and to the distribution of the study group in regions with transitional climatic conditions. CONCLUSIONS The complexity in the climatic classification of this example of the tropical-temperate transitions calls for a general climatic revision of other tropical-temperate lineages. In fact, we argue that, to properly evaluate tropical-temperate transitions across the tree of life, we cannot ignore the complexity of distribution ranges.
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Affiliation(s)
| | - Nagore G. Medina
- Departamento de BiologíaUniversidad Autónoma de MadridMadrid28049Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadrid28049Spain
| | - Jun Wen
- Department of Botany/MRC 166Smithsonian InstitutionWashington, DCUSA
| | - Virginia Valcárcel
- Departamento de BiologíaUniversidad Autónoma de MadridMadrid28049Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadrid28049Spain
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18
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Dong S, Zhou M, Zhu J, Wang Q, Ge Y, Cheng R. The complete chloroplast genomes of Tetrastigma hemsleyanum (Vitaceae) from different regions of China: molecular structure, comparative analysis and development of DNA barcodes for its geographical origin discrimination. BMC Genomics 2022; 23:620. [PMID: 36028808 PMCID: PMC9412808 DOI: 10.1186/s12864-022-08755-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tetrastigma hemsleyanum is a valuable traditional Chinese medicinal plant widely distributed in the subtropical areas of China. It belongs to the Cayratieae tribe, family Vitaceae, and exhibited significant anti-tumor and anti-inflammatory activities. However, obvious differences were observed on the quality of T. hemsleyanum root from different regions, requiring the discrimination strategy for the geographical origins. RESULT This study characterized five complete chloroplast (cp) genomes of T. hemsleynum samples from different regions, and conducted a comparative analysis with other representing species from family Vitaceae to reveal the structural variations, informative markers and phylogenetic relationships. The sequenced cp genomes of T. hemsleyanum exhibited a conserved quadripartite structure with full length ranging from 160,124 bp of Jiangxi Province to 160,618 bp of Zhejiang Province. We identified 112 unique genes (80 protein-coding, 28 tRNA and 4 rRNA genes) in the cp genomes of T. hemsleyanum with highly similar gene order, content and structure. The IR contraction/expansion events occurred on the junctions of ycf1, rps19 and rpl2 genes with different degrees, causing the differences of genome sizes in T. hemsleyanum and Vitaceae plants. The number of SSR markers discovered in T. hemsleyanum was 56-57, exhibiting multiple differences among the five geographic groups. Phylogenetic analysis based on conserved cp genome proteins strongly grouped the five T. hemsleyanum species into one clade, showing a sister relationship with T. planicaule. Comparative analysis of the cp genomes from T. hemsleyanum and Vitaceae revealed five highly variable spacers, including 4 intergenic regions and one protein-coding gene (ycf1). Furthermore, five mutational hotspots were observed among T. hemsleyanum cp genomes from different regions, providing data for designing DNA barcodes trnL and trnN. The combination of molecular markers of trnL and trnN clustered the T. hemsleyanum samples from different regions into four groups, thus successfully separating specimens of Sichuan and Zhejiang from other areas. CONCLUSION Our study obtained the chloroplast genomes of T. hemsleyanum from different regions, and provided a potential molecular tracing tool for determining the geographical origins of T. hemsleyanum, as well as important insights into the molecular identification approach and and phylogeny in Tetrastigma genus and Vitaceae family.
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Affiliation(s)
- Shujie Dong
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.,School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Manjia Zhou
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jinxing Zhu
- Bureau of Agricultural and Rural Affairs of Suichang, Suichang, China
| | - Qirui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China. .,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China.
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Dong W, Li E, Liu Y, Xu C, Wang Y, Liu K, Cui X, Sun J, Suo Z, Zhang Z, Wen J, Zhou S. Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family. BMC Biol 2022; 20:92. [PMID: 35468824 PMCID: PMC9040247 DOI: 10.1186/s12915-022-01297-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/13/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Deep-branching phylogenetic relationships are often difficult to resolve because phylogenetic signals are obscured by the long history and complexity of evolutionary processes, such as ancient introgression/hybridization, polyploidization, and incomplete lineage sorting (ILS). Phylogenomics has been effective in providing information for resolving both deep- and shallow-scale relationships across all branches of the tree of life. The olive family (Oleaceae) is composed of 25 genera classified into five tribes with tribe Oleeae consisting of four subtribes. Previous phylogenetic analyses showed that ILS and/or hybridization led to phylogenetic incongruence in the family. It was essential to distinguish phylogenetic signal conflicts, and explore mechanisms for the uncertainties concerning relationships of the olive family, especially at the deep-branching nodes. RESULTS We used the whole plastid genome and nuclear single nucleotide polymorphism (SNP) data to infer the phylogenetic relationships and to assess the variation and rates among the main clades of the olive family. We also used 2608 and 1865 orthologous nuclear genes to infer the deep-branching relationships among tribes of Oleaceae and subtribes of tribe Oleeae, respectively. Concatenated and coalescence trees based on the plastid genome, nuclear SNPs and multiple nuclear genes suggest events of ILS and/or ancient introgression during the diversification of Oleaceae. Additionally, there was extreme heterogeneity in the substitution rates across the tribes. Furthermore, our results supported that introgression/hybridization, rather than ILS, is the main factor for phylogenetic discordance among the five tribes of Oleaceae. The tribe Oleeae is supported to have originated via ancient hybridization and polyploidy, and its most likely parentages are the ancestral lineage of Jasmineae or its sister group, which is a "ghost lineage," and Forsythieae. However, ILS and ancient introgression are mainly responsible for the phylogenetic discordance among the four subtribes of tribe Oleeae. CONCLUSIONS This study showcases that using multiple sequence datasets (plastid genomes, nuclear SNPs and thousands of nuclear genes) and diverse phylogenomic methods such as data partition, heterogeneous models, quantifying introgression via branch lengths (QuIBL) analysis, and species network analysis can facilitate untangling long and complex evolutionary processes of ancient introgression, paleopolyploidization, and ILS.
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Affiliation(s)
- Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yushuang Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Xingyong Cui
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Zhili Suo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA.
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Xia MZ, Li Y, Zhang FQ, Yu JY, Khan G, Chi XF, Xu H, Chen SL. Reassessment of the Phylogeny and Systematics of Chinese Parnassia (Celastraceae): A Thorough Investigation Using Whole Plastomes and Nuclear Ribosomal DNA. FRONTIERS IN PLANT SCIENCE 2022; 13:855944. [PMID: 35371115 PMCID: PMC8971841 DOI: 10.3389/fpls.2022.855944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Parnassia L., a perennial herbaceous genus in the family Celastraceae, consists of about 60 species and is mainly distributed in the Pan-Himalayan and surrounding mountainous regions. The taxonomic position and phylogenetic relationships of the genus are still controversial. Herein, we reassessed the taxonomic status of Parnassia and its intra- and inter-generic phylogeny within Celastraceae. To that end, we sequenced and assembled the whole plastid genomes and nuclear ribosomal DNA (nrDNA) of 48 species (74 individuals), including 25 species of Parnassia and 23 species from other genera of Celastraceae. We integrated high throughput sequence data with advanced statistical toolkits and performed the analyses. Our results supported the Angiosperm Phylogeny Group IV (APG IV) taxonomy which kept the genus to the family Celastraceae. Although there were topological conflicts between plastid and nrDNA phylogenetic trees, Parnassia was fully supported as a monophyletic group in all cases. We presented a first attempt to estimate the divergence of Parnassia, and molecular clock analysis indicated that the diversification occurred during the Eocene. The molecular phylogenetic results confirmed numerous taxonomic revisions, revealing that the morphological characters used in Parnassia taxonomy and systematics might have evolved multiple times. In addition, we speculated that hybridization/introgression might exist during genus evolution, which needs to be further studied. Similarly, more in-depth studies will clarify the diversification of characters and species evolution models of this genus.
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Affiliation(s)
- Ming-Ze Xia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- School of Pharmacy, Weifang Medical University, Weifang, China
| | - Fa-Qi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
| | - Jing-Ya Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Xiao-Feng Chi
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
| | - Hao Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
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Waghole RJ, Misar AV, Kulkarni NS, Khan F, Naik DG, Jadhav SH. In vitro and in vivo anti-inflammatory activity of Tetrastigma sulcatum leaf extract, pure compound and its derivatives. Inflammopharmacology 2022; 30:291-311. [DOI: 10.1007/s10787-021-00897-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/14/2021] [Indexed: 12/19/2022]
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22
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Onyenedum JG, Pace MR. The role of ontogeny in wood diversity and evolution. AMERICAN JOURNAL OF BOTANY 2021; 108:2331-2355. [PMID: 34761812 DOI: 10.1002/ajb2.1801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Evolutionary developmental biology (evo-devo) explores the link between developmental patterning and phenotypic change through evolutionary time. In this review, we highlight the scientific advancements in understanding xylem evolution afforded by the evo-devo approach, opportunities for further engagement, and future research directions for the field. We review evidence that (1) heterochrony-the change in rate and timing of developmental events, (2) homeosis-the ontogenetic replacement of features, (3) heterometry-the change in quantity of a feature, (4) exaptation-the co-opting and repurposing of an ancestral feature, (5) the interplay between developmental and capacity constraints, and (6) novelty-the emergence of a novel feature, have all contributed to generating the diversity of woods. We present opportunities for future research engagement, which combine wood ontogeny within the context of robust phylogenetic hypotheses, and molecular biology.
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Affiliation(s)
- Joyce G Onyenedum
- School of Integrative Plant Sciences and L. H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Marcelo R Pace
- Department of Botany, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n de Ciudad Universitaria, Mexico City, 04510, Mexico
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Reichelt N, Wen J, Pätzold C, Appelhans MS. Target enrichment improves phylogenetic resolution in the genus Zanthoxylum (Rutaceae) and indicates both incomplete lineage sorting and hybridization events. ANNALS OF BOTANY 2021; 128:497-510. [PMID: 34250543 PMCID: PMC8414929 DOI: 10.1093/aob/mcab092] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/09/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS Zanthoxylum is the only pantropical genus within Rutaceae, with a few species native to temperate eastern Asia and North America. Efforts using Sanger sequencing failed to resolve the backbone phylogeny of Zanthoxylum. In this study, we employed target-enrichment high-throughput sequencing to improve resolution. Gene trees were examined for concordance and sectional classifications of Zanthoxylum were evaluated. Off-target reads were investigated to identify putative single-copy markers for bait refinement, and low-copy markers for evidence of putative hybridization events. METHODS A custom bait set targeting 354 genes, with a median of 321 bp, was designed for Zanthoxylum and applied to 44 Zanthoxylum species and one Tetradium species as the outgroup. Illumina reads were processed via the HybPhyloMaker pipeline. Phylogenetic inferences were conducted using coalescent and maximum likelihood methods based on concatenated datasets. Concordance was assessed using quartet sampling. Additional phylogenetic analyses were performed on putative single and low-copy genes extracted from off-target reads. KEY RESULTS Four major clades are supported within Zanthoxylum: the African clade, the Z. asiaticum clade, the Asian-Pacific-Australian clade and the American-eastern Asian clade. While overall support has improved, regions of conflict are similar to those previously observed. Gene tree discordances indicate a hybridization event in the ancestor of the Hawaiian lineage, and incomplete lineage sorting in the American backbone. Off-target putative single-copy genes largely confirm on-target results, and putative low-copy genes provide additional evidence for hybridization in the Hawaiian lineage. Only two of the five sections of Zanthoxylum are resolved as monophyletic. CONCLUSIONS Target enrichment is suitable for assessing phylogenetic relationships in Zanthoxylum. Our phylogenetic analyses reveal that current sectional classifications need revision. Quartet tree concordance indicates several instances of reticulate evolution. Off-target reads are proven useful to identify additional phylogenetically informative regions for bait refinement or gene tree based approaches.
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Affiliation(s)
- Niklas Reichelt
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute of Plant Sciences, University of Goettingen, Untere Karspuele 2, 37073 Goettingen, Germany
- Department of Botany, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 166, Washington, DC 20013-7012, USA
- Pharmaceutical Biology, Julius-von-Sachs-Institute for Biosciences, University of Wuerzburg, Julius-von-Sachs-Platz 2, 97082 Wuerzburg, Germany
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 166, Washington, DC 20013-7012, USA
| | - Claudia Pätzold
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute of Plant Sciences, University of Goettingen, Untere Karspuele 2, 37073 Goettingen, Germany
- Department Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Marc S Appelhans
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute of Plant Sciences, University of Goettingen, Untere Karspuele 2, 37073 Goettingen, Germany
- Department of Botany, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 166, Washington, DC 20013-7012, USA
- For correspondence. E-mail
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Ren C, Wang L, Nie ZL, Johnson G, Yang QE, Wen J. Development and phylogenetic utilities of a new set of single-/low-copy nuclear genes in Senecioneae (Asteraceae), with new insights into the tribal position and the relationships within subtribe Tussilagininae. Mol Phylogenet Evol 2021; 162:107202. [PMID: 33992786 DOI: 10.1016/j.ympev.2021.107202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/13/2021] [Accepted: 05/06/2021] [Indexed: 11/26/2022]
Abstract
The tribe Senecioneae is one of the largest tribes in Asteraceae, with a nearly cosmopolitan distribution. Despite great efforts devoted to elucidate the evolution of Senecioneae, many questions still remain concerning the systematics of this group, from the tribal circumscription and position to species relationships in many genera. The hybridization-based target enrichment method of next-generation sequencing has been accepted as a promising approach to resolve phylogenetic problems. We herein develop a set of single-/low-copy genes for Senecioneae, and test their phylogenetic utilities. Our results demonstrate that these genes work highly efficiently for Senecioneae, with a high average gene recovery of 98.8% across the tribe and recovering robust phylogenetic hypotheses at different levels. In particular, the delimitation of the Senecioneae has been confirmed to include Abrotanella and exclude Doronicum, with the former sister to core Senecioneae and the latter shown to be more closely related to Calenduleae. Moreover, Doronicum and Calenduleae are inferred to be the closest relatives of Senecioneae, which is a new hypothesis well supported by statistical topology tests, morphological evidence, and the profile of pyrrolizidine alkaloids, a special kind of chemical characters generally used to define Senecioneae. Furthermore, this study suggests a complex reticulation history in the diversification of Senecioneae, accounting for the prevalence of polyploid groups in the tribe. With subtribe Tussilagininae s.str. as a case study showing a more evident pattern of gene duplication, we further explored reconstructing the phylogeny in the groups with high ploidy levels. Our results also demonstrate that tree topologies based on sorted paralogous copies are stable across different methods of phylogenetic inference, and more congruent with the morphological evidence and the results of previous phylogenetic studies.
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Affiliation(s)
- Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Long Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Qin-Er Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Key Laboratory of Digital Botanical Garden of Guangdong Province, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China.
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
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