1
|
Veltman MA, Anthoons B, Schrøder-Nielsen A, Gravendeel B, de Boer HJ. Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids. Mol Ecol Resour 2024; 24:e13986. [PMID: 38899721 DOI: 10.1111/1755-0998.13986] [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: 06/15/2023] [Revised: 05/16/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called 'salep'. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost-effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water-soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non-exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step-up from traditional barcoding and universal markers, the genome-wide custom loci targeted by Orchidinae-205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids.
Collapse
Affiliation(s)
- Margaretha A Veltman
- Natural History Museum, Oslo, Norway
- Naturalis Biodiversity Center, Leiden, Netherlands
| | | | | | - Barbara Gravendeel
- Naturalis Biodiversity Center, Leiden, Netherlands
- Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, Netherlands
| | | |
Collapse
|
2
|
Pokorny L, Pellicer J, Woudstra Y, Christenhusz MJM, Garnatje T, Palazzesi L, Johnson MG, Maurin O, Françoso E, Roy S, Leitch IJ, Forest F, Baker WJ, Hidalgo O. Genomic incongruence accompanies the evolution of flower symmetry in Eudicots: a case study in the poppy family (Papaveraceae, Ranunculales). FRONTIERS IN PLANT SCIENCE 2024; 15:1340056. [PMID: 38947944 PMCID: PMC11212465 DOI: 10.3389/fpls.2024.1340056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/18/2024] [Indexed: 07/02/2024]
Abstract
Reconstructing evolutionary trajectories and transitions that have shaped floral diversity relies heavily on the phylogenetic framework on which traits are modelled. In this study, we focus on the angiosperm order Ranunculales, sister to all other eudicots, to unravel higher-level relationships, especially those tied to evolutionary transitions in flower symmetry within the family Papaveraceae. This family presents an astonishing array of floral diversity, with actinomorphic, disymmetric (two perpendicular symmetry axes), and zygomorphic flowers. We generated nuclear and plastid datasets using the Angiosperms353 universal probe set for target capture sequencing (of 353 single-copy nuclear ortholog genes), together with publicly available transcriptome and plastome data mined from open-access online repositories. We relied on the fossil record of the order Ranunculales to date our phylogenies and to establish a timeline of events. Our phylogenomic workflow shows that nuclear-plastid incongruence accompanies topological uncertainties in Ranunculales. A cocktail of incomplete lineage sorting, post-hybridization introgression, and extinction following rapid speciation most likely explain the observed knots in the topology. These knots coincide with major floral symmetry transitions and thus obscure the order of evolutionary events.
Collapse
Affiliation(s)
- Lisa Pokorny
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Spain
| | - Yannick Woudstra
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Maarten J. M. Christenhusz
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Spain
- Jardí Botànic Marimurtra, Fundació Carl Faust, Blanes, Spain
| | - Luis Palazzesi
- División Paleobotánica, Museo Argentino de Ciencias Naturales, CONICET, Buenos Aires, Argentina
| | - Matthew G. Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | | | | | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Spain
| |
Collapse
|
3
|
Thureborn O, Wikström N, Razafimandimbison SG, Rydin C. Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae. PLoS One 2024; 19:e0302365. [PMID: 38768140 PMCID: PMC11104678 DOI: 10.1371/journal.pone.0302365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 04/03/2024] [Indexed: 05/22/2024] Open
Abstract
In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.
Collapse
Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Niklas Wikström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
| |
Collapse
|
4
|
Ruiz-Vargas N, Ramanauskas K, Tyszka AS, Bretz EC, Yeo MTS, Mason-Gamer RJ, Walker JF. Transcriptome data from silica-preserved leaf tissue reveal gene flow patterns in a Caribbean bromeliad. ANNALS OF BOTANY 2024; 133:459-472. [PMID: 38181407 PMCID: PMC11006539 DOI: 10.1093/aob/mcae002] [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: 10/16/2023] [Accepted: 01/04/2024] [Indexed: 01/07/2024]
Abstract
BACKGROUND AND AIMS Transcriptome sequencing is a cost-effective approach that allows researchers to study a broad range of questions. However, to preserve RNA for transcriptome sequencing, tissue is often kept in special conditions, such as immediate ultracold freezing. Here, we demonstrate that RNA can be obtained from 6-month-old, field-collected samples stored in silica gel at room temperature. Using these transcriptomes, we explore the evolutionary relationships of the genus Pitcairnia (Bromeliaceae) in the Dominican Republic and infer barriers to gene flow. METHODS We extracted RNA from silica-dried leaf tissue from 19 Pitcairnia individuals collected across the Dominican Republic. We used a series of macro- and micro-evolutionary approaches to examine the relationships and patterns of gene flow among individuals. KEY RESULTS We produced high-quality transcriptomes from silica-dried material and demonstrated that evolutionary relationships on the island match geography more closely than species delimitation methods. A population genetic examination indicates that a combination of ecological and geographical features presents barriers to gene flow in Pitcairnia. CONCLUSIONS Transcriptomes can be obtained from silica-preserved tissue. The genetic diversity among Pitcairnia populations does not warrant classification as separate species, but the Dominican Republic contains several barriers to gene flow, notably the Cordillera Central mountain range.
Collapse
Affiliation(s)
- Natalia Ruiz-Vargas
- Department of Biological Sciences, the University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Karolis Ramanauskas
- Department of Biological Sciences, the University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alexa S Tyszka
- Department of Biological Sciences, the University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Eric C Bretz
- Department of Biological Sciences, the University of Illinois at Chicago, Chicago, IL 60607, USA
| | - May T S Yeo
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
- Department of Genetics, Downing Site, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Roberta J Mason-Gamer
- Department of Biological Sciences, the University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Joseph F Walker
- Department of Biological Sciences, the University of Illinois at Chicago, Chicago, IL 60607, USA
| |
Collapse
|
5
|
Becker A, Bachelier JB, Carrive L, Conde E Silva N, Damerval C, Del Rio C, Deveaux Y, Di Stilio VS, Gong Y, Jabbour F, Kramer EM, Nadot S, Pabón-Mora N, Wang W. A cornucopia of diversity-Ranunculales as a model lineage. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1800-1822. [PMID: 38109712 DOI: 10.1093/jxb/erad492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
The Ranunculales are a hyperdiverse lineage in many aspects of their phenotype, including growth habit, floral and leaf morphology, reproductive mode, and specialized metabolism. Many Ranunculales species, such as opium poppy and goldenseal, have a high medicinal value. In addition, the order includes a large number of commercially important ornamental plants, such as columbines and larkspurs. The phylogenetic position of the order with respect to monocots and core eudicots and the diversity within this lineage make the Ranunculales an excellent group for studying evolutionary processes by comparative studies. Lately, the phylogeny of Ranunculales was revised, and genetic and genomic resources were developed for many species, allowing comparative analyses at the molecular scale. Here, we review the literature on the resources for genetic manipulation and genome sequencing, the recent phylogeny reconstruction of this order, and its fossil record. Further, we explain their habitat range and delve into the diversity in their floral morphology, focusing on perianth organ identity, floral symmetry, occurrences of spurs and nectaries, sexual and pollination systems, and fruit and dehiscence types. The Ranunculales order offers a wealth of opportunities for scientific exploration across various disciplines and scales, to gain novel insights into plant biology for researchers and plant enthusiasts alike.
Collapse
Affiliation(s)
- Annette Becker
- Plant Development Group, Institute of Botany, Justus-Liebig-University, Giessen, Germany
| | - Julien B Bachelier
- Institute of Biology/Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Laetitia Carrive
- Université de Rennes, UMR CNRS 6553, Ecosystèmes-Biodiversité-Evolution, Campus de Beaulieu, 35042 Rennes cedex, France
| | - Natalia Conde E Silva
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Catherine Damerval
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Cédric Del Rio
- CR2P - Centre de Recherche en Paléontologie - Paris, MNHN - Sorbonne Université - CNRS, 43 Rue Buffon, 75005 Paris, France
| | - Yves Deveaux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190 Gif-sur-Yvette, France
| | | | - Yan Gong
- Department of Organismic and Evolutionary Biology, Harvard University, MA, 02138, USA
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP39, Paris, 75005, France
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, MA, 02138, USA
| | - Sophie Nadot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie, Systématique et Evolution, Gif-sur-Yvette, France
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China and University of Chinese Academy of Sciences, Beijing, 100049China
| |
Collapse
|
6
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
7
|
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] [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.
Collapse
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.
| |
Collapse
|
8
|
Lyu R, Xiao J, Li M, Luo Y, He J, Cheng J, Xie L. Phylogeny and Historical Biogeography of the East Asian Clematis Group, Sect. Tubulosae, Inferred from Phylogenomic Data. Int J Mol Sci 2023; 24:3056. [PMID: 36769378 PMCID: PMC9917980 DOI: 10.3390/ijms24033056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/19/2023] [Accepted: 01/29/2023] [Indexed: 02/09/2023] Open
Abstract
The evolutionary history of Clematis section Tubulosae, an East Asian endemic lineage, has not been comprehensively studied. In this study, we reconstruct the phylogeny of this section with a complete sampling using a phylogenomic approach. The genome skimming method was applied to obtain the complete plastome sequence, the nuclear ribosomal DNA (nrDNA), and the nuclear SNPs data for phylogenetic reconstruction. Using a Bayesian molecular clock approach and ancestral range reconstruction, we reconstruct biogeographical history and discuss the biotic and abiotic factors that may have shaped the distribution patterns of the section. Both nuclear datasets better resolved the phylogeny of the sect. Tubulosae than the plastome sequence. Sect. Tubulosae was resolved as a monophyletic group sister to a clade mainly containing species from the sect. Clematis and sect. Aspidanthera. Within sect. Tubulosae, two major clades were resolved by both nuclear datasets. Two continental taxa, C. heracleifolia and C. tubulosa var. ichangensis, formed one clade. One continental taxon, C. tubulosa, and all the other species from Taiwan island, the Korean peninsula, and the Japanese archipelago formed the other clade. Molecular dating results showed that sect. Tubulosae diverged from its sister clade in the Pliocene, and all the current species diversified during the Pleistocene. Our biogeographical reconstruction suggested that sect. Tubulosae evolved and began species diversification, most likely in mainland China, then dispersed to the Korean peninsula, and then expanded its range through the Japanese archipelago to Taiwan island. Island species diversity may arise through allopatric speciation by vicariance events following the range fragmentation triggered by the climatic oscillation and sea level change during the Pleistocene epoch. Our results highlight the importance of climatic oscillation during the Pleistocene to the spatial-temporal diversification patterns of the sect. Tubulosae.
Collapse
Affiliation(s)
- Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Jiamin Xiao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Mingyang Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| |
Collapse
|
9
|
Xiao J, Lyu R, He J, Li M, Ji J, Cheng J, Xie L. Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of Clematis (Ranunculaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:1059379. [PMID: 36452086 PMCID: PMC9703796 DOI: 10.3389/fpls.2022.1059379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Clematis is one of the largest genera of Ranunculaceae with many phylogenetic problems left to be resolved. Clematis species have considerable genome size of more than 7 Gbp, and there was no whole-genome reference sequence published in this genus. This raises difficulties in acquiring nuclear genome data for its phylogenetic analysis. Previous studies based on Sanger sequencing data, plastid genome data, and nrDNA sequences did not well resolve the phylogeny of Clematis. In this study, we used genome skimming and transcriptome data to assemble the plastid genome sequences, nuclear single nucleotide polymorphisms (SNPs) datasets, and single-copy nuclear orthologous genes (SCOGs) to reconstruct the phylogenetic backbone of Clematis, and test effectiveness of these genome partitioning methods. We also further analyzed the discordance among nuclear gene trees and between plastid and nuclear phylogenies. The results showed that the SCOGs datasets, assembled from transcriptome method, well resolved the phylogenetic backbone of Clematis. The nuclear SNPs datasets from genome skimming method can also produce similar results with the SCOGs data. In contrast to the plastid phylogeny, the phylogeny resolved by nuclear genome data is more robust and better corresponds to morphological characters. Our results suggested that rapid species radiation may have generated high level of incomplete lineage sorting, which was the major cause of nuclear gene discordance. Our simulation also showed that there may have been frequent interspecific hybridization events, which led to some of the cyto-nuclear discordances in Clematis. This study not only provides the first robust phylogenetic backbone of Clematis based on nuclear genome data, but also provides suggestions of genome partitioning strategies for the phylogenomic study of other plant taxa.
Collapse
Affiliation(s)
- Jiamin Xiao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Mingyang Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jiaxin Ji
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| |
Collapse
|