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Wutke S, Blank SM, Boevé JL, Faircloth BC, Koch F, Linnen CR, Malm T, Niu G, Prous M, Schiff NM, Schmidt S, Taeger A, Vilhelmsen L, Wahlberg N, Wei M, Nyman T. Phylogenomics and biogeography of sawflies and woodwasps (Hymenoptera, Symphyta). Mol Phylogenet Evol 2024; 199:108144. [PMID: 38972494 DOI: 10.1016/j.ympev.2024.108144] [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: 03/11/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
Phylogenomic approaches have recently helped elucidate various insect relationships, but large-scale comprehensive analyses on relationships within sawflies and woodwasps are still lacking. Here, we infer the relationships and long-term biogeographic history of these hymenopteran groups using a large dataset of 354 UCE loci collected from 385 species that represent all major lineages. Early Hymenoptera started diversifying during the Early Triassic ∼249 Ma and spread all over the ancient supercontinent Pangaea. We recovered Xyeloidea as a monophyletic sister group to other Hymenoptera and Pamphilioidea as sister to Unicalcarida. Within the diverse family Tenthredinidae, our taxonomically and geographically expanded taxon sampling highlights the non-monophyly of several traditionally defined subfamilies. In addition, the recent removal of Athalia and related genera from the Tenthredinidae into the separate family Athaliidae is supported. The deep historical biogeography of the group is characterised by independent dispersals and re-colonisations between the northern (Laurasia) and southern (Gondwana) palaeocontinents. The breakup of these landmasses led to ancient vicariance in several Gondwanan lineages, while interchange across the Northern Hemisphere has continued until the Recent. The little-studied African sawfly fauna is likewise a diverse mixture of groups with varying routes of colonization. Our results reveal interesting parallels in the evolution and biogeography of early hymenopterans and other ancient insect groups.
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Affiliation(s)
- Saskia Wutke
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.
| | - Stephan M Blank
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
| | - Jean-Luc Boevé
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Frank Koch
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | - Tobias Malm
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Gengyun Niu
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Marko Prous
- Museum of Natural History, University of Tartu, Estonia
| | - Nathan M Schiff
- Formerly with the USDA Forest Service, Southern Research Station, Center for Bottomland Hardwoods Research, Stoneville, MS, USA
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Andreas Taeger
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
| | - Lars Vilhelmsen
- Natural History Museum of Denmark, SCIENCE, University of Copenhagen, Denmark
| | | | - Meicai Wei
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
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2
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Xue TT, Janssens SB, Liu BB, Yu SX. Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study in the cinquefoil genus Potentilla sensu lato (Potentilleae, Rosaceae). Mol Phylogenet Evol 2024; 190:107956. [PMID: 37898296 DOI: 10.1016/j.ympev.2023.107956] [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: 07/24/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigate phylogenetic conflict analyses within and between plastid and mitochondrial genomes using Potentilla as a case study. We generated three plastid datasets (coding, noncoding, and all-region) and one mitochondrial dataset (coding regions) to infer phylogenies based on concatenated and multispecies coalescent (MSC) methods. Conflict analyses were then performed using PhyParts and Quartet Sampling (QS). Both plastid and mitochondrial genomes divided the Potentilla into eight highly supported clades, two of which were newly identified in this study. While most organellar loci were uninformative for the majority of nodes (bootstrap value < 70%), PhyParts and QS detected conflicting signals within the two organellar genomes. Regression analyses revealed that conflict signals mainly occurred among shorter loci, whereas longer loci tended to be more concordant with the species tree. In addition, two significant disagreements between the two organellar genomes were detected, likely attributed to hybridization and/or incomplete lineage sorting. Our results demonstrate that mitochondrial genes can fully resolve the phylogenetic relationships among eight major clades of Potentilla and are not always linked with plastome in evolutionary history. Stochastic inferences appear to be the primary source of observed conflicts among the gene trees. We recommend that the loci with short sequence length or containing limited informative sites should be used cautiously in MSC analysis, and suggest the joint application of concatenated and MSC methods for phylogenetic inference using organellar genomes.
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Affiliation(s)
- Tian-Tian Xue
- State Key Laboratory of Plant Diversity and Specialty Crops / 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
| | - Steven B Janssens
- Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium; Department of Biology, KU Leuven, Kasteelpark Arenberg 31, BE-3001 Leuven, Belgium.
| | - Bin-Bin Liu
- State Key Laboratory of Plant Diversity and Specialty Crops / 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.
| | - Sheng-Xiang Yu
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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3
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Flores JR, Bippus AC, de Ullivarri CF, Suárez GM, Hyvönen J, Tomescu AMF. Dating the evolution of the complex thalloid liverworts (Marchantiopsida): total-evidence dating analysis supports a Late Silurian-Early Devonian origin and post-Mesozoic morphological stasis. THE NEW PHYTOLOGIST 2023; 240:2137-2150. [PMID: 37697646 DOI: 10.1111/nph.19254] [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: 11/22/2022] [Accepted: 08/19/2023] [Indexed: 09/13/2023]
Abstract
Divergence times based on molecular clock analyses often differ from those derived from total-evidence dating (TED) approaches. For bryophytes, fossils have been excluded from previous assessments of divergence times, and thus, their utility in dating analyses remains unexplored. Here, we conduct the first TED analyses of the complex thalloid liverworts (Marchantiopsida) that include fossils and evaluate macroevolutionary trends in morphological 'diversity' (disparity) and rates. Phylogenetic analyses were performed on a combined dataset of 130 discrete characters and 11 molecular markers (sampled from nuclear, plastid and mitochondrial genomes). Taxon sampling spanned 56 extant species - representing all the orders within Marchantiophyta and extant genera within Marchantiales - and eight fossil taxa. Total-evidence dating analyses support the radiation of Marchantiopsida during Late Silurian-Early Devonian (or Middle Ordovician when the outgroup is excluded) and that of Ricciaceae in the Middle Jurassic. Morphological change rate was high early in the history of the group, but it barely increased after Late Cretaceous. Disparity-through-time analyses support a fast increase in diversity until the Middle Triassic (c. 250 Ma), after which phenotypic evolution slows down considerably. Incorporating fossils in analyses challenges previous assumptions on the affinities of extinct taxa and indicates that complex thalloid liverworts radiated c. 125 Ma earlier than previously inferred.
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Affiliation(s)
- Jorge R Flores
- Unidad Ejecutora Lillo (UEL), CONICET-Fundación Miguel Lillo, Miguel Lillo 251, San Miguel del Tucumán, CP 4000, Tucumán, Argentina
- Instituto de Paleontología y Sedimentología, Sección Paleobotánica, Fundación Miguel Lillo, Miguel Lillo 251, San Miguel del Tucumán, CP 4000, Tucumán, Argentina
| | - Alexander C Bippus
- Indian Natural Resource Science and Engineering Program + Diversity in STEM, 1 Harpst St, Arcata, CA, 95521, USA
| | - Carmen Fernández de Ullivarri
- Unidad Ejecutora Lillo (UEL), CONICET-Fundación Miguel Lillo, Miguel Lillo 251, San Miguel del Tucumán, CP 4000, Tucumán, Argentina
| | - Guillermo M Suárez
- Unidad Ejecutora Lillo (UEL), CONICET-Fundación Miguel Lillo, Miguel Lillo 251, San Miguel del Tucumán, CP 4000, Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 251, T4000JFE, San Miguel de Tucumán, Argentina
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany) & Organismal and Evolutionary Biology & Viikki Plant Science Centre, University of Helsinki, PO Box 7, FI-00014, Helsinki, Finland
| | - Alexandru M F Tomescu
- Department of Biological Sciences, California State Polytechnic University Humboldt, Arcata, CA, 95521, USA
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4
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Bechteler J, Peñaloza-Bojacá G, Bell D, Gordon Burleigh J, McDaniel SF, Christine Davis E, Sessa EB, Bippus A, Christine Cargill D, Chantanoarrapint S, Draper I, Endara L, Forrest LL, Garilleti R, Graham SW, Huttunen S, Lazo JJ, Lara F, Larraín J, Lewis LR, Long DG, Quandt D, Renzaglia K, Schäfer-Verwimp A, Lee GE, Sierra AM, von Konrat M, Zartman CE, Pereira MR, Goffinet B, Villarreal A JC. Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification. AMERICAN JOURNAL OF BOTANY 2023; 110:e16249. [PMID: 37792319 DOI: 10.1002/ajb2.16249] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/05/2023]
Abstract
PREMISE Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts, and mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns, and processes of diversification across bryophytes remain unclear. METHODS Using the GoFlag probe set, we sequenced 405 exons representing 228 nuclear genes for 531 species from 52 of the 54 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations. RESULTS The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more and propose 10 new orders of mosses. Most orders originated in the Jurassic and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene-tree topology. CONCLUSIONS We sampled hundreds of loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution; these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of this important group of plants.
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Affiliation(s)
- Julia Bechteler
- Nees-Institute for Plant Biodiversity, University of Bonn, Meckenheimer Allee 170, 53115, Bonn, Germany
- Plant Biodiversity and Ecology, iES Landau, Institute for Environmental Sciences, RPTU University of Kaiserslautern-Landau, Fortstraße 7, 76829, Landau, Germany
| | - Gabriel Peñaloza-Bojacá
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - David Bell
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - J Gordon Burleigh
- Department of Biological Sciences, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Stuart F McDaniel
- Department of Biological Sciences, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - E Christine Davis
- Department of Biological Sciences, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Emily B Sessa
- Department of Biological Sciences, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Alexander Bippus
- California State Polytechnic University, Humboldt, Arcata, CA, 95521, USA
| | - D Christine Cargill
- Australian National Herbarium, Centre for Australian National Biodiversity Research, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Sahut Chantanoarrapint
- PSU Herbarium, Division of Biological Science, Faculty of Science Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Isabel Draper
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain/Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Lorena Endara
- Department of Biological Sciences, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Laura L Forrest
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Ricardo Garilleti
- Departamento de Botánica y Geología. Universidad de Valencia, Avda. Vicente Andrés Estelles s/n, 46100, Burjassot, Spain
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Sanna Huttunen
- Herbarium (TUR), Biodiversity Unit, 20014 University of Turku, Finland
| | - Javier Jauregui Lazo
- Department of Plant Biology and Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Francisco Lara
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain/Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan Larraín
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O'Higgins, Avenida Viel 1497, Santiago, Chile
| | - Lily R Lewis
- Department of Biological Sciences, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - David G Long
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Dietmar Quandt
- Nees-Institute for Plant Biodiversity, University of Bonn, Meckenheimer Allee 170, 53115, Bonn, Germany
| | - Karen Renzaglia
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, 62901, USA
| | | | - Gaik Ee Lee
- Faculty of Science and Marine Environment/Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21020 Kuala Nerus, Terengganu, Malaysia
| | - Adriel M Sierra
- Département de Biologie, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Matt von Konrat
- Gantz Family Collections Center, Field Museum, 1400 S. DuSable Lake Shore Drive, Chicago, IL, 60605, USA
| | - Charles E Zartman
- Instituto Nacional de Pesquisas da Amazônia, Departamento de Biodiversidade, Avenida André Araújo, 2936, Aleixo, CEP 69060-001, Manaus, AM, Brazil
| | - Marta Regina Pereira
- Universidade do Estado do Amazonas, Av. Djalma Batista, 2470, Chapada, Manaus, 69050-010, Amazonas, Brazil
| | - Bernard Goffinet
- Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT, 06269-3043, USA
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Dong SS, Zhou XP, Peng T, Liu Y. Mitochondrial RNA editing sites affect the phylogenetic reconstruction of gymnosperms. PLANT DIVERSITY 2023; 45:485-489. [PMID: 37601539 PMCID: PMC10435907 DOI: 10.1016/j.pld.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 08/22/2023]
Abstract
•RNA editing sites may contain homoplasious signals that cause artifactual inferences in phylogenetic analyses.•Excluding RNA editing sites from gymnosperm mitochondrial genes restored the sister relationship of gnetophytes and Pinaceae.•Phylogenetic analysis based on mitochondrial genomic data should carefully evaluate the impact of RNA editing sites.
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Affiliation(s)
- Shan-Shan Dong
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
| | - Xu-Ping Zhou
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
- School of Life Sciences, Guizhou Normal University, Guiyang 550001, Guizhou, China
| | - Tao Peng
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
- School of Life Sciences, Guizhou Normal University, Guiyang 550001, Guizhou, China
| | - Yang Liu
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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Garrett N, Viruel J, Klimpert N, Soto Gomez M, Lam VKY, Merckx VSFT, Graham SW. Plastid phylogenomics and molecular evolution of Thismiaceae (Dioscoreales). AMERICAN JOURNAL OF BOTANY 2023; 110:e16141. [PMID: 36779918 DOI: 10.1002/ajb2.16141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Species in Thismiaceae can no longer photosynthesize and instead obtain carbon from soil fungi. Here we infer Thismiaceae phylogeny using plastid genome data and characterize the molecular evolution of this genome. METHODS We assembled five Thismiaceae plastid genomes from genome skimming data, adding to previously published data for phylogenomic inference. We investigated plastid-genome structural changes, considering locally colinear blocks (LCBs). We also characterized possible shifts in selection pressure in retained genes by considering changes in the ratio of nonsynonymous to synonymous changes (ω). RESULTS Thismiaceae experienced two major pulses of gene loss around the early diversification of the family, with subsequent scattered gene losses across descendent lineages. In addition to massive size reduction, Thismiaceae plastid genomes experienced occasional inversions, and there were likely two independent losses of the plastid inverted repeat (IR) region. Retained plastid genes remain under generally strong purifying selection (ω << 1), with significant and sporadic weakening or strengthening in several instances. The bifunctional trnE-UUC gene of Thismia huangii may retain a secondary role in heme biosynthesis, despite a probable loss of functionality in protein translation. Several cis-spliced group IIA introns have been retained, despite the loss of the plastid intron maturase, matK. CONCLUSIONS We infer that most gene losses in Thismiaceae occurred early and rapidly, following the initial loss of photosynthesis in its stem lineage. As a species-rich, fully mycoheterotrophic lineage, Thismiaceae provide a model system for uncovering the unique and divergent ways in which plastid genomes evolve in heterotrophic plants.
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Affiliation(s)
- Natalie Garrett
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - Nathaniel Klimpert
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | | | - Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Vincent S F T Merckx
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Sciencepark 904, 1098, XH, Amsterdam, The Netherlands
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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Klimpert NJ, Mayer JLS, Sarzi DS, Prosdocimi F, Pinheiro F, Graham SW. Phylogenomics and plastome evolution of a Brazilian mycoheterotrophic orchid, Pogoniopsis schenckii. AMERICAN JOURNAL OF BOTANY 2022; 109:2030-2050. [PMID: 36254561 DOI: 10.1002/ajb2.16084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Pogoniopsis likely represents an independent photosynthesis loss in orchids. We use phylogenomic data to better identify the phylogenetic placement of this fully mycoheterotrophic taxon, and investigate its molecular evolution. METHODS We performed likelihood analysis of plastid and mitochondrial phylogenomic data to localize the position of Pogoniopsis schenckii in orchid phylogeny, and investigated the evolution of its plastid genome. RESULTS All analyses place Pogoniopsis in subfamily Epidendroideae, with strongest support from mitochondrial data, which also place it near tribe Sobralieae with moderately strong support. Extreme rate elevation in Pogoniopsis plastid genes broadly depresses branch support; in contrast, mitochondrial genes are only mildly rate elevated and display very modest and localized reductions in bootstrap support. Despite considerable genome reduction, including loss of photosynthesis genes and multiple translation apparatus genes, gene order in Pogoniopsis plastomes is identical to related autotrophs, apart from moderately shifted inverted repeat (IR) boundaries. All cis-spliced introns have been lost in retained genes. Two plastid genes (accD, rpl2) show significant strengthening of purifying selection. A retained plastid tRNA gene (trnE-UUC) of Pogoniopsis lacks an anticodon; we predict that it no longer functions in translation but retains a secondary role in heme biosynthesis. CONCLUSIONS Slowly evolving mitochondrial genes clarify the placement of Pogoniopsis in orchid phylogeny, a strong contrast with analysis of rate-elevated plastome data. We documented the effects of the novel loss of photosynthesis: for example, despite massive gene loss, its plastome is fully colinear with other orchids, and it displays only moderate shifts in selective pressure in retained genes.
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Affiliation(s)
- Nathaniel J Klimpert
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Juliana Lischka Sampaio Mayer
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Deise Schroder Sarzi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, UFRJ/CCS/Bloco B33, Rio de Janeiro, RJ, 21.941-902, Brazil
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, UFRJ/CCS/Bloco B33, Rio de Janeiro, RJ, 21.941-902, Brazil
| | - Fábio Pinheiro
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
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8
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Bowman JL. The origin of a land flora. NATURE PLANTS 2022; 8:1352-1369. [PMID: 36550365 DOI: 10.1038/s41477-022-01283-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/19/2022] [Indexed: 05/12/2023]
Abstract
The origin of a land flora fundamentally shifted the course of evolution of life on earth, facilitating terrestrialization of other eukaryotic lineages and altering the planet's geology, from changing atmospheric and hydrological cycles to transforming continental erosion processes. Despite algal lineages inhabiting the terrestrial environment for a considerable preceding period, they failed to evolve complex multicellularity necessary to conquer the land. About 470 million years ago, one lineage of charophycean alga evolved complex multicellularity via developmental innovations in both haploid and diploid generations and became land plants (embryophytes), which rapidly diversified to dominate most terrestrial habitats. Genome sequences have provided unprecedented insights into the genetic and genomic bases for embryophyte origins, with some embryophyte-specific genes being associated with the evolution of key developmental or physiological attributes, such as meristems, rhizoids and the ability to form mycorrhizal associations. However, based on the fossil record, the evolution of the defining feature of embryophytes, the embryo, and consequently the sporangium that provided a reproductive advantage, may have been most critical in their rise to dominance. The long timeframe and singularity of a land flora were perhaps due to the stepwise assembly of a large constellation of genetic innovations required to conquer the terrestrial environment.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne, Victoria, Australia.
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9
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Lin Q, Braukmann TWA, Soto Gomez M, Mayer JLS, Pinheiro F, Merckx VSFT, Stefanović S, Graham SW. Mitochondrial genomic data are effective at placing mycoheterotrophic lineages in plant phylogeny. THE NEW PHYTOLOGIST 2022; 236:1908-1921. [PMID: 35731179 DOI: 10.1111/nph.18335] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/13/2022] [Indexed: 05/03/2023]
Abstract
Fully mycoheterotrophic plants can be difficult to place in plant phylogeny due to elevated substitution rates associated with photosynthesis loss. This potentially limits the effectiveness of downstream analyses of mycoheterotrophy that depend on accurate phylogenetic inference. Although mitochondrial genomic data sets are rarely used in plant phylogenetics, theory predicts that they should be resilient to long-branch artefacts, thanks to their generally slow evolution, coupled with limited rate elevation in heterotrophs. We examined the utility of mitochondrial genomes for resolving contentious higher-order placements of mycoheterotrophic lineages in two test cases: monocots (focusing on Dioscoreales) and Ericaceae. We find Thismiaceae to be distantly related to Burmanniaceae in the monocot order Dioscoreales, conflicting with current classification schemes based on few gene data sets. We confirm that the unusual Afrothismia is related to Taccaceae-Thismiaceae, with a corresponding independent loss of photosynthesis. In Ericaceae we recovered the first well supported relationships among its five major lineages: mycoheterotrophic Ericaceae are not monophyletic, as pyroloids are inferred to be sister to core Ericaceae, and monotropoids to arbutoids. Genes recovered from mitochondrial genomes collectively resolved previously ambiguous mycoheterotroph higher-order relationships. We propose that mitochondrial genomic data should be considered in standardised gene panels for inferring overall plant phylogeny.
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Affiliation(s)
- Qianshi Lin
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 2Z9, Canada
| | - Thomas W A Braukmann
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 2Z9, Canada
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Juliana Lischka Sampaio Mayer
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Fábio Pinheiro
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Vincent S F T Merckx
- Naturalis Biodiversity Center, Vondellaan 55, 2332 AA, Leiden, the Netherlands
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 2Z9, Canada
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
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10
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Harris BJ, Clark JW, Schrempf D, Szöllősi GJ, Donoghue PCJ, Hetherington AM, Williams TA. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. Nat Ecol Evol 2022; 6:1634-1643. [PMID: 36175544 PMCID: PMC9630106 DOI: 10.1038/s41559-022-01885-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 08/12/2022] [Indexed: 11/16/2022]
Abstract
The origin of plants and their colonization of land fundamentally transformed the terrestrial environment. Here we elucidate the basis of this formative episode in Earth history through patterns of lineage, gene and genome evolution. We use new fossil calibrations, a relative clade age calibration (informed by horizontal gene transfer) and new phylogenomic methods for mapping gene family origins. Distinct rooting strategies resolve tracheophytes (vascular plants) and bryophytes (non-vascular plants) as monophyletic sister groups that diverged during the Cambrian, 515-494 million years ago. The embryophyte stem is characterized by a burst of gene innovation, while bryophytes subsequently experienced an equally dramatic episode of reductive genome evolution in which they lost genes associated with the elaboration of vasculature and the stomatal complex. Overall, our analyses reveal that extant tracheophytes and bryophytes are both highly derived from a more complex ancestral land plant. Understanding the origin of land plants requires tracing character evolution across a diversity of modern lineages.
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Affiliation(s)
- Brogan J Harris
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - James W Clark
- School of Biological Sciences, University of Bristol, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Dominik Schrempf
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - Gergely J Szöllősi
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
- MTA-ELTE 'Lendület' Evolutionary Genomics Research Group, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | | | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK.
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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11
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Woudenberg S, Renema J, Tomescu AMF, De Rybel B, Weijers D. Deep origin and gradual evolution of transporting tissues: Perspectives from across the land plants. PLANT PHYSIOLOGY 2022; 190:85-99. [PMID: 35904762 PMCID: PMC9434249 DOI: 10.1093/plphys/kiac304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/08/2022] [Indexed: 05/31/2023]
Abstract
The evolution of transporting tissues was an important innovation in terrestrial plants that allowed them to adapt to almost all nonaquatic environments. These tissues consist of water-conducting cells and food-conducting cells and bridge plant-soil and plant-air interfaces over long distances. The largest group of land plants, representing about 95% of all known plant species, is associated with morphologically complex transporting tissue in plants with a range of additional traits. Therefore, this entire clade was named tracheophytes, or vascular plants. However, some nonvascular plants possess conductive tissues that closely resemble vascular tissue in their organization, structure, and function. Recent molecular studies also point to a highly conserved toolbox of molecular regulators for transporting tissues. Here, we reflect on the distinguishing features of conductive and vascular tissues and their evolutionary history. Rather than sudden emergence of complex, vascular tissues, plant transporting tissues likely evolved gradually, building on pre-existing developmental mechanisms and genetic components. Improved knowledge of the intimate structure and developmental regulation of transporting tissues across the entire taxonomic breadth of extant plant lineages, combined with more comprehensive documentation of the fossil record of transporting tissues, is required for a full understanding of the evolutionary trajectory of transporting tissues.
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Affiliation(s)
| | | | - Alexandru M F Tomescu
- Department of Biological Sciences, California State Polytechnic University–Humboldt, Arcata, California 95521, USA
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12
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Bippus AC, Flores JR, Hyvönen J, Tomescu AMF. The role of paleontological data in bryophyte systematics. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4273-4290. [PMID: 35394022 DOI: 10.1093/jxb/erac137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
Systematics reconstructs tempo and mode in biological evolution by resolving the phylogenetic fabric of biodiversity. The staggering duration and complexity of evolution, coupled with loss of information (extinction), render exhaustive reconstruction of the evolutionary history of life unattainable. Instead, we sample its products-phenotypes and genotypes-to generate phylogenetic hypotheses, which we sequentially reassess and update against new data. Current consensus in evolutionary biology emphasizes fossil integration in total-evidence analyses, requiring in-depth understanding of fossils-age, phenotypes, and systematic affinities-and a detailed morphological framework uniting fossil and extant taxa. Bryophytes present a special case: deep evolutionary history but sparse fossil record and phenotypic diversity encompassing small dimensional scales. We review how these peculiarities shape fossil inclusion in bryophyte systematics. Paucity of the bryophyte fossil record, driven primarily by phenotypic (small plant size) and ecological constraints (patchy substrate-hugging populations), and incomplete exploration, results in many morphologically isolated, taxonomically ambiguous fossil taxa. Nevertheless, instances of exquisite preservation and pioneering studies demonstrate the feasibility of including bryophyte fossils in evolutionary inference. Further progress will arise from developing extensive morphological matrices for bryophytes, continued exploration of the fossil record, re-evaluation of previously described fossils, and training specialists in identification and characterization of bryophyte fossils, and in bryophyte morphology.
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Affiliation(s)
- Alexander C Bippus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
- Department of Biological Sciences, California State Polytechnic University-Humboldt, Arcata, CA, USA
| | - Jorge R Flores
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
- Viikki Plant Science Center & Organismal & Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Alexandru M F Tomescu
- Department of Biological Sciences, California State Polytechnic University-Humboldt, Arcata, CA, USA
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13
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Wang QH, Zhang J, Liu Y, Jia Y, Jiao YN, Xu B, Chen ZD. Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4306-4322. [PMID: 35437589 DOI: 10.1093/jxb/erac127] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Bryophytes including mosses, liverworts, and hornworts are among the earliest land plants, and occupy a crucial phylogenetic position to aid in the understanding of plant terrestrialization. Despite their small size and simple structure, bryophytes are the second largest group of extant land plants. They live ubiquitously in various habitats and are highly diversified, with adaptive strategies to modern ecosystems on Earth. More and more genomes and transcriptomes have been assembled to address fundamental questions in plant biology. Here, we review recent advances in bryophytes associated with diversity, phylogeny, and ecological adaptation. Phylogenomic studies have provided increasing supports for the monophyly of bryophytes, with hornworts sister to the Setaphyta clade including liverworts and mosses. Further comparative genomic analyses revealed that multiple whole-genome duplications might have contributed to the species richness and morphological diversity in mosses. We highlight that the biological changes through gene gain or neofunctionalization that primarily evolved in bryophytes have facilitated the adaptation to early land environments; among the strategies to adapt to modern ecosystems in bryophytes, desiccation tolerance is the most remarkable. More genomic information for bryophytes would shed light on key mechanisms for the ecological success of these 'dwarfs' in the plant kingdom.
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Affiliation(s)
- Qing-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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14
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Alvarenga DO, Rousk K. Unraveling host-microbe interactions and ecosystem functions in moss-bacteria symbioses. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4473-4486. [PMID: 35728619 DOI: 10.1093/jxb/erac091] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Mosses are non-vascular plants usually found in moist and shaded areas, with great ecological importance in several ecosystems. This is especially true in northern latitudes, where mosses are responsible for up to 100% of primary production in some ecosystems. Mosses establish symbiotic associations with unique bacteria that play key roles in the carbon and nitrogen cycles. For instance, in boreal environments, more than 35% of the nitrogen fixed by diazotrophic symbionts in peatlands is transferred to mosses, directly affecting carbon fixation by the hosts, while moss-associated methanotrophic bacteria contribute 10-30% of moss carbon. Further, half of ecosystem N input may derive from moss-cyanobacteria associations in pristine ecosystems. Moss-bacteria interactions have consequences on a global scale since northern environments sequester 20% of all the carbon generated by forests in the world and stock at least 32% of global terrestrial carbon. Different moss hosts influence bacteria in distinct ways, which suggests that threats to mosses also threaten unique microbial communities with important ecological and biogeochemical consequences. Since their origin ~500 Ma, mosses have interacted with bacteria, making these associations ideal models for understanding the evolution of plant-microbe associations and their contribution to biogeochemical cycles.
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Affiliation(s)
- Danillo O Alvarenga
- Department of Biology, Terrestrial Ecology Section, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
- Centre for Permafrost, University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
| | - Kathrin Rousk
- Department of Biology, Terrestrial Ecology Section, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
- Centre for Permafrost, University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
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15
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Ke BF, Wang GJ, Labiak PH, Rouhan G, Chen CW, Shepherd LD, Ohlsen DJ, Renner MAM, Karol KG, Li FW, Kuo LY. Systematics and Plastome Evolution in Schizaeaceae. FRONTIERS IN PLANT SCIENCE 2022; 13:885501. [PMID: 35909781 PMCID: PMC9328107 DOI: 10.3389/fpls.2022.885501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
While the family Schizaeaceae (Schizaeales) represents only about 0.4% of the extant fern species diversity, it differs from other ferns greatly in gross morphologies, niche preferences, and life histories. One of the most notable features in this family is its mycoheterotrophic life style in the gametophytic stage, which appears to be associated with extensive losses of plastid genes. However, the limited number of sequenced plastomes, and the lack of a well-resolved phylogenetic framework of Schizaeaceae, makes it difficult to gain any further insight. Here, with a comprehensive sampling of ~77% of the species diversity of this family, we first inferred a plastid phylogeny of Schizaeaceae using three DNA regions. To resolve the deep relationships within this family, we then reconstructed a plastome-based phylogeny focusing on a selection of representatives that covered all the major clades. From this phylogenomic backbone, we traced the evolutionary histories of plastid genes and examined whether gene losses were associated with the evolution of gametophytic mycoheterotrophy. Our results reveal that extant Schizaeaceae is comprised of four major clades-Microschizaea, Actinostachys, Schizaea, and Schizaea pusilla. The loss of all plastid NADH-like dehydrogenase (ndh) genes was confirmed to have occurred in the ancestor of extant Schizaeaceae, which coincides with the evolution of mycoheterotrophy in this family. For chlorophyll biosynthesis genes (chl), the losses were interpreted as convergent in Schizaeaceae, and found not only in Actinostachys, a clade producing achlorophyllous gametophytes, but also in S. pusilla with chlorophyllous gametophytes. In addition, we discovered a previously undescribed but phylogenetically distinct species hidden in the Schizaea dichotoma complex and provided a taxonomic treatment and morphological diagnostics for this new species-Schizaea medusa. Finally, our phylogenetic results suggest that the current PPG I circumscription of Schizaea is non-monophyletic, and we therefore proposed a three-genus classification moving a subset of Schizaea species sensu PPG I to a third genus-Microschizaea.
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Affiliation(s)
- Bing-Feng Ke
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Paulo H. Labiak
- Depto. de Botânica, Universidade Federal do Paraná, Curitiba, Brazil
| | - Germinal Rouhan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, EPHE, UA, CNRS, Sorbonne Université, Paris, France
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Cheng-Wei Chen
- Department of Life Science, Biodiversity Program, Taiwan International Graduate Program, Biodiversity Research Center, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | | | | | - Kenneth G. Karol
- The Lewis B. and Dorothy Cullman Program for Molecular Systematics, New York Botanical Garden, Bronx, NY, United States
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, United States
- Plant Biology Section, Cornell University, Ithaca, NY, United States
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
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16
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Robison T, Nelson JM, Hauser DA, Lewis LA, Li FW. Dynamic plastid and mitochondrial genomes in Chaetopeltidales (Chlorophyceae) and characterization of a new chlorophyte taxon. AMERICAN JOURNAL OF BOTANY 2022; 109:939-951. [PMID: 35678538 DOI: 10.1002/ajb2.16015] [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: 12/15/2021] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Chaetopeltidales is a poorly characterized order in the Chlorophyceae, with only two plastid and no mitochondrial genomes published. Here we describe a new taxon in Chaetopeltidales, Gormaniella terricola gen. et sp. nov. and characterize both of its organellar genomes. METHODS Gormaniella terricola was inadvertently isolated from a surface-sterilized hornwort thallus. Light microscopy was used to characterize its vegetative morphology. Organellar genomes were assembled, annotated, and analyzed using a variety of software packages. RESULTS The mitochondrial genome (66,927 bp) represents the first complete mitochondrial genome published for Chaetopeltidales. The chloroplast genome, measuring 428,981 bp, is one of the largest plastid genomes published to date and shares this large size and an incredible number of short, dispersed repeats with the other sequenced chloroplast genomes in Chaetopeltidales. Despite these shared features, the chloroplast genomes of Chaetopeltidales appear to be highly rearranged when compared to one another, with numerous inversions, translocations, and duplications, suggesting a particularly dynamic chloroplast genome. Both the chloroplast and mitochondrial genomes of G. terricola contain a number of mobile group I and group II introns, which appear to have invaded separately. Three of the introns within the mitochondrial genome encode homing endonucleases that are phylogenetically nested within those found in fungi, rather than algae, suggesting a possible case of horizontal gene transfer. CONCLUSIONS These results help to shed light on a poorly understood group of algae and their unusual organellar genomes, raising additional questions about the unique patterns of genome evolution within Chaetopeltidales.
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Affiliation(s)
- Tanner Robison
- Plant Biology Section, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | | | | | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Fay-Wei Li
- Plant Biology Section, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
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17
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Semerikov VL, Semerikova SA, Khrunyk YY, Putintseva YA. Sequence Capture of Mitochondrial Genome with PCR-Generated Baits Provides New Insights into the Biogeography of the Genus Abies Mill. PLANTS 2022; 11:plants11060762. [PMID: 35336644 PMCID: PMC8954396 DOI: 10.3390/plants11060762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 11/18/2022]
Abstract
Mitochondrial DNA (mtDNA), being maternally inherited in plants of the family Pinaceae, is an important source of phylogeographic information. However, its use is hindered by a low mutation rate and frequent structure rearrangements. In the present study, we tested the method of genomic libraries enrichment with mtDNA via the sequence capture method yielding mtDNA data which were further used to reconstruct the phylogenetic tree of the genus Abies. The baits for hybrid capture were obtained by long-range PCR using primers designed on the basis of the assembly of Abies sibirica Ledeb. mitochondrial genome. Mitochondrial genomes of Picea sitchensis (Bong.) Carr., Larix sibirica Ledeb., and Keteleeria davidiana (Bertrand) Beissn. were used as an outgroup. The resulting phylogenetic tree consists of two sister branches, including the Eurasian and American species, respectively, with some exceptions. The subclade of A. sachalinensis (F. Schmidt) Mast. and A. veitchii Lindl. (Japan and Sakhalin islands) occupies a basal position in the branch of American firs, probably due to the complex history of fir migrations from North America to Eurasia. The tree has high support for majority of clades. For species represented by more than one sample an intraspecific variability was found which is suitable to design mtDNA markers for phylogeographic and population studies.
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Affiliation(s)
- Vladimir L. Semerikov
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, 620144 Ekaterinburg, Russia;
- Correspondence: ; Tel.: +7-908-9190472
| | - Svetlana A. Semerikova
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, 620144 Ekaterinburg, Russia;
| | - Yuliya Y. Khrunyk
- Department of Heat Treatment and Physics of Metal, Ural Federal University Named after the First President of Russia B.N. Yeltsin, 620002 Ekaterinburg, Russia;
| | - Yuliya A. Putintseva
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia;
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18
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Sadamitsu A, Inoue Y, Sakakibara K, Tsubota H, Yamaguchi T, Deguchi H, Nishiyama T, Shimamura M. The complete plastid genome sequence of the enigmatic moss, Takakia lepidozioides (Takakiopsida, Bryophyta): evolutionary perspectives on the largest collection of genes in mosses and the intensive RNA editing. PLANT MOLECULAR BIOLOGY 2021; 107:431-449. [PMID: 34817767 DOI: 10.1007/s11103-021-01214-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Complete chloroplast genome sequence of a moss, Takakia lepidozioides (Takakiopsida) is reported. The largest collection of genes in mosses and the intensive RNA editing were discussed from evolutionary perspectives. We assembled the entire plastid genome sequence of Takakia lepidozioides (Takakiopsida), emerging from the first phylogenetic split among extant mosses. The genome sequences were assembled into a circular molecule 149,016 bp in length, with a quadripartite structure comprising a large and a small single-copy region separated by inverted repeats. It contained 88 genes coding for proteins, 32 for tRNA, four for rRNA, two open reading frames, and at least one pseudogene (tufA). This is the largest number of genes of all sequenced plastid genomes in mosses and Takakia is the only moss that retains the seven coding genes ccsA, cysA, cysT, petN rpoA, rps16 and trnPGGG. Parsimonious interpretation of gene loss suggests that the last common ancestor of bryophytes had all seven genes and that mosses lost at least three of them during their diversification. Analyses of the plastid transcriptome identified the extraordinary frequency of RNA editing with more than 1100 sites. We indicated a close correlation between the monoplastidy of vegetative tissue and the intensive RNA editing sites in the plastid genome in land plant lineages. Here, we proposed a hypothesis that the small population size of plastids in each vegetative cell of some early diverging land plants, including Takakia, might cause the frequent fixation of mutations in plastid genome through the intracellular genetic drift and that deleterious mutations might be continuously compensated by RNA editing during or following transcription.
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Affiliation(s)
- Atsushi Sadamitsu
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-8526, Japan
| | - Yuya Inoue
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
- Hattori Botanical Laboratory, 6-1-26 Obi, Nichinan, Miyazaki, 889-2535, Japan
| | - Keiko Sakakibara
- Department of Life Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Hiromi Tsubota
- Miyajima Natural Botanical Garden, Graduate School of Integrated Sciences for Life, Hiroshima University, 1156-2, Mitsumaruko-yama, Miyajima-cho, Hatsukaichi, Hiroshima, 739-0543, Japan
| | - Tomio Yamaguchi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-8526, Japan
| | - Hironori Deguchi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-8526, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, 920-0934, Japan
| | - Masaki Shimamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-8526, Japan.
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19
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Fan H, Wei G, Chen X, Guo H, Crandall-Stotler B, Köllner TG, Chen F. Sesquiterpene biosynthesis in a leafy liverwort Radula lindenbergiana Gottsche ex C. Hartm. PHYTOCHEMISTRY 2021; 190:112847. [PMID: 34237478 DOI: 10.1016/j.phytochem.2021.112847] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Liverworts (Marchantiophyta) are among the earliest diverging lineages of extant land plants. Among their unique features, most liverworts contain membrane-bound oil bodies, organelles that accumulate diverse secondary metabolites, especially terpenoids. In contrast to the rich information on liverwort terpenoid chemistry, little is known about their biosynthesis. Recently, terpenoid biosynthesis was studied in a model thalloid species Marchantiapolymorpha, in which sesquiterpenes and monoterpenes are biosynthesized by a new type of terpene synthases termed microbial terpene synthase-like (MTPSL) proteins. Here we study terpenoid biosynthesis in a leafy liverwort Radula lindenbergiana. Vegetative plants of R.lindenbergiana were found to contain a mixture of sesquiterpenes, with (E,E)-α-farnesene/β-curcumene and (Z)-β-bisabolene being the most abundant constituents. From the analysis of the R. lindenbergiana transcriptome, five full-length MTPSL genes were identified. They were designated RlMTPSL1-5, respectively. Recombinant RlMTPSL proteins were produced in Escherichia coli and tested for sesquiterpene synthase activities using farnesyl diphosphate (FPP) as substrate. All except RlMTPSL5 were demonstrated to catalyze the formation of different sesquiterpenes. RlMTPSL1 produced multiple sesquiterpenes with eremophilene and an unidentified sesquiterpene as major products. The major products of RlMTPSL2 and RlMTPSL3 were β-elemene and an unidentified sesquiterpene, respectively. RlMTPSL4 was also a multi-product sesquiterpene synthase with an unidentified sesquiterpene being the major product. Homology-based structural modeling was performed to understand the structural basis underlying different product profiles of the RlMTPSLs proteins. Most of the sesquiterpene products of the four active RlMTPSLs were also detected in R. lindenbergiana plants. Expression levels of the four RlMTPSL genes encoding active enzymes in vegetative plants were compared. In phylogenetic analysis, RlMTPSL genes were found to cluster together, indicating lineage-specific expansion of MTPSL genes in lineages leading to R.lindenbergiana and M. polymorpha. This study strengthens evidence for the contribution of MTPSL genes to terpenoid biosynthesis in liverworts.
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Affiliation(s)
- Honghong Fan
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA; School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Guo Wei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Hong Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Tobias G Köllner
- Department of Biochemistry, Max-Planck-Institute for Chemical Ecology, Hans-Knöll Str. 8, D-07745, Jena, Germany
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
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20
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Flores JR, Bippus AC, Suárez GM, Hyvönen J. Defying death: incorporating fossils into the phylogeny of the complex thalloid liverworts (Marchantiidae, Marchantiophyta) confirms high order clades but reveals discrepancies in family-level relationships. Cladistics 2021; 37:231-247. [PMID: 34478198 DOI: 10.1111/cla.12442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2020] [Indexed: 12/13/2022] Open
Abstract
In recent years, the use of extensive molecular and morphological datasets has clarified the phylogenetic relationships among the orders of complex thalloid liverworts (Marchantiidae). However, previous studies excluded extinct taxa; thereby, undersampling the actual taxonomic diversity of the group. Here, we conducted a total-evidence analysis of Marchantiidae incorporating fossils. The combined dataset consisted of 11 genes-sampled from the nuclear, mitochondrial and plastid genomes-and 128 morphological characters. Sixty-two species, representing all classes and orders within Marchantiophyta and genera within Marchantiidae were included in the analyses. Six fossils were scored from literature: two assigned to the outgroup (Metzgeriothallus sharonae and Pallaviciniites sandaolingensis) and four to the ingroup (Marchantites cyathodoides, M. huolinhensis, Ricciopsis ferganica and R. sandaolingensis). Tree searches were conducted using parsimony as the optimality criterion. Clade sensitivity was assessed across a wide range of weighting regimes. Also, we evaluated the influence of fossils on the inferred topologies and branch support. Our results were congruent with previously inferred clades above the order level: Neohodgsoniales was sister to a clade formed by Sphaerocarpales and Marchantiales. However, relationships among families within Marchantiales contradicted recent studies. For instance, a clade consisting of Monosoleniaceae, Wiesnerellaceae and Targioniaceae was sister to the morphologically simple taxa instead of being nested within them as in previous studies. Novel synapomorphies were found for several clades within Marchantiales. Outgroup fossils were more influential than Marchantiidae fossils on overall topologies and branch support values. Except for a single weighting scheme, sampling continuous characters and down-weighting characters improved fossil stability. Ultimately, our results challenge the widespread notion that bryophyte fossils are problematic for phylogenetic inference.
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Affiliation(s)
- Jorge R Flores
- Finnish Museum of Natural History (Botany), University of Helsinki, PO Box 7, Helsinki, FI-00014, Finland
| | - Alexander C Bippus
- Department of Botany and Plant Pathology, Oregon State University, 2701 SW Campus Way, Corvallis, OR, 97331, USA
| | - Guillermo M Suárez
- Unidad Ejecutora Lillo (CONICET - Fundación Miguel Lillo), Miguel Lillo 251, San Miguel de Tucumán, Tucumán, 4000, Argentina.,Facultad de Ciencias Naturales, Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán, Tucumán, 4000, Argentina
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany), University of Helsinki, PO Box 7, Helsinki, FI-00014, Finland.,Organismal and Evolutionary Biology, Viikki Plant Science Centre, University of Helsinki, PO Box 65, Helsinki, FI-00014, Finland
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21
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Baker WJ, Dodsworth S, Forest F, Graham SW, Johnson MG, McDonnell A, Pokorny L, Tate JA, Wicke S, Wickett NJ. Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants. AMERICAN JOURNAL OF BOTANY 2021; 108:1059-1065. [PMID: 34293179 DOI: 10.1002/ajb2.1703] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Affiliation(s)
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Angela McDonnell
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Jennifer A Tate
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Susann Wicke
- Plant Evolutionary Biology, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Plant Systematics and Biodiversity, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
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22
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Jin XJ, Zhu RL. The complete plastome of Polytrichum commune Hedw. (Polytrichaceae, Bryophyta). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1645-1647. [PMID: 34027080 PMCID: PMC8128170 DOI: 10.1080/23802359.2021.1927223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Polytrichum commune, one of hair-cap mosses, is the type species of the genus Polytrichum Hedw. (Polytrichaceae). Here we present its complete plastome. The plastome of P. commune is successfully assembled from raw reads sequenced by HiSeq X ten system. Its total length is 126,323 bp consisting of four regions: large single copy (LSC) region (88,070 bp), small single copy (SSC) region (16,717 bp), and inverted repeats (IRs; 9,680 bp per each). It contains 128 genes (84 coding genes, eight rRNAs, and 36 tRNAs); nine genes (four rRNAs and five tRNAs) are duplicated in IR regions. The overall GC content is 28.9% and in the LSC, SSC and IR regions is 26.1%, 25.1%, and 45.5%, respectively. This plastome is an important sequence resource for further studies on the class Polytrichopsida.
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Affiliation(s)
- Xin-Jie Jin
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, China
| | - Rui-Liang Zhu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, China
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23
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Su D, Yang L, Shi X, Ma X, Zhou X, Hedges SB, Zhong B. Large-Scale Phylogenomic Analyses Reveal the Monophyly of Bryophytes and Neoproterozoic Origin of Land Plants. Mol Biol Evol 2021; 38:3332-3344. [PMID: 33871608 PMCID: PMC8321542 DOI: 10.1093/molbev/msab106] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The relationships among the four major embryophyte lineages (mosses, liverworts, hornworts, vascular plants) and the timing of the origin of land plants are enigmatic problems in plant evolution. Here, we resolve the monophyly of bryophytes by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions. We then estimate the divergence time of crown embryophytes based on three fossil calibration strategies, and reveal that maximum calibration constraints have a major effect on estimating the time of origin of land plants. Moreover, comparison of priors and posteriors provides a guide for evaluating the optimal calibration strategy. By considering the reliability of fossil calibrations and the influences of molecular data, we estimate that land plants originated in the Precambrian (980–682 Ma), much older than widely recognized. Our study highlights the important contribution of molecular data when faced with contentious fossil evidence, and that fossil calibrations used in estimating the timescale of plant evolution require critical scrutiny.
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Affiliation(s)
- Danyan Su
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuan Shi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - S Blair Hedges
- Center for Biodiversity, Temple University, Philadelphia, PA, USA
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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24
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Ignatov MS, Spirina UN, Kolesnikova MA, Larraín J, Ignatova EA. Cell Division Patterns in the Peristomial Layers of the Moss Genus Costesia: Two Hypotheses and a Third Solution. FRONTIERS IN PLANT SCIENCE 2020; 11:536862. [PMID: 33013962 PMCID: PMC7498844 DOI: 10.3389/fpls.2020.536862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
The Chilean endemic genus Costesia belongs to the Gigaspermaceae, one of the most basal groups of arthrodontous mosses. While none of the species in this family has a peristome, earlier stages of sporophyte development often disclose its basic structure. The study of Costesia sporophytes at the early stages of development was conducted to identify possible similarities with Diphyscium, the genus sister to Gigaspermaceae plus all other arthrodontous mosses in the moss phylogenetic tree. Diphyscium shares a strongly unequal cell division pattern with the Dicranidae. In groups more closely related to Diphyscium, as it is the case of Costesia, this pattern is not known. Our study of Costesia found only irregular presence of slightly unequal cell divisions that may then be considered as a plesiomorphic state in peristomate mosses. The most frequently present pattern revealed in Costesia is common with the Polytrichaceae, a more basal moss group with nematodontous peristomes.
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Affiliation(s)
- Michael S. Ignatov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Tsitsin Main Botanical Garden, Russian Academy of Sciences, Moscow, Russia
| | - Ulyana N. Spirina
- Tsitsin Main Botanical Garden, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Tver State University, Tver, Russia
| | | | - Juan Larraín
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Elena A. Ignatova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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25
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Soto Gomez M, Lin Q, Silva Leal E, Gallaher TJ, Scherberich D, Mennes CB, Smith SY, Graham SW. A bi‐organellar phylogenomic study of Pandanales: inference of higher‐order relationships and unusual rate‐variation patterns. Cladistics 2020; 36:481-504. [DOI: 10.1111/cla.12417] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Marybel Soto Gomez
- Department of Botany University of British Columbia 6270 University Boulevard Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research University of British Columbia 6804 Marine Drive SW Vancouver BC V6T 1Z4 Canada
| | - Qianshi Lin
- Department of Botany University of British Columbia 6270 University Boulevard Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research University of British Columbia 6804 Marine Drive SW Vancouver BC V6T 1Z4 Canada
| | - Eduardo Silva Leal
- Universidade Federal Rural da Amazônia, Campus Capanema Avenida Barão de Capanema s/n Capanema68700-665 PA Brazil
| | | | - David Scherberich
- Jardin Botanique de la Ville de Lyon Mairie de Lyon69205 Lyon Cedex 01 France
| | | | - Selena Y. Smith
- Department of Earth & Environmental Sciences and Museum of Paleontology University of Michigan Ann Arbor MI 48109 USA
| | - Sean W. Graham
- Department of Botany University of British Columbia 6270 University Boulevard Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research University of British Columbia 6804 Marine Drive SW Vancouver BC V6T 1Z4 Canada
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26
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Sousa F, Civáň P, Brazão J, Foster PG, Cox CJ. The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models. PeerJ 2020; 8:e8995. [PMID: 32377448 PMCID: PMC7194085 DOI: 10.7717/peerj.8995] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/26/2020] [Indexed: 01/04/2023] Open
Abstract
Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics. Recent analyses of both nuclear and chloroplast genome data of land plants (embryophytes) have, controversially, been shown to support monophyly of both bryophytes (mosses, liverworts, and hornworts) and tracheophytes (lycopods, ferns, and seed plants), with mosses and liverworts forming the clade Setaphyta. However, relationships inferred from mitochondria are incongruent with these results, and typically indicate paraphyly of bryophytes with liverworts alone resolved as the earliest-branching land plant group. Here, we reconstruct the mitochondrial land plant phylogeny from a newly compiled data set. When among-lineage composition heterogeneity is accounted for in analyses of codon-degenerate nucleotide and amino acid data, the clade Setaphyta is recovered with high support, and hornworts are supported as the earliest-branching lineage of land plants. These new mitochondrial analyses demonstrate partial congruence with current hypotheses based on nuclear and chloroplast genome data, and provide further incentive for revision of how plants arose on land.
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Affiliation(s)
- Filipe Sousa
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Peter Civáň
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
- INRAE-Université Clermont-Auvergne, Clermont-Ferrand, France
| | - João Brazão
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Peter G. Foster
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Cymon J. Cox
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
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