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Zuntini AR, Carruthers T, Maurin O, Bailey PC, Leempoel K, Brewer GE, Epitawalage N, Françoso E, Gallego-Paramo B, McGinnie C, Negrão R, Roy SR, Simpson L, Toledo Romero E, Barber VMA, Botigué L, Clarkson JJ, Cowan RS, Dodsworth S, Johnson MG, Kim JT, Pokorny L, Wickett NJ, Antar GM, DeBolt L, Gutierrez K, Hendriks KP, Hoewener A, Hu AQ, Joyce EM, Kikuchi IABS, Larridon I, Larson DA, de Lírio EJ, Liu JX, Malakasi P, Przelomska NAS, Shah T, Viruel J, Allnutt TR, Ameka GK, Andrew RL, Appelhans MS, Arista M, Ariza MJ, Arroyo J, Arthan W, Bachelier JB, Bailey CD, Barnes HF, Barrett MD, Barrett RL, Bayer RJ, Bayly MJ, Biffin E, Biggs N, Birch JL, Bogarín D, Borosova R, Bowles AMC, Boyce PC, Bramley GLC, Briggs M, Broadhurst L, Brown GK, Bruhl JJ, Bruneau A, Buerki S, Burns E, Byrne M, Cable S, Calladine A, Callmander MW, Cano Á, Cantrill DJ, Cardinal-McTeague WM, Carlsen MM, Carruthers AJA, de Castro Mateo A, Chase MW, Chatrou LW, Cheek M, Chen S, Christenhusz MJM, Christin PA, Clements MA, Coffey SC, Conran JG, Cornejo X, Couvreur TLP, Cowie ID, Csiba L, Darbyshire I, Davidse G, Davies NMJ, Davis AP, van Dijk KJ, Downie SR, Duretto MF, Duvall MR, Edwards SL, Eggli U, Erkens RHJ, Escudero M, de la Estrella M, Fabriani F, Fay MF, Ferreira PDL, Ficinski SZ, Fowler RM, Frisby S, Fu L, Fulcher T, Galbany-Casals M, Gardner EM, German DA, Giaretta A, Gibernau M, Gillespie LJ, González CC, Goyder DJ, Graham SW, Grall A, Green L, Gunn BF, Gutiérrez DG, Hackel J, Haevermans T, Haigh A, Hall JC, Hall T, Harrison MJ, Hatt SA, Hidalgo O, Hodkinson TR, Holmes GD, Hopkins HCF, Jackson CJ, James SA, Jobson RW, Kadereit G, Kahandawala IM, Kainulainen K, Kato M, Kellogg EA, King GJ, Klejevskaja B, Klitgaard BB, Klopper RR, Knapp S, Koch MA, Leebens-Mack JH, Lens F, Leon CJ, Léveillé-Bourret É, Lewis GP, Li DZ, Li L, Liede-Schumann S, Livshultz T, Lorence D, Lu M, Lu-Irving P, Luber J, Lucas EJ, Luján M, Lum M, Macfarlane TD, Magdalena C, Mansano VF, Masters LE, Mayo SJ, McColl K, McDonnell AJ, McDougall AE, McLay TGB, McPherson H, Meneses RI, Merckx VSFT, Michelangeli FA, Mitchell JD, Monro AK, Moore MJ, Mueller TL, Mummenhoff K, Munzinger J, Muriel P, Murphy DJ, Nargar K, Nauheimer L, Nge FJ, Nyffeler R, Orejuela A, Ortiz EM, Palazzesi L, Peixoto AL, Pell SK, Pellicer J, Penneys DS, Perez-Escobar OA, Persson C, Pignal M, Pillon Y, Pirani JR, Plunkett GM, Powell RF, Prance GT, Puglisi C, Qin M, Rabeler RK, Rees PEJ, Renner M, Roalson EH, Rodda M, Rogers ZS, Rokni S, Rutishauser R, de Salas MF, Schaefer H, Schley RJ, Schmidt-Lebuhn A, Shapcott A, Al-Shehbaz I, Shepherd KA, Simmons MP, Simões AO, Simões ARG, Siros M, Smidt EC, Smith JF, Snow N, Soltis DE, Soltis PS, Soreng RJ, Sothers CA, Starr JR, Stevens PF, Straub SCK, Struwe L, Taylor JM, Telford IRH, Thornhill AH, Tooth I, Trias-Blasi A, Udovicic F, Utteridge TMA, Del Valle JC, Verboom GA, Vonow HP, Vorontsova MS, de Vos JM, Al-Wattar N, Waycott M, Welker CAD, White AJ, Wieringa JJ, Williamson LT, Wilson TC, Wong SY, Woods LA, Woods R, Worboys S, Xanthos M, Yang Y, Zhang YX, Zhou MY, Zmarzty S, Zuloaga FO, Antonelli A, Bellot S, Crayn DM, Grace OM, Kersey PJ, Leitch IJ, Sauquet H, Smith SA, Eiserhardt WL, Forest F, Baker WJ. Phylogenomics and the rise of the angiosperms. Nature 2024; 629:843-850. [PMID: 38658746 PMCID: PMC11111409 DOI: 10.1038/s41586-024-07324-0] [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: 09/15/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.
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Affiliation(s)
| | | | | | | | | | | | | | - Elaine Françoso
- Royal Botanic Gardens, Kew, Richmond, UK
- Centre for Ecology, Evolution and Behaviour, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, London, UK
| | | | | | | | | | - Lalita Simpson
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | | | | | - Laura Botigué
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | | | | | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | | | - Jan T Kim
- School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield, UK
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC), Madrid, Spain
| | - Norman J Wickett
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Guilherme M Antar
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Ciências Agrárias e Biológicas, Centro Universitário Norte do Espírito Santo, Universidade Federal do Espírito Santo, São Mateus, Brazil
| | | | | | - Kasper P Hendriks
- Department of Biology, University of Osnabrück, Osnabrück, Germany
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Alina Hoewener
- Plant Biodiversity, Technical University Munich, Freising, Germany
| | - Ai-Qun Hu
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Elizabeth M Joyce
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
- Systematic, Biodiversity and Evolution of Plants, Ludwig Maximilian University of Munich, Munich, Germany
| | - Izai A B S Kikuchi
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Drew A Larson
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Elton John de Lírio
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | | | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, Richmond, UK
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Toral Shah
- Royal Botanic Gardens, Kew, Richmond, UK
| | | | | | - Gabriel K Ameka
- Department of Plant and Environmental Biology, University of Ghana, Accra, Ghana
| | - Rose L Andrew
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
| | - Marc S Appelhans
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute of Plant Sciences, University of Göttingen, Göttingen, Germany
| | - Montserrat Arista
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - María Jesús Ariza
- General Research Services, Herbario SEV, CITIUS, Universidad de Sevilla, Seville, Spain
| | - Juan Arroyo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | | | | | - C Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Helen F Barnes
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Matthew D Barrett
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | - Russell L Barrett
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Randall J Bayer
- Department of Biological Sciences, University of Memphis, Memphis, TN, USA
| | - Michael J Bayly
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ed Biffin
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | | | - Joanne L Birch
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Diego Bogarín
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, Costa Rica
| | | | | | - Peter C Boyce
- Centro Studi Erbario Tropicale, Dipartimento di Biologia, University of Florence, Florence, Italy
| | | | | | - Linda Broadhurst
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Gillian K Brown
- Queensland Herbarium and Biodiversity Science, Brisbane Botanic Gardens, Toowong, Queensland, Australia
| | - Jeremy J Bruhl
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, University of Montreal, Montreal, Quebec, Canada
| | - Sven Buerki
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Edie Burns
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | | | - Ainsley Calladine
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | | | - Ángela Cano
- Cambridge University Botanic Garden, Cambridge, UK
| | | | - Warren M Cardinal-McTeague
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Alejandra de Castro Mateo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Mark W Chase
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | | | | | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, China
| | - Maarten J M Christenhusz
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
- Plant Gateway, Den Haag, The Netherlands
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Mark A Clements
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Skye C Coffey
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | - John G Conran
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Xavier Cornejo
- Herbario GUAY, Facultad de Ciencias Naturales, Universidad de Guayaquil, Guayaquil, Ecuador
| | | | - Ian D Cowie
- Northern Territory Herbarium Department of Environment Parks & Water Security, Northern Territory Government, Palmerston, Northern Territory, Australia
| | | | | | | | | | | | - Kor-Jent van Dijk
- The University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Stephen R Downie
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Marco F Duretto
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Melvin R Duvall
- Department of Biological Sciences and Institute for the Study of the Environment, Sustainability and Energy, Northern Illinois University, DeKalb, IL, USA
| | | | - Urs Eggli
- Sukkulenten-Sammlung Zürich/ Grün Stadt Zürich, Zürich, Switzerland
| | - Roy H J Erkens
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
- System Earth Science, Maastricht University, Venlo, The Netherlands
| | - Marcial Escudero
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Manuel de la Estrella
- Departamento de Botánica, Ecología y Fisiología Vegetal, Facultad de Ciencias, Universidad de Córdoba, Córdoba, Spain
| | | | | | - Paola de L Ferreira
- Departamento de Biologia, Faculdade de Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Rachael M Fowler
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Sue Frisby
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Lin Fu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | - Mercè Galbany-Casals
- Systematics and Evolution of Vascular Plants (UAB)-Associated Unit to CSIC by IBB, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Elliot M Gardner
- Department of Biology, Case Western Reserve University, Cleveland, OH, USA
| | | | - Augusto Giaretta
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, Dourados, Brazil
| | - Marc Gibernau
- Laboratoire Sciences Pour l'Environnement, Université de Corse, Ajaccio, France
| | | | - Cynthia C González
- Herbario Trelew, Universidad Nacional de la Patagonia San Juan Bosco, Trelew, Argentina
| | | | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Bee F Gunn
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Diego G Gutiérrez
- Museo Argentino de Ciencias Naturales (MACN-CONICET), Buenos Aires, Argentina
| | - Jan Hackel
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biology, Universität Marburg, Marburg, Germany
| | - Thomas Haevermans
- Institut de Systématique, Evolution, Biodiversité, Muséum National d'Histoire Naturelle, Paris, France
| | - Anna Haigh
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tony Hall
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Melissa J Harrison
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | | | - Oriane Hidalgo
- Institut Botànic de Barcelona (IBB CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Trevor R Hodkinson
- Botany, School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Gareth D Holmes
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | | | | | - Shelley A James
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | - Richard W Jobson
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Gudrun Kadereit
- Prinzessin Therese von Bayern-Lehrstuhl für Systematik, Biodiversität & Evolution der Pflanzen, Ludwig-Maximilians-Universität München, Botanische Staatssammlung München, Botanischer Garten München-Nymphenburg, Munich, Germany
| | | | | | - Masahiro Kato
- National Museum of Nature and Science, Tsukuba, Japan
| | | | - Graham J King
- Southern Cross University, Lismore, New South Wales, Australia
| | | | | | - Ronell R Klopper
- Foundational Biodiversity Science Division, South African National Biodiversity Institute, Pretoria, South Africa
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Marcus A Koch
- Centre for Organismal Studies, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
| | | | - Frederic Lens
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | | | | | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lan Li
- CSIRO, Canberra, Australian Capital Territory, Australia
| | | | - Tatyana Livshultz
- Department of Biodiversity, Earth and Environmental Sciences, Drexel University, Philadelphia, PA, USA
- Academy of Natural Science, Drexel University, Philadelphia, PA, USA
| | - David Lorence
- National Tropical Botanical Garden, Kalaheo, HI, USA
| | - Meng Lu
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Patricia Lu-Irving
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Jaquelini Luber
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Mabel Lum
- Bioplatforms Australia Ltd, Sydney, New South Wales, Australia
| | - Terry D Macfarlane
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | | | - Vidal F Mansano
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Kristina McColl
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Angela J McDonnell
- Department of Biological Sciences, Saint Cloud State University, Saint Cloud, MN, USA
| | - Andrew E McDougall
- The University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Todd G B McLay
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Hannah McPherson
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Rosa I Meneses
- Instituto de Arqueología y Antropología, Universidad Católica del Norte, San Pedro de Atacama, Chile
| | | | | | | | | | | | - Taryn L Mueller
- Department of Ecology, Evolution & Behavior, University of Minnesota, St. Paul, MN, USA
| | - Klaus Mummenhoff
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Jérôme Munzinger
- AMAP Lab, Université Montpellier, IRD, CIRAD, CNRS INRAE, Montpellier, France
| | - Priscilla Muriel
- Laboratorio de Ecofisiología, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | - Francis J Nge
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | - Reto Nyffeler
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Andrés Orejuela
- Royal Botanic Garden Edinburgh, Edinburgh, UK
- Grupo de Investigación en Recursos Naturales Amazónicos, Instituto Tecnológico del Putumayo, Mocoa, Colombia
| | - Edgardo M Ortiz
- Plant Biodiversity, Technical University Munich, Freising, Germany
| | - Luis Palazzesi
- Museo Argentino de Ciencias Naturales (MACN-CONICET), Buenos Aires, Argentina
| | - Ariane Luna Peixoto
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Jaume Pellicer
- Institut Botànic de Barcelona (IBB CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Darin S Penneys
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | | | - Claes Persson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Marc Pignal
- Institut de Systématique, Evolution, Biodiversité, Muséum National d'Histoire Naturelle, Paris, France
| | - Yohan Pillon
- LSTM Université Montpellier, CIRADIRD, Montpellier, France
| | - José R Pirani
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Carmen Puglisi
- Royal Botanic Gardens, Kew, Richmond, UK
- Missouri Botanical Garden, St. Louis, MO, USA
| | - Ming Qin
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Richard K Rabeler
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Matthew Renner
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michele Rodda
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | | | - Saba Rokni
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Rolf Rutishauser
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Miguel F de Salas
- Tasmanian Herbarium, University of Tasmania, Sandy Bay, Tasmania, Australia
| | - Hanno Schaefer
- Plant Biodiversity, Technical University Munich, Freising, Germany
| | | | - Alexander Schmidt-Lebuhn
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Alison Shapcott
- School of Science Technology and Engineering, Center for Bioinnovation, University Sunshine Coast, Sippy Downs, Queensland, Australia
| | | | - Kelly A Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - André O Simões
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, Brazil
| | | | - Michelle Siros
- Royal Botanic Gardens, Kew, Richmond, UK
- University of California, San Francisco, San Francisco, CA, USA
| | - Eric C Smidt
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Brazil
| | - James F Smith
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Neil Snow
- Pittsburg State University, Pittsburg, KS, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | | | | | - Julian R Starr
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | | | | | - Ian R H Telford
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
| | - Andrew H Thornhill
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Ifeanna Tooth
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | | | - Frank Udovicic
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | | | - Jose C Del Valle
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - G Anthony Verboom
- Department of Biological Sciences and Bolus Herbarium, University of Cape Town, Cape Town, South Africa
| | - Helen P Vonow
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | | | - Jurriaan M de Vos
- Department of Environmental Sciences-Botany, University of Basel, Basel, Switzerland
| | | | - Michelle Waycott
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Cassiano A D Welker
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Adam J White
- Australian National Herbarium, Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | | | - Luis T Williamson
- The University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Trevor C Wilson
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Sin Yeng Wong
- Institute of Biodiversity And Environmental Conservation, Universiti Malaysia Sarawak, Samarahan, Malaysia
| | - Lisa A Woods
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | | | - Stuart Worboys
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | | | - Ya Yang
- University of Minnesota-Twin Cities, St. Paul, MN, USA
| | | | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | | | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Darren M Crayn
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | - Olwen M Grace
- Royal Botanic Gardens, Kew, Richmond, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | | | - Hervé Sauquet
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - William J Baker
- Royal Botanic Gardens, Kew, Richmond, UK.
- Department of Biology, Aarhus University, Aarhus, Denmark.
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2
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Han S, Zhang S, Yi R, Bi D, Ding H, Yang J, Ye Y, Xu W, Wu L, Zhuo R, Kan X. Phylogenomics and plastomics offer new evolutionary perspectives on Kalanchoideae (Crassulaceae). ANNALS OF BOTANY 2024; 133:585-604. [PMID: 38359907 PMCID: PMC11037489 DOI: 10.1093/aob/mcae017] [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: 01/05/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND AND AIMS Kalanchoideae is one of three subfamilies within Crassulaceae and contains four genera. Despite previous efforts, the phylogeny of Kalanchoideae remains inadequately resolved with persistent issues including low support, unstructured topologies and polytomies. This study aimed to address two central objectives: (1) resolving the pending phylogenetic questions within Kalanchoideae by using organelle-scale 'barcodes' (plastomes) and nuclear data; and (2) investigating interspecific diversity patterns among Kalanchoideae plastomes. METHODS To explore the plastome evolution in Kalanchoideae, we newly sequenced 38 plastomes representing all four constituent genera (Adromischus, Cotyledon, Kalanchoe and Tylecodon). We performed comparative analyses of plastomic features, including GC and gene contents, gene distributions at the IR (inverted repeat) boundaries, nucleotide divergence, plastomic tRNA (pttRNA) structures and codon aversions. Additionally, phylogenetic inferences were inferred using both the plastomic dataset (79 genes) and nuclear dataset (1054 genes). KEY RESULTS Significant heterogeneities were observed in plastome lengths among Kalanchoideae, strongly correlated with LSC (large single copy) lengths. Informative diversities existed in the gene content at SSC/IRa (small single copy/inverted repeat a), with unique patterns individually identified in Adromischus leucophyllus and one major Kalanchoe clade. The ycf1 gene was assessed as a shared hypervariable region among all four genera, containing nine lineage-specific indels. Three pttRNAs exhibited unique structures specific to Kalanchoideae and the genera Adromischus and Kalanchoe. Moreover, 24 coding sequences revealed a total of 41 lineage-specific unused codons across all four constituent genera. The phyloplastomic inferences clearly depicted internal branching patterns in Kalanchoideae. Most notably, by both plastid- and nuclear-based phylogenies, our research offers the first evidence that Kalanchoe section Eukalanchoe is not monophyletic. CONCLUSIONS This study conducted comprehensive analyses on 38 newly reported Kalanchoideae plastomes. Importantly, our results not only reconstructed well-resolved phylogenies within Kalanchoideae, but also identified highly informative unique markers at the subfamily, genus and species levels. These findings significantly enhance our understanding of the evolutionary history of Kalanchoideae.
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Affiliation(s)
- Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ran Yi
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - De Bi
- Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
| | - Hengwu Ding
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jianke Yang
- School of Basic Medical Sciences, Wannan Medical College, Wuhu 241000, China
| | - Yuanxin Ye
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Wenzhong Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Longhua Wu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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3
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Choi TY, Lee SR. Complete plastid genome of Iris orchioides and comparative analysis with 19 Iris plastomes. PLoS One 2024; 19:e0301346. [PMID: 38578735 PMCID: PMC10997070 DOI: 10.1371/journal.pone.0301346] [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: 12/10/2023] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
Iris is a cosmopolitan genus comprising approximately 280 species distributed throughout the Northern Hemisphere. Although Iris is the most diverse group in the Iridaceae, the number of taxa is debatable owing to various taxonomic issues. Plastid genomes have been widely used for phylogenetic research in plants; however, only limited number of plastid DNA markers are available for phylogenetic study of the Iris. To understand the genomic features of plastids within the genus, including its structural and genetic variation, we newly sequenced and analyzed the complete plastid genome of I. orchioides and compared it with those of 19 other Iris taxa. Potential plastid markers for phylogenetic research were identified by computing the sequence divergence and phylogenetic informativeness. We then tested the utility of the markers with the phylogenies inferred from the markers and whole-plastome data. The average size of the plastid genome was 152,926 bp, and the overall genomic content and organization were nearly identical among the 20 Iris taxa, except for minor variations in the inverted repeats. We identified 10 highly informative regions (matK, ndhF, rpoC2, ycf1, ycf2, rps15-ycf, rpoB-trnC, petA-psbJ, ndhG-ndhI and psbK-trnQ) and inferred a phylogeny from each region individually, as well as from their concatenated data. Remarkably, the phylogeny reconstructed from the concatenated data comprising three selected regions (rpoC2, ycf1 and ycf2) exhibited the highest congruence with the phylogeny derived from the entire plastome dataset. The result suggests that this subset of data could serve as a viable alternative to the complete plastome data, especially for molecular diagnoses among closely related Iris taxa, and at a lower cost.
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Affiliation(s)
- Tae-Young Choi
- Department of Biology Education, Chosun University, Gwangju, South Korea
| | - Soo-Rang Lee
- Department of Biology Education, Chosun University, Gwangju, South Korea
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4
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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 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.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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5
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Do VM, Thieu VD, Mai VH. Research on Passiflora foetida L. as a Pharmaceutical Treatment for Neurasthenia in Humans. Pak J Biol Sci 2023; 26:504-509. [PMID: 38110555 DOI: 10.3923/pjbs.2023.504.509] [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] [Indexed: 12/20/2023]
Abstract
<b>Background and Objective:</b> This plant is known in many parts of the world and is used as medicine in some countries. In Vietnam, people know how to use <i>Passiflora foetida </i>L.,<i> </i>as an herb. There are many research works in the world, most of them focus on medicinal properties. The objective of this study was to determine the genetic diversity of samples of <i>Passiflora foetida </i>L., yellow fruit based on agronomic traits and the gene region of "<i>rbcL</i>". <b>Materials and Methods:</b> Seed samples were arranged in a completely randomized design with three replications. The trial was a sample of <i>Passiflora foetida </i>L., species. The distance between sample plant is 3×2 m, so the total number of trees is 1,330 trees ha<sup>1</sup>. The genetic relationship between them was determined through the construction of a phylogenetic tree in the "<i>rbcL</i>" gene region sequence. Data analysis and processing methods done by using X software. <b>Results:</b> The PCR results that amplify the "<i>rbcL</i>" gene region around 670 bp, the PCR products were then sequenced. The sequence results were compared with the sequences on the NCBI gene bank, showing that the sequences of the nine varieties/species all coincided with the <i>Passiflora foetida </i>Sims species sequences with a high similarity coefficient from 98.77 to 99.9%. Genetically shows that all nine species samples belong to <i>Passiflora foetida</i> which can be classified into three genetic samples of An Giang (LA1), Ca Mau (LA2) and Can Tho (LA3) which are genetically close to each other, have the same index. <b>Conclusion:</b> The heritability in the broad sense is high in the two traits of stem height and leaf length, so it can be considered that these two traits are controlled by genes. The cultivation of algae seeds to improve the productivity of these medicinal plant varieties is important in providing raw materials for the oriental medicine industry.
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6
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Frazão A, Thode VA, Lohmann LG. Comparative chloroplast genomics and insights into the molecular evolution of Tanaecium (Bignonieae, Bignoniaceae). Sci Rep 2023; 13:12469. [PMID: 37528152 PMCID: PMC10394017 DOI: 10.1038/s41598-023-39403-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
Species of Tanaecium (Bignonieae, Bignoniaceae) are lianas distributed in the Neotropics and centered in the Amazon. Members of the genus exhibit exceptionally diverse flower morphology and pollination systems. Here, we sequenced, assembled, and annotated 12 complete and four partial chloroplast genomes representing 15 Tanaecium species and more than 70% of the known diversity in the genus. Gene content and order were similar in all species of Tanaecium studied, with genome sizes ranging between 158,470 and 160,935 bp. Tanaecium chloroplast genomes have 137 genes, including 80-81 protein-coding genes, 37 tRNA genes, and four rRNA genes. No rearrangements were found in Tanaecium plastomes, but two different patterns of boundaries between regions were recovered. Tanaecium plastomes show nucleotide variability, although only rpoA was hypervariable. Multiple SSRs and repeat regions were detected, and eight genes were found to have signatures of positive selection. Phylogeny reconstruction using 15 Tanaecium plastomes resulted in a strongly supported topology, elucidating several relationships not recovered previously and bringing new insights into the evolution of the genus.
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Affiliation(s)
- Annelise Frazão
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
- Departamento de Biodiversidade e Bioestatística, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil.
| | - Verônica A Thode
- Programa de Pós-Graduação em Botânica, Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lúcia G Lohmann
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
- Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, USA.
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7
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Zhou S, Zhi X, Yu R, Liu Y, Zhou R. Factors contributing to mitogenome size variation and a recurrent intracellular DNA transfer in Melastoma. BMC Genomics 2023; 24:370. [PMID: 37393222 DOI: 10.1186/s12864-023-09488-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/27/2023] [Indexed: 07/03/2023] Open
Abstract
BACKGROUND Mitogenome sizes of seed plants vary substantially even among closely related species, which are often related to horizontal or intracellular DNA transfer (HDT or IDT) events. However, the mechanisms of this size variation have not been well characterized. RESULTS Here we assembled and characterized the mitogenomes of three species of Melastoma, a tropical shrub genus experiencing rapid speciation. The mitogenomes of M. candidum (Mc), M. sanguineum (Ms) and M. dodecandrum (Md) were assembled to a circular mapping chromosome of 391,595 bp, 395,542 bp and 412,026 bp, respectively. While the mitogenomes of Mc and Ms showed good collinearity except for a large inversion of ~ 150 kb, there were many rearrangements in the mitogenomes between Md and either Mc or Ms. Most non-alignable sequences (> 80%) between Mc and Ms are from gain or loss of mitochondrial sequences. Whereas, between Md and either Mc or Ms, non-alignable sequences in Md are mainly chloroplast derived sequences (> 30%) and from putative horizontal DNA transfers (> 30%), and those in both Mc and Ms are from gain or loss of mitochondrial sequences (> 80%). We also identified a recurrent IDT event in another congeneric species, M. penicillatum, which has not been fixed as it is only found in one of the three examined populations. CONCLUSIONS By characterizing mitochondrial genome sequences of Melastoma, our study not only helps understand mitogenome size evolution in closely related species, but also cautions different evolutionary histories of mitochondrial regions due to potential recurrent IDT events in some populations or species.
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Affiliation(s)
- Shuaixi Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xueke Zhi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Runxian Yu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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8
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Xia Q, Zhang H, Lv D, El-Kassaby YA, Li W. Insights into phylogenetic relationships in Pinus inferred from a comparative analysis of complete chloroplast genomes. BMC Genomics 2023; 24:346. [PMID: 37349702 DOI: 10.1186/s12864-023-09439-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Pinus is the largest genus of Pinaceae and the most primitive group of modern genera. Pines have become the focus of many molecular evolution studies because of their wide use and ecological significance. However, due to the lack of complete chloroplast genome data, the evolutionary relationship and classification of pines are still controversial. With the development of new generation sequencing technology, sequence data of pines are becoming abundant. Here, we systematically analyzed and summarized the chloroplast genomes of 33 published pine species. RESULTS Generally, pines chloroplast genome structure showed strong conservation and high similarity. The chloroplast genome length ranged from 114,082 to 121,530 bp with similar positions and arrangements of all genes, while the GC content ranged from 38.45 to 39.00%. Reverse repeats showed a shrinking evolutionary trend, with IRa/IRb length ranging from 267 to 495 bp. A total of 3,205 microsatellite sequences and 5,436 repeats were detected in the studied species chloroplasts. Additionally, two hypervariable regions were assessed, providing potential molecular markers for future phylogenetic studies and population genetics. Through the phylogenetic analysis of complete chloroplast genomes, we offered novel opinions on the genus traditional evolutionary theory and classification. CONCLUSION We compared and analyzed the chloroplast genomes of 33 pine species, verified the traditional evolutionary theory and classification, and reclassified some controversial species classification. This study is helpful in analyzing the evolution, genetic structure, and the development of chloroplast DNA markers in Pinus.
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Affiliation(s)
- Qijing Xia
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hongbin Zhang
- Gansu Province Academy of Qilian Water Resource Conservation Forests Research Institute, Zhangye, 734031, China
| | - Dong Lv
- Gansu Province Academy of Qilian Water Resource Conservation Forests Research Institute, Zhangye, 734031, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, Canada
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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9
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Waswa EN, Mkala EM, Odago WO, Amenu SG, Mutinda ES, Muthui SW, Ding SX, Hu GW, Wang QF. Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume. FRONTIERS IN PLANT SCIENCE 2023; 14:1179510. [PMID: 37396648 PMCID: PMC10313135 DOI: 10.3389/fpls.2023.1179510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023]
Abstract
Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine-cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.
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Affiliation(s)
- Emmanuel Nyongesa Waswa
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Elijah Mbandi Mkala
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Wyclif Ochieng Odago
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Sara Getachew Amenu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Elizabeth Syowai Mutinda
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Samuel Wamburu Muthui
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Shi-Xiong Ding
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
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10
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Waswa EN, Mkala EM, Odago WO, Amenu SG, Mutinda ES, Muthui SW, Ding SX, Hu GW, Wang QF. Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume. FRONTIERS IN PLANT SCIENCE 2023; 14. [DOI: https:/doi.org/10.3389/fpls.2023.1179510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine–cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.
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11
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Zhao SW, Guo JF, Kong L, Nie S, Yan XM, Shi TL, Tian XC, Ma HY, Bao YT, Li ZC, Chen ZY, Zhang RG, Ma YP, El-Kassaby YA, Porth I, Zhao W, Mao JF. Haplotype-resolved genome assembly of Coriaria nepalensis a non-legume nitrogen-fixing shrub. Sci Data 2023; 10:259. [PMID: 37156769 PMCID: PMC10167230 DOI: 10.1038/s41597-023-02171-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/20/2023] [Indexed: 05/10/2023] Open
Abstract
Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.
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Affiliation(s)
- Shi-Wei Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jing-Fang Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Lei Kong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuai Nie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xue-Mei Yan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Tian-Le Shi
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xue-Chan Tian
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hai-Yao Ma
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yu-Tao Bao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhi-Chao Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhao-Yang Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ren-Gang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yong-Peng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå, SE-901 87, Sweden.
| | - Jian-Feng Mao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, SE-901 87, Sweden.
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12
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Chen Q, Chen L, Teixeira da Silva JA, Yu X. The plastome reveals new insights into the evolutionary and domestication history of peonies in East Asia. BMC PLANT BIOLOGY 2023; 23:243. [PMID: 37150831 PMCID: PMC10165817 DOI: 10.1186/s12870-023-04246-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/24/2023] [Indexed: 05/09/2023]
Abstract
BACKGROUD Paeonia holds considerable value in medicinal, ornamental horticultural, and edible oil industries, but the incomplete state of phylogenetic research in this genus poses a challenge to the effective conservation and development of wild germplasm, and also impedes the practical utilization of existing cultivars. Due to its uniparental inheritance and lack of recombination, the plastome (i.e., plastid genome), which is a valuable molecular marker for phylogenetic analyses, is characterized by an appropriate rate of nucleotide evolution. METHODS In this study, 10 newly assembled data and available reported data were combined to perform a comparative genomics and phylogenetics analysis of 63 plastomes of 16 Paeonia species, primarily from East Asia, which is the origin and diversity center of Paeonia. RESULTS Ranging between 152,153 and 154,405 bp, most plastomes displayed a conserved structure and relatively low nucleotide diversity, except for six plastomes, which showed obvious IR construction or expansion. A total of 111 genes were annotated in the Paeonia plastomes. Four genes (rpl22, rps3, rps19 and ycf1) showed different copy numbers among accessions while five genes (rpl36, petN, psbI, rpl33 and psbJ) showed strong codon usage biases (ENC < 35). Additional selection analysis revealed that no genes were under positive selection during the domestication of tree peony cultivars whereas four core photosynthesis-related genes (petA, psaA, psaB and rbcL) were under positive selection in herbaceous peony cultivars. This discovery might contribute to the wide adaption of these cultivars. Two types of molecular markers (SSR and SNP) were generated from the 63 plastomes. Even though SSR was more diverse than SNP, it had a weaker ability to delimit Paeonia species than SNP. The reconstruction of a phylogenetic backbone of Paeonia in East Asia revealed significant genetic divergence within the P. ostii groups. Evidence also indicated that the majority of P. suffruticosa cultivars had a maternal origin, from P. ostii. The results of this research also suggest that P. delavayi var. lutea, which likely resulted from hybridization with P. ludlowii, should be classified as a lineage within the broader P. delavayi group. CONCLUSIONS Overall, this study's research findings suggest that the Paeonia plastome is highly informative for phylogenetic and comparative genomic analyses, and could be useful in future research related to taxonomy, evolution, and domestication.
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Affiliation(s)
- Qihang Chen
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, 100083, China
- National Engineering Research Center for Floriculture, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, China
| | - Le Chen
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, 100083, China
- National Engineering Research Center for Floriculture, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, China
| | | | - Xiaonan Yu
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, 100083, China.
- National Engineering Research Center for Floriculture, Beijing, 100083, China.
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, China.
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Abouseada HH, Mohamed ASH, Teleb SS, Badr A, Tantawy ME, Ibrahim SD, Ellmouni FY, Ibrahim M. Genetic diversity analysis in wheat cultivars using SCoT and ISSR markers, chloroplast DNA barcoding and grain SEM. BMC PLANT BIOLOGY 2023; 23:193. [PMID: 37041463 PMCID: PMC10088244 DOI: 10.1186/s12870-023-04196-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Wheat is a major cereal that can narrow the gap between the increasing human population and food production. In this connection, assessing genetic diversity and conserving wheat genetic resources for future exploitation is very important for breeding new cultivars that may withstand the expected climate change. The current study evaluates the genetic diversity in selected wheat cultivars using ISSR and SCoT markers, the rbcL and matK chloroplast DNA barcoding, and grain surface sculpture characteristics. We anticipate that these objectives may prioritize using the selected cultivars to improve wheat production. The selected collection of cultivars may lead to the identification of cultivars adapted to a broad spectrum of climatic environments. RESULTS Multivariate clustering analyses of the ISSR and SCoT DNA fingerprinting polymorphism grouped three Egyptian cultivars with cultivar El-Nielain from Sudan, cultivar Aguilal from Morocco, and cultivar Attila from Mexico. In the other group, cultivar Cook from Australia and cultivar Chinese-166 were differentiated from four other cultivars: cultivar Cham-10 from Syria, cultivar Seri-82 from Mexico, cultivar Inqalab-91 from Pakistan, and cultivar Sonalika from India. In the PCA analysis, the Egyptian cultivars were distinct from the other studied cultivars. The rbcL and matK sequence variation analysis indicated similarities between Egyptian cultivars and cultivar Cham-10 from Syria and cultivar Inqalab-91 from Pakistan, whereas cultivar Attila from Mexico was distinguished from all other cultivars. Combining the data of ISSR and SCoT with the rbcL and matK results retained the close resemblance among the two Egyptian cultivars EGY1: Gemmeiza-9 and EGY3: Sakha-93, and the Moroccan cultivar Aguilal, and the Sudanese cultivar El-Nielain and between Seri-82, Inqalab-91, and Sonalika cultivars. The analysis of all data distinguished cultivar Cham-10 from Syria from all other cultivars, and the analysis of grain traits indicated a close resemblance between cv. Cham-10 from and the two Egyptian cultivars Gemmeiza-9 and Sakha-93. CONCLUSIONS The analysis of rbcL and matK chloroplast DNA barcoding agrees with the ISSR and the SCoT markers in supporting the close resemblance between the Egyptian cultivars, particularly Gemmeiza-9 and Sakha-93. The ISSR and SCoT data analyses significantly expressed high differentiation levels among the examined cultivars. Cultivars with closer resemblance may be recommended for breeding new wheat cultivars adapted to various climatic environments.
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Affiliation(s)
- Heba H Abouseada
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Al-Safa H Mohamed
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Samir S Teleb
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Sharqia, Egypt
| | - Abdelfattah Badr
- Botany and Microbiology Department, Faculty of Science, Helwan University, Cairo, Egypt
| | - Mohamed E Tantawy
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Shafik D Ibrahim
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Faten Y Ellmouni
- Botany Department, Faculty of Science, Fayoum University, 63514, Fayoum, Egypt.
| | - Mohamed Ibrahim
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, Egypt.
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14
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Goloboff PA, Morales ME. TNT version 1.6, with a graphical interface for MacOS and Linux, including new routines in parallel. Cladistics 2023; 39:144-153. [PMID: 36682054 DOI: 10.1111/cla.12524] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/21/2022] [Indexed: 01/23/2023] Open
Abstract
A new graphical user interface (GUI) for the parsimony program TNT is presented that works under the Linux and Mac operating systems, as well as the Cygwin environment (which runs under Windows). The new interface is based on the GIMP Tool Kit, GTK (version 3). Formerly, only Windows versions of TNT had a GUI. The new interface improves upon the existing Windows GUI in several respects. These changes, together with several additions to the program since the publication of version 1.5, warrant a change in minor version, thus moving from version 1.5 to 1.6. Among the most notable improvements are the possibility to access graphical user dialogs by means of simple commands, to easily save trees in SVG format ("Scalable Vector Graphics") directly from any tree-diagram being displayed, and to manage analyses in parallel (using multiple processors, by means of the PVM system or "Parallel Virtual Machine"), as well as a generally more stable and consistent behaviour. As the binaries for the new version are compiled as native 64-bit applications, this removes the limitations for accessing large amounts of memory in the previous GUI Windows interface (which is a 32-bit application).
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Affiliation(s)
- Pablo A Goloboff
- Unidad Ejecutora Lillo (Consejo Nacional de Investigaciones Científicas y Técnicas - Fundación Miguel Lillo), Miguel Lillo 251, 4000 S.M. de Tucumán, Argentina.,American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Martín E Morales
- Unidad Ejecutora Lillo (Consejo Nacional de Investigaciones Científicas y Técnicas - Fundación Miguel Lillo), Miguel Lillo 251, 4000 S.M. de Tucumán, Argentina
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15
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Bartish IV, Bonnefoi S, Aïnouche A, Bruelheide H, Bartish M, Prinzing A. Fewer chromosomes, more co-occurring species within plant lineages: A likely effect of local survival and colonization. AMERICAN JOURNAL OF BOTANY 2023; 110:e16139. [PMID: 36758168 DOI: 10.1002/ajb2.16139] [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: 10/28/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Plant lineages differ markedly in species richness globally, regionally, and locally. Differences in whole-genome characteristics (WGCs) such as monoploid chromosome number, genome size, and ploidy level may explain differences in global species richness through speciation or global extinction. However, it is unknown whether WGCs drive species richness within lineages also in a recent, postglacial regional flora or in local plant communities through local extinction or colonization and regional species turnover. METHODS We tested for relationships between WGCs and richness of angiosperm families across the Netherlands/Germany/Czechia as a region, and within 193,449 local vegetation plots. RESULTS Families that are species-rich across the region have lower ploidy levels and small monoploid chromosomes numbers or both (interaction terms), but the relationships disappear after accounting for continental and local richness of families. Families that are species-rich within occupied localities have small numbers of polyploidy and monoploid chromosome numbers or both, independent of their own regional richness and the local richness of all other locally co-occurring species in the plots. Relationships between WGCs and family species-richness persisted after accounting for niche characteristics and life histories. CONCLUSIONS Families that have few chromosomes, either monoploid or holoploid, succeed in maintaining many species in local communities and across a continent and, as indirect consequence of both, across a region. We suggest evolutionary mechanisms to explain how small chromosome numbers and ploidy levels might decrease rates of local extinction and increase rates of colonization. The genome of a macroevolutionary lineage may ultimately control whether its species can ecologically coexist.
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Affiliation(s)
- Igor V Bartish
- Université de Rennes 1, CNRS Research Unit Ecosystèmes Biodiversité Evolution (ECOBIO), Campus de Beaulieu, 35042, Rennes, France
- Department of Genetic Ecology, Institute of Botany, Academy of Sciences, CZ-25243 Pruhonice 1, Czech Republic
| | - Salomé Bonnefoi
- Université de Rennes 1, CNRS Research Unit Ecosystèmes Biodiversité Evolution (ECOBIO), Campus de Beaulieu, 35042, Rennes, France
| | - Abdelkader Aïnouche
- Université de Rennes 1, CNRS Research Unit Ecosystèmes Biodiversité Evolution (ECOBIO), Campus de Beaulieu, 35042, Rennes, France
| | - Helge Bruelheide
- Institute of Biology/Geobotany & Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103, Leipzig, Germany
| | - Mark Bartish
- Royal Institute of Technology, Stockholm, SE-100 44, Sweden
| | - Andreas Prinzing
- Université de Rennes 1, CNRS Research Unit Ecosystèmes Biodiversité Evolution (ECOBIO), Campus de Beaulieu, 35042, Rennes, France
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16
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Tyszka AS, Bretz EC, Robertson HM, Woodcock-Girard MD, Ramanauskas K, Larson DA, Stull GW, Walker JF. Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1125107. [PMID: 37063179 PMCID: PMC10098128 DOI: 10.3389/fpls.2023.1125107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles' evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles' evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.
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Affiliation(s)
- Alexa S. Tyszka
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Eric C. Bretz
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Holly M. Robertson
- Sainsbury Laboratory, School of Biological Sciences, University of Cambridge, Cambridge, England, United Kingdom
| | - Miles D. Woodcock-Girard
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Karolis Ramanauskas
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Drew A. Larson
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Gregory W. Stull
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Joseph F. Walker
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
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17
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Joyce EM, Appelhans MS, Buerki S, Cheek M, de Vos JM, Pirani JR, Zuntini AR, Bachelier JB, Bayly MJ, Callmander MW, Devecchi MF, Pell SK, Groppo M, Lowry PP, Mitchell J, Siniscalchi CM, Munzinger J, Orel HK, Pannell CM, Nauheimer L, Sauquet H, Weeks A, Muellner-Riehl AN, Leitch IJ, Maurin O, Forest F, Nargar K, Thiele KR, Baker WJ, Crayn DM. Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication. FRONTIERS IN PLANT SCIENCE 2023; 14:1063174. [PMID: 36959945 PMCID: PMC10028101 DOI: 10.3389/fpls.2023.1063174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order's spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.
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Affiliation(s)
- Elizabeth M. Joyce
- Systematics, Biodiversity and Evolution of Plants, Ludwig-Maximilians-Universität München, Munich, Germany
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Marc S. Appelhans
- Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Goettingen, Germany
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Sven Buerki
- Department of Biological Sciences, Boise State University, Boise, ID, United States
| | - Martin Cheek
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Jurriaan M. de Vos
- Department of Environmental Sciences, University Basel, Basel, Switzerland
| | - José R. Pirani
- Departamento de Botaênica, Universidade de Saão Paulo, Herbário SPF, Saão Paulo, Brazil
| | | | | | - Michael J. Bayly
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | | | - Marcelo F. Devecchi
- Departamento de Botaênica, Universidade de Saão Paulo, Herbário SPF, Saão Paulo, Brazil
| | - Susan K. Pell
- United States Botanic Garden, Washington, DC, United States
| | - Milton Groppo
- Departamento de Botaênica, Universidade de Saão Paulo, Herbário SPF, Saão Paulo, Brazil
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, MO, United States
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, Paris, France
| | - John Mitchell
- New York Botanical Garden, New York, NY, United States
| | - Carolina M. Siniscalchi
- Department of Biological Sciences, Harned Hall, Mississippi State University, Mississippi State, MS, United States
| | - Jérôme Munzinger
- AMAP, Université Montpellier, Institut de Recherche pour le Développement (IRD), Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Centre National de la Recherche Scientifique (CNRS), Institut national de la recherche agronomique (INRAE), Montpellier, France
| | - Harvey K. Orel
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Caroline M. Pannell
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Biology, Oxford University, Oxford, United Kingdom
- Marine Laboratory, Queen’s University Belfast, Portaferry, United Kingdom
| | - Lars Nauheimer
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Andrea Weeks
- Department of Biology, George Mason University, Fairfax, VA, United States
| | - Alexandra N. Muellner-Riehl
- Department of Molecular Evolution and Plant Systematics & Herbarium, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organization (CSIRO), Canberra, ACT, Australia
| | - Kevin R. Thiele
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | | | - Darren M. Crayn
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
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Du ZY, Jenny Xiang QY, Cheng J, Zhou W, Wang QF, Soltis DE, Soltis PS. An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data. AMERICAN JOURNAL OF BOTANY 2023; 110:e16116. [PMID: 36480351 DOI: 10.1002/ajb2.16116] [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: 07/12/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
PREMISE A major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome-wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s.l.), reconstruct the biogeographic history of the clade, and provide a revised classification using the PhyloCode to stabilize names for this taxonomically controversial group. METHODS We conducted phylogenetic analyses using 312 single-copy nuclear genes and 70 plastid genes from Angiosperms353 Hyb-Seq, plus numerous loci from RAD-Seq. We integrated fossils using morphological data and produced a dated phylogeny for biogeographical analysis. RESULTS A well-resolved, strongly supported, comprehensive phylogeny was obtained. Biogeographic analyses support an origin and rapid diversification of Cornus into four morphologically distinct major clades in the Northern Hemisphere (with an eastern Asian ancestor) during the late Cretaceous. Dispersal into Africa from eastern Asia likely occurred along the Tethys Seaway during the Paleogene, whereas dispersal into South America likely occurred during the Neogene. Diversification within the northern hemisphere likely involved repeated independent colonization of new areas during the Paleogene and Neogene along the Bering Land Bridge, the North Atlantic Land Bridge, and the Tethys Seaway. Thirteen strongly supported clades were named following rules of the PhyloCode. CONCLUSIONS Our study provides an example of integrating genomic and morphological data to produce a robust, explicit species phylogeny that includes fossil taxa, which we translate into an updated classification scheme using the PhyloCode to stabilize names.
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Affiliation(s)
- Zhi-Yuan Du
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jin Cheng
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Wenbin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Qing-Feng Wang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611 FL, USA
- Department of Biology, University of Florida, Gainesville, 32611 FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611 FL, USA
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19
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Guo C, Luo Y, Gao LM, Yi TS, Li HT, Yang JB, Li DZ. Phylogenomics and the flowering plant tree of life. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:299-323. [PMID: 36416284 DOI: 10.1111/jipb.13415] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.
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Affiliation(s)
- Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
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20
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Hu H, Sun P, Yang Y, Ma J, Liu J. Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36647606 DOI: 10.1111/jipb.13455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation.
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Affiliation(s)
- Hongyin Hu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Pengchuan Sun
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Jianxiang Ma
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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21
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Knox EB. DNA Sequence Analysis of an Inversion Hot Spot in Lobeliaceae Plastomes. PLANTS (BASEL, SWITZERLAND) 2022; 11:2863. [PMID: 36365316 PMCID: PMC9653739 DOI: 10.3390/plants11212863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
The evolution of plastid genomes (plastomes) in land plants is typically conservative, with extensive structural rearrangements present in only a few groups. Early Southern blot analysis identified two Lobelia species that minimally required deletion of the plastid gene accD and five inversions to account for their plastome arrangement relative to the ancestral organization. Sixty alternative 5-step inversion scenarios could account for the observed arrangement, but only one scenario was consistent with the criterion of 'common cause' attributable to a putative rearrangement hot spot at the accD deletion-site. Plastome sequencing demonstrated that this previously hypothesized inversion order is historically accurate. Detailed reconstructions of the ancestral plastome organization before and after each inversion are presented herein. Stem-loop and disruption-rescue models were evaluated for each inversion. One inversion has an obvious stem-loop basis, but the other four inversions were primarily caused by serial insertion of foreign (extra-plastid) DNA bearing large open-reading frames that disrupted plastome organization at the accD deletion-site, and complete plastomes were rescued by seemingly arbitrary ligation or fortuitous recombination at the other inversion endpoint. Transposed copies of DNA segments from elsewhere in the plastome are frequently inserted at inversion junctions, and four junctions are consistent with the stem-loop ligation model.
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Affiliation(s)
- Eric B Knox
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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22
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Montenegro JD, Julca I, Chumbe-Nolasco LD, Rodríguez-Pérez LM, Sevilla Panizo R, Medina-Hoyos A, Gutiérrez-Reynoso DL, Guerrero-Abad JC, Amasifuen Guerra CA, García-Serquén AL. Phylogenomic Analysis of the Plastid Genome of the Peruvian Purple Maize Zea mays subsp. mays cv. 'INIA 601'. PLANTS (BASEL, SWITZERLAND) 2022; 11:2727. [PMID: 36297753 PMCID: PMC9612013 DOI: 10.3390/plants11202727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Peru is an important center of diversity for maize; its different cultivars have been adapted to distinct altitudes and water availability and possess an array of kernel colors (red, blue, and purple), which are highly appreciated by local populations. Specifically, Peruvian purple maize is a collection of native landraces selected and maintained by indigenous cultures due to its intense purple color in the seed, bract, and cob. This color is produced by anthocyanin pigments, which have gained interest due to their potential use in the food, agriculture, and pharmaceutical industry. It is generally accepted that the Peruvian purple maize originated from a single ancestral landrace 'Kculli', but it is not well understood. To study the origin of the Peruvian purple maize, we assembled the plastid genomes of the new cultivar 'INIA 601' with a high concentration of anthocyanins, comparing them with 27 cultivars/landraces of South America, 9 Z. mays subsp. parviglumis, and 5 partial genomes of Z. mays subsp. mexicana. Using these genomes, plus four other maize genomes and two outgroups from the NCBI database, we reconstructed the phylogenetic relationship of Z. mays. Our results suggest a polyphyletic origin of purple maize in South America and agree with a complex scenario of domestication with recurrent gene flow from wild relatives. Additionally, we identify 18 plastid positions that can be used as high-confidence genetic markers for further studies. Altogether, these plastid genomes constitute a valuable resource to study the evolution and domestication of Z. mays in South America.
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Affiliation(s)
- Juan D. Montenegro
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
- Department of Neurosciences and Developmental Biology, University of Vienna, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Irene Julca
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Lenin D. Chumbe-Nolasco
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Lila M. Rodríguez-Pérez
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Ricardo Sevilla Panizo
- Departamento de Fitotecnia, Facultad de Agronomía, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima 15024, Peru
| | - Alicia Medina-Hoyos
- Estación Experimental Agraria “Baños del Inca”, Instituto Nacional de Innovación Agraria (INIA), Km. 5.5 Carretera Cajamarca–Celendín, Cajamarca 06000, Peru
| | - Dina L. Gutiérrez-Reynoso
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Juan Carlos Guerrero-Abad
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Carlos A. Amasifuen Guerra
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Aura L. García-Serquén
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
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23
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Fan W, Liu F, Jia Q, Du H, Chen W, Ruan J, Lei J, Li DZ, Mower JP, Zhu A. Fragaria mitogenomes evolve rapidly in structure but slowly in sequence and incur frequent multinucleotide mutations mediated by microinversions. THE NEW PHYTOLOGIST 2022; 236:745-759. [PMID: 35731093 DOI: 10.1111/nph.18334] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Plant mitochondrial DNA has been described as evolving rapidly in structure but slowly in sequence. However, many of the noncoding portions of plant mitogenomes are not homologous among species, raising questions about the rate and spectrum of mutations in noncoding regions. Recent studies have suggested that the lack of homology in noncoding regions could be due to increased sequence divergence. We compared 30 kb of coding and 200 kb of noncoding DNA from 13 sequenced Fragaria mitogenomes, followed by analysis of the rate of sequence divergence, microinversion events and structural variations. Substitution rates in synonymous sites and nongenic sites are nearly identical, suggesting that the genome-wide point mutation rate is generally consistent. A surprisingly high number of large multinucleotide substitutions were detected in Fragaria mitogenomes, which may have resulted from microinversion events and could affect phylogenetic signal and local rate estimates. Fragaria mitogenomes preferentially accumulate deletions relative to insertions and substantial genomic arrangements, whereas mutation rates could positively associate with these sequence and structural changes among species. Together, these observations suggest that plant mitogenomes exhibit low point mutations genome-wide but exceptionally high structural variations, and our results favour a gain-and-loss model for the rapid loss of homology among plant mitogenomes.
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Affiliation(s)
- Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiaoya Jia
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, China
| | - Haiyuan Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wu Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiwei Ruan
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Jiajun Lei
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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24
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Pelosi JA, Kim EH, Barbazuk WB, Sessa EB. Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:882441. [PMID: 35909764 PMCID: PMC9330400 DOI: 10.3389/fpls.2022.882441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/16/2022] [Indexed: 05/31/2023]
Abstract
Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree-species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.
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Affiliation(s)
- Jessie A. Pelosi
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Emily H. Kim
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - W. Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Emily B. Sessa
- Department of Biology, University of Florida, Gainesville, FL, United States
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25
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Sokoloff DD, El ES, Pechenyuk EV, Carrive L, Nadot S, Rudall PJ, Remizowa MV. Refined Interpretation of the Pistillate Flower in Ceratophyllum Sheds Fresh Light on Gynoecium Evolution in Angiosperms. Front Cell Dev Biol 2022; 10:868352. [PMID: 35573671 PMCID: PMC9098228 DOI: 10.3389/fcell.2022.868352] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Molecular phylogenetic analyses have revealed a superclade of mesangiosperms with five extant lineages: monocots, eudicots, magnoliids, Ceratophyllum and Chloranthaceae. Both Ceratophyllum and Chloranthaceae are ancient lineages with a long fossil record; their precise placement within mesangiosperms is uncertain. Morphological studies have suggested that they form a clade together with some Cretaceous fossils, including Canrightia, Montsechia and Pseudoasterophyllites. Apart from Canrightia, members of this clade share unilocular gynoecia commonly interpreted as monomerous with ascidiate carpels. Alternatively, the gynoecium of Ceratophyllum has also been interpreted as syncarpous with a single fertile carpel (pseudomonomerous). We investigate patterns of morphological, anatomical and developmental variation in gynoecia of three Ceratophyllum species to explore the controversial interpretation of its gynoecium as either monomerous or pseudomonomerous. We use an angiosperm-wide morphological data set and contrasting tree topologies to estimate the ancestral gynoecium type in both Ceratophyllum and mesangiosperms. Gynoecia of all three Ceratophyllum species possess a small (sometimes vestigial) glandular appendage on the abaxial side and an occasionally bifurcating apex. The ovary is usually unilocular with two procambium strands, but sometimes bilocular and/or with three strands in C. demersum. None of the possible phylogenetic placements strongly suggest apocarpy in the stem lineage of Ceratophyllum. Rescoring Ceratophyllum as having two united carpels affects broader-scale reconstructions of the ancestral gynoecium in mesangiosperms. Our interpretation of the glandular appendage as a tepal or staminode homologue makes the Ceratophyllum ovary inferior, thus resembling (semi)inferior ovaries of most Chloranthaceae and potentially related fossils Canrightia and Zlatkocarpus. The entire structure of the flower of Ceratophyllum suggests strong reduction following a long and complex evolutionary history. The widely accepted notion that apocarpy is ancestral in mesangiosperms (and angiosperms) lacks robust support, regardless of which modes of carpel fusion are considered. Our study highlights the crucial importance of incorporating fossils into large-scale analyses to understand character evolution.
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Affiliation(s)
- Dmitry D Sokoloff
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Elena S El
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | | | - Laetitia Carrive
- Université Paris-Saclay, CNRS, AgroParisTech, Écologie, Systématique et Évolution, Orsay, France
| | - Sophie Nadot
- Université Paris-Saclay, CNRS, AgroParisTech, Écologie, Systématique et Évolution, Orsay, France
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26
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Du XY, Kuo LY, Zuo ZY, Li DZ, Lu JM. Structural Variation of Plastomes Provides Key Insight Into the Deep Phylogeny of Ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:862772. [PMID: 35645990 PMCID: PMC9134734 DOI: 10.3389/fpls.2022.862772] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/04/2022] [Indexed: 06/02/2023]
Abstract
Structural variation of plastid genomes (plastomes), particularly large inversions and gene losses, can provide key evidence for the deep phylogeny of plants. In this study, we investigated the structural variation of fern plastomes in a phylogenetic context. A total of 127 plastomes representing all 50 recognized families and 11 orders of ferns were sampled, making it the most comprehensive plastomic analysis of fern lineages to date. The samples included 42 novel plastomes of 15 families with a focus on Hymenophyllales and Gleicheniales. We reconstructed a well-supported phylogeny of all extant fern families, detected significant structural synapomorphies, including 9 large inversions, 7 invert repeat region (IR) boundary shifts, 10 protein-coding gene losses, 7 tRNA gene losses or anticodon changes, and 19 codon indels (insertions or deletions) across the deep phylogeny of ferns, particularly on the backbone nodes. The newly identified inversion V5, together with the newly inferred expansion of the IR boundary R5, can be identified as a synapomorphy of a clade composed of Dipteridaceae, Matoniaceae, Schizaeales, and the core leptosporangiates, while a unique inversion V4, together with an expansion of the IR boundary R4, was verified as a synapomorphy of Gleicheniaceae. This structural evidence is in support of our phylogenetic inference, thus providing key insight into the paraphyly of Gleicheniales. The inversions of V5 and V7 together filled the crucial gap regarding how the "reversed" gene orientation in the IR region characterized by most extant ferns (Schizaeales and the core leptosporangiates) evolved from the inferred ancestral type as retained in Equisetales and Osmundales. The tRNA genes trnR-ACG and trnM-CAU were assumed to be relicts of the early-divergent fern lineages but intact in most Polypodiales, particularly in eupolypods; and the loss of the tRNA genes trnR-CCG, trnV-UAC, and trnR-UCU in fern plastomes was much more prevalent than previously thought. We also identified several codon indels in protein-coding genes within the core leptosporangiates, which may be identified as synapomorphies of specific families or higher ranks. This study provides an empirical case of integrating structural and sequence information of plastomes to resolve deep phylogeny of plants.
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Affiliation(s)
- Xin-Yu Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Zheng-Yu Zuo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jin-Mei Lu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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27
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Xia MZ, Li Y, Zhang FQ, Yu JY, Khan G, Chi XF, Xu H, Chen SL. Reassessment of the Phylogeny and Systematics of Chinese Parnassia (Celastraceae): A Thorough Investigation Using Whole Plastomes and Nuclear Ribosomal DNA. FRONTIERS IN PLANT SCIENCE 2022; 13:855944. [PMID: 35371115 PMCID: PMC8971841 DOI: 10.3389/fpls.2022.855944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Parnassia L., a perennial herbaceous genus in the family Celastraceae, consists of about 60 species and is mainly distributed in the Pan-Himalayan and surrounding mountainous regions. The taxonomic position and phylogenetic relationships of the genus are still controversial. Herein, we reassessed the taxonomic status of Parnassia and its intra- and inter-generic phylogeny within Celastraceae. To that end, we sequenced and assembled the whole plastid genomes and nuclear ribosomal DNA (nrDNA) of 48 species (74 individuals), including 25 species of Parnassia and 23 species from other genera of Celastraceae. We integrated high throughput sequence data with advanced statistical toolkits and performed the analyses. Our results supported the Angiosperm Phylogeny Group IV (APG IV) taxonomy which kept the genus to the family Celastraceae. Although there were topological conflicts between plastid and nrDNA phylogenetic trees, Parnassia was fully supported as a monophyletic group in all cases. We presented a first attempt to estimate the divergence of Parnassia, and molecular clock analysis indicated that the diversification occurred during the Eocene. The molecular phylogenetic results confirmed numerous taxonomic revisions, revealing that the morphological characters used in Parnassia taxonomy and systematics might have evolved multiple times. In addition, we speculated that hybridization/introgression might exist during genus evolution, which needs to be further studied. Similarly, more in-depth studies will clarify the diversification of characters and species evolution models of this genus.
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Affiliation(s)
- Ming-Ze Xia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- School of Pharmacy, Weifang Medical University, Weifang, China
| | - Fa-Qi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
| | - Jing-Ya Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Xiao-Feng Chi
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
| | - Hao Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
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A Review on Application of DNA Barcoding Technology for Rapid Molecular Diagnostics of Adulterants in Herbal Medicine. Drug Saf 2021; 45:193-213. [PMID: 34846701 DOI: 10.1007/s40264-021-01133-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2021] [Indexed: 10/19/2022]
Abstract
The rapid molecular diagnostics of adulterants in herbal medicine using DNA barcoding forms the core of this meticulously detailed review, based on two decades of data. With 80% of the world's population using some form of herbal medicine, authentication, quality control, and detection of adulterants warrant DNA barcoding. A combined group of keywords were used for literature review using the PubMed, the ISI Web of Knowledge, Web of Science (WoS), and Google Scholar databases. All the papers (N = 210) returned by the search engines were downloaded and systematically analyzed. Detailed analysis of conventional DNA barcodes were based on retrieved sequences for internal transcribed spacer (ITS) (412,189), rbcL (251,598), matK (210,835), and trnH-psbA (141,846). The utility of databases such as The Barcode of Life Data System (BOLD), NCBI, GenBank, and Medicinal Materials DNA Barcode Database (MMDBD) has been critically examined for the identification of unknown species from known databases. The current review gives an overview of the ratio of adulterated to authentic drugs for some countries along with the state of the art technology currently being used in the identification of adulterated medicines. In this review, efforts were made to systematically analyze and arrange the research and reviews on the basis of technical progress. The review concludes with the future of DNA-based herbal medicine adulteration detection, forecasting the reliance on the metabarcoding technology. DNA barcoding technology for differentiating adulterated herbal medicine.
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Graper AL, Noyszewski AK, Anderson NO, Smith AG. Variability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae). BMC PLANT BIOLOGY 2021; 21:515. [PMID: 34742253 PMCID: PMC8571858 DOI: 10.1186/s12870-021-03284-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Phalaris species (Poaceae) occupy diverse environments throughout all continents except Antarctica. Phalaris arundinacea is an important forage, ornamental, wetland restoration and biofuel crop grown globally as well as being a wetland invasive. The nuclear ribosomal internal transcribed spacer (ITS) region has been used for Phalaris barcoding as a DNA region with high nucleotide diversity for Phalaris species identification. Recent findings that P. arundinacea populations in Minnesota USA are most likely native and not European prompted this analysis to determine whether Eurasian vs. native North American P. arundinacea differed in ITS regions. Our objectives were to amplify and compare ITS regions (ITS1 and ITS2) of historic herbaria (1882-2001) and extant (fresh) Phalaris specimens; analyze ITS regions for species-specific polymorphisms (diagnostic SNPs) and compare ITS regions of historic Phalaris specimens with known, extant Phalaris species. RESULTS We obtained complete ITS1 and ITS2 sequences from 31 Phalaris historic (herbaria samples, 1908 to 2001) and five extant (fresh) specimens. Herbaria Phalaris specimens did not produce new SNPs (single nucleotide polymorphisms) not present in extant specimens. Diagnostic SNPs were identified in 8/12 (66.6%) Phalaris species. This study demonstrates the use of herbaria tissue for barcoding as a means for improved species identification of Phalaris herbaria specimens. No significant correlation between specimen age and genomic DNA concentration was found. Phalaris arundinacea showed high SNP variation within its clade, with the North American being distinctly different than other USA and most Eurasian types, potentially allowing for future identification of specific SNPs to geographic origin. CONCLUSIONS While not as efficient as extant specimens to obtain DNA, Phalaris herbaria specimens can produce high quality ITS sequences to evaluate historic genetic resources and facilitate identification of new species-specific barcodes. No correlation between DNA concentration and age of historic samples (119 year range) occurred. Considerable polymorphism was exhibited in the P. arundinacea clade with several N. American accessions being distinct from Eurasian types. Further development of within species- and genus-specific barcodes could contribute to designing PCR primers for efficient and accurate identification of N. American P. arundinacea. Our finding of misidentified Phalaris species indicates the need to exercise stringent quality control measures on newly generated sequence data and to approach public sequence databases in a critical way.
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Affiliation(s)
- Allison L Graper
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, Saint Paul, MN, 55108, USA
| | - Andrzej K Noyszewski
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, Saint Paul, MN, 55108, USA
- Present Address: Quality Control Analyst III, Aldevron, ND, Fargo, USA
| | - Neil O Anderson
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, Saint Paul, MN, 55108, USA.
| | - Alan G Smith
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, Saint Paul, MN, 55108, USA
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Gibson K, Olofsson J, Mooers AØ, Monroe MJ. Pulse grazing by reindeer ( Rangifer tarandus) can increase the phylogenetic diversity of vascular plant communities in the Fennoscandian tundra. Ecol Evol 2021; 11:14598-14614. [PMID: 34765128 PMCID: PMC8571604 DOI: 10.1002/ece3.8131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 08/03/2021] [Accepted: 08/23/2021] [Indexed: 12/24/2022] Open
Abstract
Herbivore grazing is an important determinant of plant community assemblages. Thus, it is essential to understand its impact to direct conservation efforts in regions where herbivores are managed. While the impacts of reindeer (Rangifer tarandus) grazing on plant biodiversity and community composition in the Fennoscandian tundra are well studied, the impact of reindeer grazing on phylogenetic community structure is not. We used data from a multiyear quasi-experimental study in northern Fennoscandia to analyze the effect of reindeer grazing on plant community diversity including its phylogenetic structure. Our study design used a permanent fence constructed in the 1960s and temporary fences constructed along the permanent fence to expose plant communities to three different grazing regimes: light (almost never grazed), pulse (grazed every other year), and press (chronic grazing for over 40 years). Similar to previous studies on low productivity ecosystems in this region, the species richness and evenness of plant communities with pulse and press grazing did not differ from communities with light grazing. Also consistent with previous studies in this region, we observed a transition from shrub-dominated communities with light grazing to graminoid-dominated communities with pulse and press grazing. Interestingly, communities with pulse, but not press, grazing were more phylogenetically dispersed than communities with light grazing. If grazing pulses can increase the phylogenetic diversity of plant communities, our result suggests changes in reindeer management allowing for pulses of grazing to increase phylogenetic diversity of plant communities.
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Affiliation(s)
- Kate Gibson
- Department of BiologySimon Fraser UniversityBurnabyBCCanada
| | - Johan Olofsson
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
| | - Arne Ø. Mooers
- Department of BiologySimon Fraser UniversityBurnabyBCCanada
| | - Melanie J. Monroe
- Department of BiologySimon Fraser UniversityBurnabyBCCanada
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
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Li HT, Luo Y, Gan L, Ma PF, Gao LM, Yang JB, Cai J, Gitzendanner MA, Fritsch PW, Zhang T, Jin JJ, Zeng CX, Wang H, Yu WB, Zhang R, van der Bank M, Olmstead RG, Hollingsworth PM, Chase MW, Soltis DE, Soltis PS, Yi TS, Li DZ. Plastid phylogenomic insights into relationships of all flowering plant families. BMC Biol 2021; 19:232. [PMID: 34711223 PMCID: PMC8555322 DOI: 10.1186/s12915-021-01166-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades. RESULTS Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation. CONCLUSIONS We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.
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Affiliation(s)
- Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lu Gan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lian-Ming Gao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Lijiang Forest Ecosystem National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Matthew A Gitzendanner
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76017, USA
| | - Ting Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jian-Jun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10025, USA
| | - Chun-Xia Zeng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hong Wang
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Michelle van der Bank
- Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Richard G Olmstead
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, 98195-5325, USA
| | | | - Mark W Chase
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, England, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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Physiological and Molecular Analysis Reveals the Differences of Photosynthesis between Colored and Green Leaf Poplars. Int J Mol Sci 2021; 22:ijms22168982. [PMID: 34445687 PMCID: PMC8396459 DOI: 10.3390/ijms22168982] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/09/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
Leaf coloration changes evoke different photosynthetic responses among different poplar cultivars. The aim of this study is to investigate the photosynthetic difference between a red leaf cultivar (ZHP) and a green leaf (L2025) cultivar of Populus deltoides. In this study, ‘ZHP’ exhibited wide ranges and huge potential for absorption and utilization of light energy and CO2 concentration which were similar to those in ‘L2025’ and even showed a stronger absorption for weak light. However, with the increasing light intensity and CO2 concentration, the photosynthetic capacity in both ‘L2025’ and ‘ZHP’ was gradually restricted, and the net photosynthetic rate (Pn) in ‘ZHP’ was significantly lower than that in ‘L2025’under high light or high CO2 conditions, which was mainly attributed to stomatal regulation and different photosynthetic efficiency (including the light energy utilization efficiency and photosynthetic CO2 assimilation efficiency) in these two poplars. Moreover, the higher anthocyanin content in ‘ZHP’ than that in ‘L2025’ was considered to be closely related to the decreased photosynthetic efficiency in ‘ZHP’. According to the results from the JIP-test, the capture efficiency of the reaction center for light energy in ‘L2025’ was significantly higher than that in ‘ZHP’. Interestingly, the higher levels of light quantum caused relatively higher accumulation of QA- in ‘L2025’, which blocked the electron transport and weakened the photosystem II (PSII) performance as compared with ‘ZHP’; however, the decreased capture of light quantum also could not promote the utilization of light energy, which was the key to the low photosynthetic efficiency in ‘ZHP’. The differential expressions of a series of photosynthesis-related genes further promoted these specific photosynthetic processes between ‘L2025’ and ‘ZHP’.
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Combining molecular and geographical data to infer the phylogeny of Lamiales and its dispersal patterns in and out of the tropics. Mol Phylogenet Evol 2021; 164:107287. [PMID: 34365014 DOI: 10.1016/j.ympev.2021.107287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/25/2021] [Accepted: 08/03/2021] [Indexed: 11/22/2022]
Abstract
Lamiales is one of the most intractable orders of flowering plants, with several changes in family composition, and circumscription throughout history. The order is worldwide distributed, occurring in tropical forests and frozen habitats. In this study, a comprehensive phylogeny of Lamiales was reconstructed using DNA sequences. The tree was used to infer dispersal patterns, focusing on the tropics and extratropics. Molecular and species geographic data available from public repositories were combined to address both objectives. A total of 6,910 species, and 842 genera of Lamiales were sampled using the Python tool PyPHLAWD. The tree was inferred using RAxML, and recovered a monophyletic Lamiales. All 26 families were recovered as monophyletic with high support. The families Bignoniaceae, and Plantaginaceae are remarkable examples. The first emerged as monophyletic and included tribe Jacarandeae, while the later emerged as monophyletic in its sensu lato and included both the tribes Angelonieae, and Gratioleae. Distribution points for all species were retrieved from GBIF. After filtering, 1,136,425 records were retained. Species were coded as present in extratropical or tropical environments. The in and out of the tropics dispersal patterns were inferred using a maximum likelihood approach that identifies hidden rate changes. The model recovered higher rates of transition from extratropics to tropics, estimating two rates of state transitions. When ancestral states are considered, more discrete transitions from extratropics to tropics were observed. The extratropical state was also inferred for the crown node of Lamiales and old nested nodes, revealing a rare pattern of transitions to the tropics throughout the upper Cretaceous and Tertiary. A significant phylogenetic signal was recovered for the in and out of the tropics dispersal patterns, showing that state transitions are not frequent enough to erase the effect of tree structure on the data.
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Pérez-Escobar OA, Dodsworth S, Bogarín D, Bellot S, Balbuena JA, Schley RJ, Kikuchi IA, Morris SK, Epitawalage N, Cowan R, Maurin O, Zuntini A, Arias T, Serna-Sánchez A, Gravendeel B, Torres Jimenez MF, Nargar K, Chomicki G, Chase MW, Leitch IJ, Forest F, Baker WJ. Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. AMERICAN JOURNAL OF BOTANY 2021; 108:1166-1180. [PMID: 34250591 DOI: 10.1002/ajb2.1702] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed. METHODS We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses. RESULTS Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes. CONCLUSIONS Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution.
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Affiliation(s)
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2UP, UK
| | - Diego Bogarín
- Lankester Botanic Garden, University of Costa Rica, Cartago, Costa Rica
| | | | | | | | | | | | | | - Robyn Cowan
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
| | | | | | | | | | | | | | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Australia
- National Research Collections, Commonwealth Industrial and Scientific Research Organization, Australia
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Mark W Chase
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia
| | | | - Félix Forest
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
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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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Antonelli A, Clarkson JJ, Kainulainen K, Maurin O, Brewer GE, Davis AP, Epitawalage N, Goyder DJ, Livshultz T, Persson C, Pokorny L, Straub SCK, Struwe L, Zuntini AR, Forest F, Baker WJ. Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes. AMERICAN JOURNAL OF BOTANY 2021; 108:1143-1165. [PMID: 34254285 DOI: 10.1002/ajb2.1697] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies. METHODS Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees. RESULTS We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order's classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). CONCLUSIONS The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.
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Affiliation(s)
- Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | | | - Kent Kainulainen
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22 A, Gothenburg, 413 19, Sweden
| | | | | | | | | | | | - Tatyana Livshultz
- Department of Biodiversity Earth and Environmental Sciences and Academy of Natural Sciences, Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA, 19103, USA
| | - Claes Persson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
| | | | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, 300 Pulteney Street, Geneva, NY, 14456, USA
| | - Lena Struwe
- Department of Ecology, Evolution, and Natural Resources & Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901, USA
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Shah T, Schneider JV, Zizka G, Maurin O, Baker W, Forest F, Brewer GE, Savolainen V, Darbyshire I, Larridon I. Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits. AMERICAN JOURNAL OF BOTANY 2021; 108:1201-1216. [PMID: 34180046 DOI: 10.1002/ajb2.1682] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/23/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Both universal and family-specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships. METHODS We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support. RESULTS For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. Merging of data obtained with the two kits resulted in a well-supported phylogenetic tree. CONCLUSIONS The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.
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Affiliation(s)
- Toral Shah
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | - Julio V Schneider
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
| | - Georg Zizka
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - William Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Grace E Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Vincent Savolainen
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | | | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L., Ledeganckstraat 35, Gent, 9000, Belgium
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Zuntini AR, Frankel LP, Pokorny L, Forest F, Baker WJ. A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae. AMERICAN JOURNAL OF BOTANY 2021; 108:1066-1086. [PMID: 34278560 DOI: 10.1002/ajb2.1698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/02/2021] [Indexed: 05/03/2023]
Abstract
PREMISE Resolving relationships within order Commelinales has posed quite a challenge, as reflected in its unstable infra-familial classification. Thus, we investigated (1) relationships across families and genera of Commelinales; (2) phylogenetic placement of never-before sequenced genera; (3) how well off-target plastid data integrate with other plastid-based data sets; and (4) how the novel inferences coincide with the infra-familial classification. METHODS We generated two large data sets (nuclear and plastome) by means of target sequence capture using the Angiosperms353 probe set, with additional sequences mined from publicly available transcriptomes and full plastomes. A third extended-plastid data set was considered, including all species with sequences in public repositories. Species trees were inferred under a multispecies coalescent framework from individual gene trees and also using maximum likelihood analyses from concatenated and partitioned data. RESULTS The nuclear, plastome, and extended-plastid data sets include 52, 53, and 58 genera, respectively, and up to 290 species of Commelinales, representing the most comprehensive molecular sampling for the order to date, which includes seven never-before sequenced genera. CONCLUSIONS We inferred robust phylogenies supporting the monophyly of Commelinales and its five constituent families, and we recovered the clades Pontederiaceae-Haemodoraceae and Hanguanaceae-Commelinaceae, as previously reported. The placement of Philydraceae remains contentious. Relationships within the two largest families, Commelinaceae and Haemodoraceae, are resolved. Based on the latter results, we confirm the subfamilial classification of Haemodoraceae and propose a new classification for Commelinaceae, which includes the synonymization of Tapheocarpa in Commelina.
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Affiliation(s)
| | - Lorna P Frankel
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Faculty of Life and Environmental Sciences, University of Southampton Highfield Campus, Southampton, SO17 1BJ, UK
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Centre for Plant Biotechnology and Genomics (CBGP UPM - INIA), Autopista M-40, Km 38, Pozuelo de Alarcón (Madrid), 28223, Spain
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Yang YY, Qu XJ, Zhang R, Stull GW, Yi TS. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol Phylogenet Evol 2021; 163:107232. [PMID: 34129935 DOI: 10.1016/j.ympev.2021.107232] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
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Affiliation(s)
- Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, Shangdong 250014, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Baker WJ, Bailey P, Barber V, Barker A, Bellot S, Bishop D, Botigué LR, Brewer G, Carruthers T, Clarkson JJ, Cook J, Cowan RS, Dodsworth S, Epitawalage N, Françoso E, Gallego B, Johnson MG, Kim JT, Leempoel K, Maurin O, McGinnie C, Pokorny L, Roy S, Stone M, Toledo E, Wickett NJ, Zuntini AR, Eiserhardt WL, Kersey PJ, Leitch IJ, Forest F. A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life. Syst Biol 2021; 71:301-319. [PMID: 33983440 PMCID: PMC8830076 DOI: 10.1093/sysbio/syab035] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/22/2022] Open
Abstract
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96\documentclass[12pt]{minimal}
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}{}$\%$\end{document}). A “first pass” angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.]
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Affiliation(s)
- William J Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Paul Bailey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Vanessa Barber
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Abigail Barker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - David Bishop
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Laura R Botigué
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Centre for Research in Agricultural Genomics, Campus UAB, Edifici CRAG, Bellaterra Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Grace Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Tom Carruthers
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - James J Clarkson
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Jeffrey Cook
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Robyn S Cowan
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,School of Life Sciences, University of Bedfordshire, University Square, Luton LU1 3JU, United Kingdom
| | | | - Elaine Françoso
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Berta Gallego
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Jan T Kim
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Department of Computer Science, School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield, Hertfordshire, AL10 9AB, United Kingdom
| | - Kevin Leempoel
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | | | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Centre for Plant Biotechnology and Genomics (CBGP) UPM-INIA, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Malcolm Stone
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Eduardo Toledo
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA
| | | | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Ali MA. Phylotranscriptomic analysis of Dillenia indica L. (Dilleniales, Dilleniaceae) and its systematics implication. Saudi J Biol Sci 2021; 28:1557-1560. [PMID: 33732040 PMCID: PMC7938110 DOI: 10.1016/j.sjbs.2021.01.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/17/2021] [Accepted: 01/18/2021] [Indexed: 11/21/2022] Open
Abstract
The recent massive development in the next-generation sequencing platforms and bioinformatics tools including cloud based computing have proven extremely useful in understanding the deeper-level phylogenetic relationships of angiosperms. The present phylotranscriptomic analyses address the poorly known evolutionary relationships of the order Dilleniales to order of the other angiosperms using the minimum evolution method. The analyses revealed the nesting of the representative taxon of Dilleniales in the MPT but distinct from the representative of the order Santalales, Caryophyllales, Asterales, Cornales, Ericales, Lamiales, Saxifragales, Fabales, Malvales, Vitales and Berberidopsidales.
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Affiliation(s)
- Mohammad Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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Lai Y, Gandolfo MA, Crepet WL, Nixon KC. Paleoaltingia gen. nov., a new genus of Altingiaceae from the Late Cretaceous of New Jersey. AMERICAN JOURNAL OF BOTANY 2021; 108:461-471. [PMID: 33660257 DOI: 10.1002/ajb2.1618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/30/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Altingiaceae is a small family with a bimodal Northern Hemisphere distribution in eastern North America and eastern Asia, and a rich Cenozoic fossil record. The charcoalified fossil infructescence Paleoaltingia gen. nov. from Turonian (Late Cretaceous) deposits of New Jersey, provides new evidence of early Altingiaceae reproductive structures and has biogeographical implications in understanding modern distribution. METHODS Fossils were prepared using standard methods for obtaining and processing mesofossils. The fossils were examined with light microscopy, and scanning electron microscopy for observing structural and anatomical details. Phylogenetic analyses were performed using a combined matrix of molecular and morphological data. RESULTS Based on morphological features of the fossil and the phylogenetic analyses, the new genus, Paleoaltingia, with two species (Paleoaltingia ovum-dinosauri and P. polyodonta) is erected. The phylogenetic position of Paleoaltingia confirms affinities with living Altingiaceae. CONCLUSIONS The combination of characters-simple capitate infructescence, syncarpous bicarpellate, and bilocular ovary, unique sterile phyllome structures-indicates that the fossil taxa have close affinities to modern Altingiaceae. The unique characters of the phyllomes provide new information on the floral diversity of Altingiaceae. The emergence of Paleoaltingia in Late Cretaceous sediments of Northeastern North America represents the earliest fossil record of Altingiaceae and provides new insights into its biogeography.
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Affiliation(s)
- Yangjun Lai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- L. H. Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Maria A Gandolfo
- L. H. Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - William L Crepet
- L. H. Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Kevin C Nixon
- L. H. Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
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Daniell H, Jin S, Zhu X, Gitzendanner MA, Soltis DE, Soltis PS. Green giant-a tiny chloroplast genome with mighty power to produce high-value proteins: history and phylogeny. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:430-447. [PMID: 33484606 PMCID: PMC7955891 DOI: 10.1111/pbi.13556] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 05/04/2023]
Abstract
Free-living cyanobacteria were entrapped by eukaryotic cells ~2 billion years ago, ultimately giving rise to chloroplasts. After a century of debate, the presence of chloroplast DNA was demonstrated in the 1960s. The first chloroplast genomes were sequenced in the 1980s, followed by ~100 vegetable, fruit, cereal, beverage, oil and starch/sugar crop chloroplast genomes in the past three decades. Foreign genes were expressed in isolated chloroplasts or intact plant cells in the late 1980s and stably integrated into chloroplast genomes, with typically maternal inheritance shown in the 1990s. Since then, chloroplast genomes conferred the highest reported levels of tolerance or resistance to biotic or abiotic stress. Although launching products with agronomic traits in important crops using this concept has been elusive, commercial products developed include enzymes used in everyday life from processing fruit juice, to enhancing water absorption of cotton fibre or removal of stains as laundry detergents and in dye removal in the textile industry. Plastid genome sequences have revealed the framework of green plant phylogeny as well as the intricate history of plastid genome transfer events to other eukaryotes. Discordant historical signals among plastid genes suggest possible variable constraints across the plastome and further understanding and mitigation of these constraints may yield new opportunities for bioengineering. In this review, we trace the evolutionary history of chloroplasts, status of autonomy and recent advances in products developed for everyday use or those advanced to the clinic, including treatment of COVID-19 patients and SARS-CoV-2 vaccine.
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Affiliation(s)
- Henry Daniell
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xin‐Guang Zhu
- State Key Laboratory for Plant Molecular Genetics and Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | | | - Douglas E. Soltis
- Florida Museum of Natural History and Department of BiologyUniversity of FloridaGainesvilleFLUSA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
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Bernabeu M, Rosselló JA. Molecular Evolution of rbcL in Orthotrichales (Bryophyta): Site Variation, Adaptive Evolution, and Coevolutionary Patterns of Amino Acid Replacements. J Mol Evol 2021; 89:225-237. [PMID: 33611663 DOI: 10.1007/s00239-021-09998-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 01/31/2021] [Indexed: 11/24/2022]
Abstract
Molecular evolution of the large subunit of the RuBisCO enzyme is understudied in early diverging land plants. These groups show morphological and eco-physiological adaptations to the uneven and intermittent distribution of water in the terrestrial environment. This might have prompted a continuous fine-tuning of RuBisCO under a selective pressure modifying the species-specific optima for photosynthesis in contrasting microdistributions and environmental niches. To gain a better insight into the molecular evolution of RuBisCO large subunits, the aim of this study was to assess the pattern of evolutionary change in the amino acid residues in a monophyletic group of Bryophyta (Orthotrichaceae). Tests for positive, neutral, or purifying selection at the amino acid level were assessed by comparing rates (ω) of non-synonymous (dN) and synonymous (dS) nucleotide substitutions along a Maximum Likelihood phylogenetic tree. Molecular adaptation tests using likelihood ratio tests, reconstruction of ancestral amino acid sites, and intra-protein coevolution analyses were performed. Variable amino acid sites (39) were unevenly distributed across the LSU. The residues are located on rbcL sites that are highly variable in higher plants and close to key regions implying dimer-dimer (L2L2), RuBisCO-activase interactions, and conformational functions during catalysis. Ten rbcL sites (32, 33, 91, 230, 247, 251, 255, 424, 449 and 475) have been identified by the Bayesian Empirical Bayes inference to be under positive selection and under adaptive evolution under the M8 model. The pattern of amino acid variation suggests that it is not lineage specific, but rather representative of a case of convergent evolution, suggesting recurrent changes that potentially favor the same amino acid substitutions that are likely optimized the RuBisCO activity.
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Affiliation(s)
- Moisès Bernabeu
- Departament de Genètica, Universitat de València, c/ Doctor Moliner 50, Burjassot, 46100, ,València, Spain
| | - Josep A Rosselló
- Jardín Botánico, ICBiBE, Universitat de València, c/ Quart 80, 46008, València, Spain.
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Assis ACRD, Gasparino EC, Saba MD. Pollen morphology of selected species of Anacardiaceae and its taxonomic significance. RODRIGUÉSIA 2021. [DOI: 10.1590/2175-7860202172115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract In the present work, the pollen morphology of 22 species of Anacardiaceae was analysed, occurring in the state of Bahia, Brazil. The palynological material was obtained from specimens deposited in herbaria. The pollen grains were acetolysed, measured, illustrated and described under light and scanning electron microscopies. The quantitative data were statistically analysed according to sample size. The analysed species presented pollen grains in monads, small to medium sized, isopolar, amb circular to subtriangular, with shapes varying from oblate-spheroidal to prolate, 3-colporate, with fastigium in some species. The exine ornamentation was characterized as psilate, striate, microreticulate-striate, striato-perforate, suprastriato-infra(micro)reticulate. The pollen morphology variation confirms the eurypalynous character of the family. The attributes of the apertures and exine may collaborate in the taxonomic circumscription and provide a clarification of the phylogenetic relationships of the group.
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The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements. Genome Biol 2020; 21:291. [PMID: 33267872 PMCID: PMC7709256 DOI: 10.1186/s13059-020-02198-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 11/06/2020] [Indexed: 12/25/2022] Open
Abstract
Background Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species. Results Here, we report a chromosome-scale assembly of the T. sinense genome. We assemble the 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes. Phylogenomic analyses verify that the Trochodendrales and core eudicots are sister lineages and showed that two whole-genome duplications occurred in the Trochodendrales approximately 82 and 59 million years ago. Synteny analyses suggest that the γ event, resulting in paleohexaploidy, may have only happened in core eudicots. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. T. sinense also has several key genes regulated by or regulating TsVND7.2 and their regulatory relationship resembles that in Arabidopsis thaliana. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China. Conclusions The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation. Population genomics analysis of T. sinense reveals its genetic diversity and geographic structure with implications for conservation. Supplementary information The online version contains supplementary material available at 10.1186/s13059-020-02198-7.
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Koenen EJ, Kidner C, de Souza ÉR, Simon MF, Iganci JR, Nicholls JA, Brown GK, de Queiroz LP, Luckow M, Lewis GP, Pennington RT, Hughes CE. Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation. AMERICAN JOURNAL OF BOTANY 2020; 107:1710-1735. [PMID: 33253423 PMCID: PMC7839790 DOI: 10.1002/ajb2.1568] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/07/2020] [Indexed: 05/05/2023]
Abstract
PREMISE Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the "tree of life" are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have shown extensive lack of resolution, especially among the species-rich and taxonomically challenging ingoids. METHODS We generated transcriptomes to select low-copy nuclear genes, enrich these via hybrid capture for representative species of most mimosoid genera, and analyze the resulting data using de novo assembly and various phylogenomic tools for species tree inference. We also evaluate gene tree support and conflict for key internodes and use phylogenetic network analysis to investigate phylogenetic signal across the ingoids. RESULTS Our selection of 964 nuclear genes greatly improves phylogenetic resolution across the mimosoid phylogeny and shows that the ingoid clade can be resolved into several well-supported clades. However, nearly all loci show lack of phylogenetic signal for some of the deeper internodes within the ingoids. CONCLUSIONS Lack of resolution in the ingoid clade is most likely the result of hyperfast diversification, potentially causing a hard polytomy of six or seven lineages. The gene set for targeted sequencing presented here offers great potential to further enhance the phylogeny of mimosoids and the wider Caesalpinioideae with denser taxon sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation.
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Affiliation(s)
- Erik J. M. Koenen
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Catherine Kidner
- School of Biological SciencesUniversity of EdinburghKing’s Buildings, Mayfield RoadEdinburghUK
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
| | - Élvia R. de Souza
- Departamento Ciências BiológicasUniversidade Estadual de Feira de SantanaAvenida Transnordestina s/n—Novo Horizonte44036‐900Feira de SantanaBrazil
| | - Marcelo F. Simon
- Embrapa Recursos Genéticos e BiotecnologiaParque Estação Biológica (PqEB)Avenida W5 norte70770‐917BrasíliaBrazil
| | - João R. Iganci
- Instituto de BiologiaUniversidade Federal de PelotasCampus Universitário Capão do LeãoTravessa André Dreyfus s/nCapão do Leão96010‐900Rio Grande do SulBrazil
| | - James A. Nicholls
- School of Biological SciencesUniversity of EdinburghKing’s Buildings, Mayfield RoadEdinburghUK
- Australian National Insect CollectionCSIROClunies Ross StActonACT 2601Australia
| | - Gillian K. Brown
- Queensland HerbariumBrisbane Botanic GardensMount Coot‐tha, Mt Coot‐tha RoadToowong4066QueenslandAustralia
| | - Luciano P. de Queiroz
- Departamento Ciências BiológicasUniversidade Estadual de Feira de SantanaAvenida Transnordestina s/n—Novo Horizonte44036‐900Feira de SantanaBrazil
| | - Melissa Luckow
- L.H. Bailey HortoriumDepartment of Plant BiologyCornell University412 Mann Library BuildingIthacaNew York14853USA
| | - Gwilym P. Lewis
- Comparative Plant and Fungal Biology DepartmentRoyal Botanic GardensKew, RichmondSurreyTW9 3AEUK
| | - R. Toby Pennington
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
- GeographyUniversity of ExeterAmory Building, Rennes DriveExeterEX4 4RJUK
| | - Colin E. Hughes
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
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Molecular Study of Selected Taxonomically Critical Taxa of the Genus Iris L. from the Broader Alpine-Dinaric Area. PLANTS 2020; 9:plants9091229. [PMID: 32961899 PMCID: PMC7570032 DOI: 10.3390/plants9091229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 12/15/2022]
Abstract
Some wild, morphologically diverse taxa of the genus Iris in the broad Alpine-Dinaric area have never been explored molecularly, and/or have ambiguous systematic status. The main aims of our research were to perform a molecular study of critical Iris taxa from that area (especially a narrow endemic accepted species I. adriatica, for which we also analysed genome size) and to explore the contribution of eight microsatellites and highly variable chloroplast DNA (ndhJ, rpoC1) markers to the understanding of the Iris taxa taxonomy and phylogeny. Both the microsatellite-based UPGMA and plastid markers-based maximum likelihood analysis discriminated three main clusters in the set of 32 analysed samples, which correspond well to the lower taxonomic categories of the genus, and support separate status of ambiguous regional taxa (e.g., I. sibirica subsp. erirrhiza, I. x croatica and I. x rotschildii). The first molecular data on I. adriatica revealed its genome size (2C = 12.639 ± 0.202 pg) and indicated the existence of ecotypes. For future molecular characterisation of the genus we recommend the utilisation of microsatellite markers supplemented with a combination of plastid markers.
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Mir RA, Bhat KA, Rashid G, Ebinezer LB, Masi A, Rakwal R, Shah AA, Zargar SM. DNA barcoding: a way forward to obtain deep insights about the realistic diversity of living organisms. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00330-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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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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