A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

Olivier Maurin¹, Artemis Anest^{2

3}, Sidonie Bellot¹, Edward Biffin^{4

5}, Grace Brewer¹, Tristan Charles-Dominique⁶, Robyn S Cowan¹, Steven Dodsworth⁷, Niroshini Epitawalage¹, Berta Gallego¹, Augusto Giaretta⁸, Renato Goldenberg⁹, Deise J P Gonçalves¹⁰, Shirley Graham¹¹, Peter Hoch¹¹, Fiorella Mazine¹², Yee Wen Low^{1

13

14}, Catherine McGinnie¹, Fabián A Michelangeli¹⁵, Sarah Morris¹, Darin S Penneys¹⁶, Oscar Alejandro Pérez Escobar¹, Yohan Pillon¹⁷, Lisa Pokorny^{1

18}, Gustavo Shimizu¹⁹, Vanessa G Staggemeier²⁰, Andrew H Thornhill^{4

5}, Kyle W Tomlinson^{2

21}, Ian M Turner^{13

22}, Thais Vasconcelos²³, Peter G Wilson²⁴, Alexandre R Zuntini¹, William J Baker¹, Félix Forest¹, Eve Lucas¹

Affiliations

¹ Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK.
² Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China.
³ University of Chinese Academy of Sciences, Beijing, 100049, China.
⁴ School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia.
⁵ State Herbarium of South Australia, PO Box 1047, Adelaide, South Australia, 5001, Australia.
⁶ Centre National de la Recherche Scientifique (CNRS), Sorbonne University, 4 Place Jussieu, Paris, 75005, France.
⁷ School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK.
⁸ Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados - UFGD, Dourados, MS, Brazil.
⁹ Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, Brazil.
¹⁰ Department of Ecology and Evolutionary Biology, University of Michigan, USA.
¹¹ Missouri Botanical Garden, St. Louis, MO, 63110, USA.
¹² Departamento de Ciências Ambientais, Centro de Ciências e Tecnologias para a Sustentabilidade, Universidade Federal de São Carlos - campus Sorocaba, Sorocaba, SP, 18052-780, Brazil.
¹³ Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore.
¹⁴ School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK.
¹⁵ Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458-5126, USA.
¹⁶ Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28403, USA.
¹⁷ LSTM, IRD, INRAE, CIRAD, Institut Agro, Univ. Montpellier, Montpellier, France.
¹⁸ Centre for Plant Biotechnology and Genomics (CBGP UPM - INIA), Autopista M-40, Km 38, Pozuelo de Alarcón (Madrid), 28223, Spain.
¹⁹ Department of Plant Biology, University of Campinas, Campinas, São Paulo, 13083-970, Brazil.
²⁰ Departamento de Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-970, Brazil.
²¹ Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China.
²² Singapore Botanical Liaison Officer, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK.
²³ Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
²⁴ Royal Botanic Gardens Sydney, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia.

PMID: 34297852
DOI: 10.1002/ajb2.1699

Free article

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

Olivier Maurin et al. Am J Bot. 2021 Jul.

Free article

. 2021 Jul;108(7):1087-1111.

doi: 10.1002/ajb2.1699. Epub 2021 Jul 23.

Authors

Affiliations

¹ Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK.
² Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China.
³ University of Chinese Academy of Sciences, Beijing, 100049, China.
⁴ School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia.
⁵ State Herbarium of South Australia, PO Box 1047, Adelaide, South Australia, 5001, Australia.
⁶ Centre National de la Recherche Scientifique (CNRS), Sorbonne University, 4 Place Jussieu, Paris, 75005, France.
⁷ School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK.
⁸ Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados - UFGD, Dourados, MS, Brazil.
⁹ Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, Brazil.
¹⁰ Department of Ecology and Evolutionary Biology, University of Michigan, USA.
¹¹ Missouri Botanical Garden, St. Louis, MO, 63110, USA.
¹² Departamento de Ciências Ambientais, Centro de Ciências e Tecnologias para a Sustentabilidade, Universidade Federal de São Carlos - campus Sorocaba, Sorocaba, SP, 18052-780, Brazil.
¹³ Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore.
¹⁴ School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK.
¹⁵ Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458-5126, USA.
¹⁶ Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28403, USA.
¹⁷ LSTM, IRD, INRAE, CIRAD, Institut Agro, Univ. Montpellier, Montpellier, France.
¹⁸ Centre for Plant Biotechnology and Genomics (CBGP UPM - INIA), Autopista M-40, Km 38, Pozuelo de Alarcón (Madrid), 28223, Spain.
¹⁹ Department of Plant Biology, University of Campinas, Campinas, São Paulo, 13083-970, Brazil.
²⁰ Departamento de Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-970, Brazil.
²¹ Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China.
²² Singapore Botanical Liaison Officer, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK.
²³ Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
²⁴ Royal Botanic Gardens Sydney, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia.

PMID: 34297852
DOI: 10.1002/ajb2.1699

Abstract

Premise: To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit.

Methods: We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order).

Results: Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed.

Conclusions: High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.

Keywords: Alzateaceae; Combretaceae; Crypteroniaceae; Lythraceae; Melastomataceae; Myrtaceae; Onagraceae; Penaeaceae; Vochysiaceae; phylogenomics.

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References

LITERATURE CITED

1. Antonelli, A., J. J. Clarkson, K. Kainulainen, O. Maurin, G. E. Brewer, A. P. Davis, N. Epitawalage, et al. 2021. Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes. American Journal of Botany 108: 1143-1165.
1. APG III. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 161: 105-121.
1. APG IV. 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society 181: 1-20.
1. Bacci, L. F., F. A. Michelangeli, and R. Goldenberg. 2019. Revisiting the classification of Melastomataceae: implications for habit and fruit evolution. Botanical Journal of the Linnean Society 190: 1-24.
1. Baker, W. J., P. Bailey, B. Barber, A. Barker, S. Bellot, D. Bishop, L. R. Botigué, et al. 2021. A comprehensive phylogenomic platform for exploring the angiosperm tree of life. Systematic Biology syab035. https://doi.org/10.1093/sysbio/syab035.

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A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

Affiliations

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

Authors

Affiliations

Abstract

References

LITERATURE CITED

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources