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

• Published in: American Journal of Botany
• Main Authors: Maurin, Olivier, Anest, Artemis, Bellot, Sidonie, Biffin, Edward, Brewer, Grace, Charles-Dominique, Tristan, Cowan, Robyn, S., Dodsworth, Steven, Epitawalage, Niroshini, Gallego, Berta, Giaretta, Augusto, Goldenberg, Renato, Gonçalves, Deise J.P., Graham, Shirley, Hoch, Peter, Mazine, Fiorella, Low, Yee Wen, McGinnie, Catherine, Michelangeli, Fabián, A., Morris, Sarah, Penneys, Darin, S., Pérez Escobar, Oscar Alejandro, Pillon, Yohan, Pokorny, Lisa, Shimizu, Gustavo, Staggemeier, Vanessa, G., Thornhill, Andrew, H., Tomlinson, Kyle, W., Turner, Ian, M., Vasconcelos, Thais, Wilson, Peter, G., Zuntini, Alexandre, Baker, William, J., Forest, Félix, Lucas, Eve
• Other Authors: Royal Botanic Gardens Kew, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences Beijing (CAS), University of Chinese Academy of Sciences Beijing (UCAS), University of Adelaide, State Herbarium of South Australia, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Bedfordshire, Federal University of Grande Dourados (UFGD), Universidade Federal do Parana Curitiba (UFPR), Universidade Federal do Paraná Curitiba, Brasil = Federal University of Paraná Curitiba, Brazil = Université fédérale du Paraná Curitiba, Brésil (UFPR), University of Michigan Ann Arbor, University of Michigan System, Missouri Botanical Garden, Universidade Federal de São Carlos São Carlos (UFSCar), Singapore Botanic Gardens, University of Aberdeen, New York Botanical Garden (NYBG), Institute of Systematic Botany, University of North Carolina Wilmington (UNC), University of North Carolina System (UNC), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Universidad Politécnica de Madrid (UPM), Universidade Estadual de Campinas = University of Campinas (UNICAMP), Universidade Federal do Rio Grande do Norte Natal (UFRN), University of Arkansas Fayetteville, Royal Botanic Gardens and Domain Trust, Sydney, Australia, This work was funded by grants from the Calleva Foundation and the Sackler Trust to the Plant and Fungal Trees of Life Project (PAFTOL) at the Royal Botanic Gardens, Kew, with additional funding from the Garfield Weston Foundation. A.A. received support from the 2018 CAS-TWAS President's Fellowship for International Doctoral Students. E.L. and A.G. received support from the Bentham-Moxon Trust providing funds for sequencing Eugenia species and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq - proc. 155480/2018-9). Support from the National Science Foundation is acknowledged (DEB-0515665, DEB-0818399, DEB-1146409, DEB-1343612, DEB-1754667). We also thank the Assemblée de la Province Nord, Assemblée de la Province Sud (New Caledonia) for relevant collection permits. F.M. received support from the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES/PriInt) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq - proc. 302309/2018-7). K.W.T. received support by a joint Natural Science Foundation of China-Yunnan Government research grant (U1502264).
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2021
• Subjects: Alzateaceae; Combretaceae; Crypteroniaceae; Lythraceae; Melastomataceae; Myrtaceae; Onagraceae; Penaeaceae; phylogenomics; Vochysiaceae; [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics; Phylogenetics and taxonomy; [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics; [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]; Antarc*; Antarctica
• Online Access: https://hal.science/hal-03372269; https://hal.science/hal-03372269/document; https://hal.science/hal-03372269/file/Maurin%20et%20al.%202021.pdf; https://doi.org/10.1002/ajb2.1699

All Sequences files (fastq) generated for this study are deposited in the European Nucleotide Archive (ENA accession PRJEB35285; Appendix S1). All alignments, Newick tree files generated and scripts used in this research are available at Zenodo (https://doi.org/10.5281/zenodo.4268317). International audience 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.