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, 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, Morris, Sarah, Penneys, Darin, Pérez Escobar, Oscar Alejandro, Pillon, Yohan, Pokorny, Lisa, Shimizu, Gustavo, Staggemeier, Vanessa, Thornhill, Andrew, Tomlinson, Kyle, Turner, Ian, Vasconcelos, Thais, Wilson, Peter, Zuntini, Alexandre, Baker, William, Forest, Félix, Lucas, Eve
• Other Authors: Royal Botanic Gardens Kew, Institute of Deep-Sea Science and Engineering Chinese Academy of Sciences Sanya (IDSSE), Chinese Academy of Sciences Beijing (CAS), University of Chinese Academy of Sciences Beijing (UCAS), State Herbarium South Australia, Sorbonne Université (SU), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), 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)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2021
• Subjects: Alzateaceae; Combretaceae; Crypteroniaceae; Lythraceae; Melastomataceae; Myrtaceae; Onagraceae; Penaeaceae; phylogenomics; Vochysiaceae; [SDV]Life Sciences [q-bio]; 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

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.