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

Olivier Maurin (1) , Artemis Anest (2, 3) , Sidonie Bellot (1) , Edward Biffin (4, 5) , Grace Brewer (1) , Tristan Charles-Dominique (6) , Robyn S. Cowan (1) , Steven Dodsworth (7) , Niroshini Epitawalage (1) , Berta Gallego (1) , Augusto Giaretta (8) , Renato Goldenberg (9) , Deise J.P. Gonçalves (10) , Shirley Graham (11) , Peter Hoch (11) , Fiorella Mazine (12) , Yee Wen Low (1, 13, 14) , Catherine McGinnie (1) , Fabián A. Michelangeli (15, 16) , Sarah Morris (1) , Darin S. Penneys (17) , Oscar Alejandro Pérez Escobar (1) , Yohan Pillon (18) , Lisa Pokorny (1, 19, 20) , Gustavo Shimizu (21) , Vanessa G. Staggemeier (22) , Andrew H. Thornhill (4, 5) , Kyle W. Tomlinson (2) , Ian M. Turner (1, 13) , Thais Vasconcelos (23) , Peter G. Wilson (24) , Alexandre Zuntini (1) , William J. Baker (1) , Félix Forest (1) , Eve Lucas (1)

1 Royal Botanic Gardens [Kew]
2 Xishuangbanna Tropical Botanical Garden
3 UCAS - University of Chinese Academy of Sciences [Beijing]
4 University of Adelaide
5 State Herbarium of South Australia
6 iEES Paris - Institut d'écologie et des sciences de l'environnement de Paris
7 University of Bedfordshire
8 UFGD - Federal University of Grande Dourados
9 UFPR - Universidade Federal do Parana [Curitiba]
10 University of Michigan [Ann Arbor]
11 Missouri Botanical Garden
12 UFSCar - Universidade Federal de São Carlos [São Carlos]
13 Singapore Botanic Gardens
14 University of Aberdeen
15 NYBG - New York Botanical Garden
16 Institute of Systematic Botany
17 UNC - University of North Carolina [Wilmington]
18 UMR LSTM - Laboratoire des symbioses tropicales et méditerranéennes
19 INIA - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology
20 UPM - Universidad Politécnica de Madrid
21 UNICAMP - Universidade Estadual de Campinas = University of Campinas
22 UFRN - Universidade Federal do Rio Grande do Norte [Natal]
23 University of Arkansas [Fayetteville]
24 Royal Botanic Gardens and Domain Trust, Sydney, Australia

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.

Mots clés: Alzateaceae; Combretaceae; Crypteroniaceae; Lythraceae; Melastomataceae; Myrtaceae; Onagraceae; Penaeaceae; phylogenomics; Vochysiaceae

Domaines: Systématique, phylogénie et taxonomie; Génétique des plantes; Génétique des populations [q-bio.PE]

Olivier Maurin, Artemis Anest, Sidonie Bellot, Edward Biffin, Grace Brewer, et al.. A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set. American Journal of Botany, 2021, 108 (7), pp.1087-1111. ⟨10.1002/ajb2.1699⟩. ⟨hal-03372269⟩