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

Abstract

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.

Phylogenetic Relationships Within the Hyper-Diverse Genus Eugenia (Myrtaceae: Myrteae) Based on Target Enrichment Sequencing

“…Seven outgroup taxa were used, such as Myrcianthes, which is shown as sister to Eugenia in previous molecular phylogenies based on Sanger sequencing (e.g., Mazine et al, 2014;Giaretta et al, 2019b). Outgroup sequence data are taken from the Myrtales-focused study of Maurin et al (2021) and are available on the Kew Tree of Life Explorer (https://treeoflife.kew.org; Baker et al, 2021). Sample voucher details are provided in Supplementary Table 1.…”

Phylogenomics and continental biogeographic disjunctions: insight from the Australian starflowers (Calytrix)

“…Phylogenomic approaches are currently reinvigorating systematic research. Target capture methods (e.g., Johnson et al 2019) have potential to provide unprecedented resolution and node support across both deep and shallow scales across the tree of life (e.g., Antonelli et al, 2021; Maurin et al, 2021; Nge et al, 2021b; Thomas et al, 2021). Applying these methods to resolve the phylogenetic relationships of Calytrix is especially timely in addressing a range of phylogenetic, taxonomic, and biogeographic questions, as well as provide a robust framework to guide further research on this species‐rich Australian genus and the evolution of the Australian flora more broadly.…”

Genomic insights into rapid speciation within the world’s largest tree genus

“…S6). Based on phylogenetic relationships recently solidified for Myrtales families 36 , we conclude that earlier genome-based determinations of shared polyploid status within Myrtales are correct in indicating one basal WGD, and that the transcriptome-based 1KP study erroneously inflated the number of WGDs within the clade (Fig. 1C).…”

“…The ASTRAL tree of BUSCO genes, and selected traits, were loaded into Mesquite 70 version 3.61 and the Trace Character Evolution option with parsimony was selected to predict ancestral states. 36 . Genera of Myrtaceae used in genome structural and phylogenetic analyses are also depicted.…”