A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae

Abstract

Resolving relationships within order Commelinales has posed quite a challenge, as reflected in its unstable infra-familial classification. Thus, we investigated (1) relationships across families and genera of Commelinales; (2) phylogenetic placement of never-before sequenced genera; (3) how well off-target plastid data integrate with other plastid-based data sets; and (4) how the novel inferences coincide with the infra-familial classification. METHODS:We generated two large data sets (nuclear and plastome) by means of target sequence capture using the Angiosperms353 probe set, with additional sequences mined from publicly available transcriptomes and full plastomes. A third extended-plastid data set was considered, including all species with sequences in public repositories. Species trees were inferred under a multispecies coalescent framework from individual gene trees and also using maximum likelihood analyses from concatenated and partitioned data. RESULTS:The nuclear, plastome, and extended-plastid data sets include 52, 53, and 58 genera, respectively, and up to 290 species of Commelinales, representing the most comprehensive molecular sampling for the order to date, which includes seven neverbefore sequenced genera. CONCLUSIONS:We inferred robust phylogenies supporting the monophyly of Commelinales and its five constituent families, and we recovered the clades Pontederiaceae-Haemodoraceae and Hanguanaceae-Commelinaceae, as previously reported. The placement of Philydraceae remains contentious. Relationships within the two largest families, Commelinaceae and Haemodoraceae, are resolved. Based on the latter results, we confirm the subfamilial classification of Haemodoraceae and propose a new classification for Commelinaceae, which includes the synonymization of Tapheocarpa in Commelina.

Settling a family feud: a high‐level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes

“…Recovery statistics were generated using two scripts from HybPiper v1.3 get_seq_lengths.py and hybpiper_stats.py (Johnson et al, 2016), and additional statistics were prepared using custom scripts (available at GitHub: https://github.com/sidonieB/). The recovery of plastid off‐target coding sequences followed the same approach as for nuclear recovery, except for using BWA (instead of BLASTx), as no significant improvement on the recovery is observed (Zuntini et al, 2021). A plastid target file for Gentianales was produced, extracting coding and ribosomal sequences from complete plastomes of Loganiaceae ( Mitreola yangchunensis ; MT471262), Gentianaceae ( Gentiana officinalis ; MH261261) and Gelsemiaceae ( Gelsemium sempervirens ; MG963263), as well as a plastome for each of the main clades in Apocynaceae ( Asclepias syriaca ; KF386166, Hemidesmus indicus ; MN736959, Plumeria rubra ; MN812495, Nerium oleander ; KJ953907) and in Rubiaceae ( Coffea arabica ; KY085909, Rubia cordifolia ; MN736957, Uncaria rhynchophylla ; MT991006).…”

A Bird’s Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data

“…While some key higher-level relationships are for the first time here consolidated, it is clear that a top-down reclassification of the family can now only be possible once this phylogenomic approach is expanded to additional taxa, with deeper sampling at generic and species level. Addition of key taxa in Convolvulaceae may lead to substantial taxonomic changes, paralleling those observed in Apiaceae ( Clarkson et al, 2021 ) and Commelinaceae ( Zuntini et al, 2021 ).…”

“…In plants, the development of the Angiosperms353 ( Johnson et al, 2019 ), a universal target capture probe set, has allowed standardization of genomic data generated for phylogenetic inference in angiosperms ( Baker et al, 2021 ), enabling easier combination of different datasets and materials, including old herbarium specimens that are proven to be great source of genetic data ( Brewer et al, 2019 ). This probe set has demonstrated its potential to advance phylogenetic studies and significantly resolve relationships with outstanding uncertainty across different taxonomic levels, from ordinal (e.g., Commelinales: Zuntini et al, 2021 ; Cornales: Thomas et al, 2021 ; Dipsacales: Lee et al, 2021 ) to familial (Orchidaceae: Eserman et al, 2021 ; Pérez-Escobar et al, 2021 ; Cyperaceae: Larridon et al, 2021 ) and even infra-generic levels ( Shee et al, 2020 ; Slimp et al, 2021 ). Based on this universal probe set, large collaborative efforts such as Plant and Fungal Tree of Life Project (PAFTOL, Baker et al, 2022 1 ) and Genomics for Australian Plants (GAP 2 ) have generated an incomparable amount of genomic data for nearly all families and more than seven thousand genera of flowering plants, on which relationships among all plant families of angiosperms are being analyzed, at taxonomic and phylogenetic scales never attempted before.…”

Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants

“…They can also be analyzed using multispecies coalescent (MSC) approaches (e.g., ASTRAL‐III, Zhang et al, 2018), which assume that genes are unlinked, whereas plastid genomes are generally considered to be single‐linkage groups (e.g., Birky, 2001). However, analyzing plastid data in parallel with Angiosperms353 data is useful as it permits integration with existing large‐scale data sets (e.g., Zuntini et al, 2021), creating opportunities for comparison and contrast. The vast back‐catalog of plastid data produced primarily in the pre‐genomic era remains extremely relevant as the foundation of much current phylogenetic thinking (e.g., APG IV, 2016, and its predecessors, which relied extensively on plastid gene data sets), and because plastid phylogenomic data continue to be actively collected (e.g., Gitzendanner et al, 2018; Lam et al, 2018).…”