Plastid phylogenomic insights into relationships of all flowering plant families

Abstract

Background Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades. Results Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation. Conclusions We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.

Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics

“…These studies have deepened our understanding of evolutionary relationships across many branches in the plant Tree of Life, from the most recalcitrant deep relationships at and within the family level (e.g., Xi et al, 2012 ; Goremykin et al, 2015 ; Duvall et al, 2020 ; Koenen et al, 2020a ; Yang et al, 2020 ; Antonelli et al, 2021 ; Orton et al, 2021 ; Schneider et al, 2021 ; Serna-Sánchez et al, 2021 ) to long, unresolved radiations at the species level (e.g., Nicholls et al, 2015 ; Welch et al, 2016 ; Villaverde et al, 2018 ; Thode et al, 2020 ; Pereira et al, 2021 ). While massive amounts of plastid genome (plastome) sequence data have filled the family level sampling gap for angiosperms (e.g., Li et al, 2021 ), infra-family levels remain less well covered. This is particularly true of the economically important, ecologically successful, morphologically diverse, species-rich legume family Fabaceae (Leguminosae), from which the plastomes of only 319 species in 184 genera have been deposited in the GenBank database 1 (Accessed Sep. 09, 2021) thus far, of the more than 22,000 species and 770 genera in six subfamilies ( LPWG et al, 2017 , LPWG, 2021 ).…”

Phylogenomic analyses of Alismatales shed light into adaptations to aquatic environments

“…Analyses using chloroplast (cp) and mitochondrial markers supported a relationship of (Tofieldiaceae, (Araceae, core Alismatids)) (Iles et al 2013; Ross et al 2016; Petersen et al 2015; Luo et al 2016; Li et al 2019). However, studies using cp and/or nuclear markers supported a relationship of (Araceae, (Tofieldiaceae, core Alismatids)) (Nauheimer et al 2012; Hertweck et al 2015; Azuma and Tobe, 2011; Li et al 2021). Conflicting phylogenetic relationships also exist in Alismataceae, Potamogetonaceae, and Hydrocharitaceae (Tanaka et al 1997; Les et al 2006; Chen et al 2012; Ross et al 2016).…”

“…However, studies using cp and/or nuclear markers supported a relationship of (Araceae, (Tofieldiaceae, core Alismatids)) (Nauheimer et al 2012;Hertweck et al 2015;Azuma and Tobe, 2011;Li et al 2021).…”

Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis

“…Due to its lack of recombination, usually uniparental inheritance, and large copy numbers in plant cells [ 1 , 2 ], the plastid genome has been widely applied in phylogenomics for rebuilding the plant tree of life in the recent decade [ 3 – 5 ]. It has also facilitated the progress of resolving deep relationships of particularly recalcitrant lineages, such as those that have undergone recent radiations [ 6 , 7 ].…”