One ring to rule them all? Dissecting evolutionary relationships of all flowering plant families using plastomes

<b>Background:</b> Flowering plants (angiosperms) are dominant components of the global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our understanding of their evolution and early diversification. The plastome, typically mapped as a ring-shaped genome, has been the most important molecular data source for plant phylogenetic reconstruction for decades. Here we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4,792 plastomes of 4,660 species representing all currently recognized families. <b>Results:</b> 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 radiation. <b>Conclusions:</b> The robust phylogenetic relationships resolved here will serve as a firm basis for future evolutionary studies of flowering plants.