Plastid phylogenomic insights into relationships of all flowering plant families

Background: 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.

Results: Here we assembled by
far the largest plastid dataset of angiosperms, composed of 80 genes from 4,792 plastomes of 4,660 species in 2,024 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 radiation.

Conclusions: We provide the most comprehensive dataset of plastome to date and
robust phylogenetic relationships, which will serve as a firm basis for future
evolutionary studies of flowering
plants.