Mitochondrial genes from eighteen angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants

The early diversification of angiosperms is a rapid yet complicated
process and thus it renders the phylogenetic analyses of early-diverging
angiosperms much difficulty. Plastid and nuclear phylogenomic studies have
raised several controversial hypotheses regarding the angiosperm
phylogeny, whereas mitochondrial genomes have been largely ignored. In
this study, we newly sequenced mitochondrial genomes from 18 angiosperms
to fill the sampling gaps in magnoliids, Austrobaileyales, Chloranthales,
Ceratophyllales, and early-diverging lineages of eudicots and monocots. A
data matrix of 38 mitochondrial genes from 107 taxa was assembled to
address this question. Although conflicting phylogenies were recovered in
this study from different datasets and analytical methods, congruence was
achieved regarding the deep relationships of several major angiosperm
lineages: Chloranthales always groups with Ceratophyllales,
Austrobaileyales is sister to mesangiosperms, and a previously unplaced
clade—Dilleniales—is consistently resolved as a sister to superasterids.
Substitutional saturation, GC compositional heterogeneity, and codon-usage
bias are suggested as common reasons for the noisy signals that impact
phylogenetic reconstructions, and angiosperm mitochondrial genes seem to
hardly suffer from these factors. In addition, the 3rd codon positions of
the mitochondrial genes contained more phylogenetic signals than the 1st
and 2nd codon positions, which might be responsible for the incongruent
results recovered among different datasets. Due to the rapid radiation
process, the relationships among these early lineages are not well
resolved. Nevertheless, this study based on mitochondrial genomes provides
additional evidence and alternative hypotheses for the early evolution and
diversification of angiosperms.