The increasing availability of plastid genomes represents a new opportunity to explore molecular evolution in plants (Tonti-Filippini et al., 2017;Twyford & Ness, 2017). For example, plastid phylogenomics has resolved some persistent taxonomic uncertainties in challenging plant groups (e.g., in Rosaceae; Zhang et al., 2017), and more generally led to a better understanding of major events in plant
Recovering phylogenetic relationships in lineages experiencing intense diversification has always been a persistent challenge in evolutionary studies, including in
Gentiana
section
Chondrophyllae
sensu lato (s.l.). Indeed, this subcosmopolitan taxon encompasses more than 180 mostly annual species distributed around the world. We sequenced and assembled 22 new plastomes representing 21 species in section
Chondrophyllae
s.l. In addition to previously released plastome data, our study includes all main lineages within the section. We reconstructed their phylogenetic relationships based on protein‐coding genes and recombinant DNA (rDNA) cistron sequences, and then investigated plastome structural evolution as well as divergence time. Despite an admittedly humble species cover overall, we recovered a well‐supported phylogenetic tree based on plastome data, and found significant discordance between phylogenetic relationships and taxonomic treatments. Our results show that
G. capitata
and
G. leucomelaena
diverged early within the section, which is then further divided into two clades. The divergence time estimation showed that section
Chondrophyllae
s.l. evolved in the second half of the Oligocene. We found that section
Chondrophyllae
s.l. had the smallest average plastome size (128 KB) in tribe Gentianeae (Gentianaceae), with frequent gene and sequence losses such as the
ndh
complex and its flanking regions. In addition, we detected both expansion and contraction of the inverted repeat (IR) regions. Our study suggests that plastome degradation parallels the diversification of this group, and illustrates the strong discordance between phylogenetic relationships and taxonomic treatments, which now need to be carefully revised.
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