Background
Robust phylogenies for species with giant genomes and closely related taxa can build evolutionary frameworks for investigating the origin and evolution of these genomic gigantisms.
Paris japonica
(Melanthiaceae) has the largest genome that has been confirmed in eukaryotes to date; however, its phylogenetic position remains unresolved. As a result, the evolutionary history of the genomic gigantisms in
P. japonica
remains poorly understood.
Results
We used next-generation sequencing to generate complete plastomes of
P. japonica
,
P. verticillata
,
Trillium govanianum
,
Ypsilandra thibetica
and
Y. yunnanensis
. Together with published plastomes, the infra-familial relationships in Melanthiaceae and infra-generic phylogeny in
Paris
were investigated, and their divergence times were calculated. The results indicated that the expansion of the ancestral genome of extant
Paris
and
Trillium
occurred approximately from 59.16 Mya to 38.21 Mya. The sister relationship between
P. japonica
and the section
Euthyra
was recovered, and they diverged around the transition of the Oligocene/Miocene (20 Mya), when the Japan Islands were separated from the continent of Asia.
Conclusions
The genome size expansion in the most recent common ancestor for
Paris
and
Trillium
was most possibly a gradual process that lasted for approximately 20 million years. The divergence of
P. japonica
(section
Kinugasa
) and other taxa with thick rhizome may have been triggered by the isolation of the Japan Islands from the continent of Asia. This long-term separation, since the Oligocene/Miocene boundary, would have played an important role in the formation and evolution of the genomic gigantism in
P. japonica.
Moreover, our results support the taxonomic treatment of
Paris
as a genus rather than dividing it into three genera, but do not support the recognition of
T. govanianum
as the separate genus
Trillidium
.
Electronic supplementary material
The online version of this article (10.1186/s12870-019-1879-7) contains supplementary material, which is available to authorized users.