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The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions
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The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions
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Journal Article
The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions
2021
Overview
Background
Paphiopedilum
is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat
(
IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of
Paphiopedilum
.
Results
Here, we sequenced, assembled, and annotated 77 plastomes of
Paphiopedilum
species (size range of 152,130 – 164,092 bp). The phylogeny based on the plastome resolved the relationships of the genus except for the phylogenetic position of two unstable species. We used phylogenetic and comparative genomic approaches to elucidate the plastome evolution of
Paphiopedilum
. The plastomes of
Paphiopedilum
have a conserved genome structure and gene content except in the SSC region. The large single copy/inverted repeat (LSC/IR) boundaries are relatively stable, while the boundaries of the inverted repeat and small single copy region (IR/SSC) varied among species. Corresponding to the IR/SSC boundary shifts, the chloroplast genomes of the genus experienced IR expansion and SSC contraction. The IR region incorporated one to six genes of the SSC region. Unexpectedly, great variation in the size, gene order, and gene content of the SSC regions was found, especially in the subg.
Parvisepalum
. Furthermore,
Paphiopedilum
provides evidence for the ongoing degradation of the
ndh
genes in the photoautotrophic plants. The estimated substitution rates of the protein coding genes show accelerated rates of evolution in
clpP
,
psbH
, and
psbZ
. Genes transferred to the IR region due to the boundary shift also have higher substitution rates.
Conclusions
We found IR expansion and SSC contraction in the chloroplast genomes of
Paphiopedilum
with dense sampling, and the genus shows variation in the size, gene order, and gene content of the SSC region. This genus provides an ideal system to investigate the dynamics of plastome evolution.
