The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions

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