Yan-Yan Guo1, Jia-Xing Yang2, Ming-Zhu Bai2, Guo-Qiang Zhang3, Zhong-Jian Liu4,5. 1. College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China. guoyy@henau.edu.cn. 2. College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China. 3. Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China. 4. Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization At College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. zjliu@fafu.edu.cn. 5. College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. zjliu@fafu.edu.cn.
Abstract
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.
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.
Authors: Hyoung Tae Kim; Jung Sung Kim; Michael J Moore; Kurt M Neubig; Norris H Williams; W Mark Whitten; Joo-Hwan Kim Journal: PLoS One Date: 2015-11-11 Impact factor: 3.240
Authors: Marcin Górniak; Dariusz L Szlachetko; Natalia Olędrzyńska; Aleksandra M Naczk; Agata Mieszkowska; Lidia Boss; Marek S Ziętara Journal: Int J Mol Sci Date: 2021-10-21 Impact factor: 5.923