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

Yan-Yan Guo,Zhong-Jian Liu,Ming-Zhu Bai,Jia-Xing Yang,Guo-Qiang Zhang

doi:10.1186/s12870-021-03053-y

Abstract

BackgroundPaphiopedilum 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.ResultsHere, 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.ConclusionsWe 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.

Highlights

Paphiopedilum is the largest genus of slipper orchids
The goals of this study are to 1) reconstruct the phylogenetic relationships of the genus, especially the systematic positions of the phylogenetically unstable taxa (P. canhii, P. fairrieanum, P. hirsutissimum, and P. rungiyasanum), and test whether the chloroplast genome could resolve the recently diverged taxa of the genus; 2) characterize the chloroplast genome evolution pattern of Paphiopedilum; and 3) calculate the substitution rate of the coding genes, evaluate the impact of inverted repeat (IR)/small single copy (SSC) boundary shift, and test whether the genes transferred to the IR region due to boundary shift have decreased substitution rates
The other 11 plastome sequences had one or two gaps located in regions of high Adenosine Thymine (AT) content within the three intergeneric regions

Summary

Introduction

Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expan‐ sion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum. Many studies have used plastome data to address the phylogenetic relationships among land plants, chloroplast genome evolution, and patterns and rates of nucleotide substitutions [2,3,4,5]. These studies indicate that the chloroplast genome has striking variations in genome size, genome structure, and gene substitution rate across the angiosperms. High throughout sequencing provides a good opportunity to test the plastome evolution in more groups

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