Chloroplast Genome Evolution in Four Montane Zingiberaceae Taxa in China.

Qian Yang,Zhi-Qiang Wu,Jian-Li Zhao,Li Li,Gao-Fei Fu,Qing-Jun Li

doi:10.3389/fpls.2021.774482

Abstract

Chloroplasts are critical to plant survival and adaptive evolution. The comparison of chloroplast genomes could provide insight into the adaptive evolution of closely related species. To identify potential adaptive evolution in the chloroplast genomes of four montane Zingiberaceae taxa (Cautleya, Roscoea, Rhynchanthus, and Pommereschea) that inhabit distinct habitats in the mountains of Yunnan, China, the nucleotide sequences of 13 complete chloroplast genomes, including five newly sequenced species, were characterized and compared. The five newly sequenced chloroplast genomes (162,878–163,831 bp) possessed typical quadripartite structures, which included a large single copy (LSC) region, a small single copy (SSC) region, and a pair of inverted repeat regions (IRa and IRb), and even though the structure was highly conserved among the 13 taxa, one of the rps19 genes was absent in Cautleya, possibly due to expansion of the LSC region. Positive selection of rpoA and ycf2 suggests that these montane species have experienced adaptive evolution to habitats with different sunlight intensities and that adaptation related to the chloroplast genome has played an important role in the evolution of Zingiberaceae taxa.

Highlights

Even though the chloroplast genome is typically far smaller than most plant nuclear genomes, chloroplasts play a crucial role in plant survival, adaptation, and evolution (Wicke et al, 2011; Gao et al, 2019; Zhao C. et al, 2019; Dopp et al, 2021)
Chloroplast genomes typically exhibit a conserved quadripartite structure, which includes two inverted repeat regions (IRs), a small single copy (SSC) region, and a large single copy (LSC) region (Shinozaki et al, 1986), as well as a relatively conserved set of genes, which can be categorized according to their involvement in photosynthesis, transcription, translation, and biosynthesis (Sassenrath-Cole, 1998)
This study aimed to investigate the hypothesis that two pairs of sister genera (Cautleya vs. Roscoea and Rhynchanthus vs. Pommereschea) have common chloroplast genes associated with adaptive divergence to contrast habitats

Summary

Introduction

Even though the chloroplast genome is typically far smaller than most plant nuclear genomes, chloroplasts play a crucial role in plant survival, adaptation, and evolution (Wicke et al, 2011; Gao et al, 2019; Zhao C. et al, 2019; Dopp et al, 2021). The absence of the ndh gene and one of the IR regions in the chloroplast genome of Cassytha (Lauraceae) taxa and the absence of almost all photosynthesis-related genes in Aeginetia indica (Orobanchaceae) are associated with parasitic lifestyles (Song et al, 2017; Chen et al, 2020), and many chloroplasts are absent from the chloroplast genome of Gastrodia elata (Orchidaceae), which is mycoheterotrophic and does not rely on photosynthesis, thereby resulting in a relatively small chloroplast genome (35,326 bp; Yuan et al, 2018) These extreme examples suggest that changes in chloroplast gene content are closely associated with plant adaptation. The adaptive evolution of most angiosperm groups, especially the Zingiberaceae, remains largely unknown

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