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. 2022 Jan 10:12:774482.
doi: 10.3389/fpls.2021.774482. eCollection 2021.

Chloroplast Genome Evolution in Four Montane Zingiberaceae Taxa in China

Qian Yang  1   2 , Gao-Fei Fu  3 , Zhi-Qiang Wu  3 , Li Li  1   2 , Jian-Li Zhao  1   2 , Qing-Jun Li  1   2
Affiliations

Chloroplast Genome Evolution in Four Montane Zingiberaceae Taxa in China

Qian Yang et al. Front Plant Sci. .

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.

Keywords: Zingiberaceae; adaptive evolution; chloroplast genome; gene loss; genomic variation.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Comparison of chloroplast genome structure in Zingiberaceae. IR (inverted repeat), LSC (large single copy) and SSC (small single copy) regions and border genes are indicated.
FIGURE 2
FIGURE 2
Variation level of the Zingiberaceae chloroplast genome sequences, the y-axis indicates the level of variation (between 50 and 100%) and the x-axis represents the coordinate in the chloroplast genome.
FIGURE 3
FIGURE 3
The Ka/Ks ratio of protein-coding genes of four species chloroplast genomes, and Ka/Ks > 1 suggests positive selection.
FIGURE 4
FIGURE 4
The phylogenetic tree ML (maximum likelihood) and BI (Bayesian Inference) based on 47 complete chloroplast genomes (left) and 54 ITS (internal transcribed spacer) sequences (right). Supporting values of > 50% and > 0.5 for ML and BI, respectively, were shown on the branch.
See this image and copyright information in PMC

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