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. 2023 Oct 27;24(1):648.
doi: 10.1186/s12864-023-09563-3.

Comparative chloroplast genomics reveals the phylogeny and the adaptive evolution of Begonia in China

Chao Xiong #  1 , Yang Huang #  2 , Zhenglong Li  3 , Lan Wu  4 , Zhiguo Liu  1 , Wenjun Zhu  1 , Jianhui Li  5 , Ran Xu  6 , Xin Hong  7
Affiliations

Comparative chloroplast genomics reveals the phylogeny and the adaptive evolution of Begonia in China

Chao Xiong et al. BMC Genomics. .

Abstract

Background: The Begonia species are common shade plants that are mostly found in southwest China. They have not been well studied despite their medicinal and decorative uses because gene penetration, decreased adaptability, and restricted availability are all caused by frequent interspecific hybridization.

Result: To understand the patterns of mutation in the chloroplast genomes of different species of Begonia, as well as their evolutionary relationships, we collected seven Begonia species in China and sequenced their chloroplast genomes. Begonia species exhibit a quadripartite structure of chloroplast genomes (157,634 - 169,694 bp), consisting of two pairs of inverted repeats (IR: 26,529 - 37,674 bp), a large single copy (LSC: 75,477 - 86,500 bp), and a small single copy (SSC: 17,861 - 18,367 bp). 128-143 genes (comprising 82-93 protein-coding genes, 8 ribosomal RNAs, and 36-43 transfer RNAs) are found in the chloroplast genomes. Based on comparative analyses, this taxon has a relatively similar genome structure. A total of six substantially divergent DNA regions (trnT-UGU-trnL-UAA, atpF-atpH, ycf4-cemA, psbC-trnS-UGA, rpl32-trnL-UAG, and ccsA-ndhD) are found in the seventeen chloroplast genomes. These regions are suitable for species identification and phylogeographic analysis. Phylogenetic analysis shows that Begonia species that were suited to comparable environments grouped in a small clade and that all Begonia species formed one big clade in the phylogenetic tree, supporting the genus' monophyly. In addition, positive selection sites were discovered in eight genes (rpoC1, rpoB, psbE, psbK, petA, rps12, rpl2, and rpl22), the majority of which are involved in protein production and photosynthesis.

Conclusion: Using these genome resources, we can resolve deep-level phylogenetic relationships between Begonia species and their families, leading to a better understanding of evolutionary processes. In addition to enhancing species identification and phylogenetic resolution, these results demonstrate the utility of complete chloroplast genomes in phylogenetically and taxonomically challenging plant groupings.

Keywords: Begonia; Chloroplast; Evolutionary; Phylogeny; Positive selection.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Structural map of the Begonia chloroplast genome. Genes shown outside the outer circle are transcribed clockwise and those inside are transcribed counterclockwise. Genes belonging to different functional groups are color-coded. B. cathayana is used as the template for Fig. 1. The dark grey plot in the inner circle corresponds to GC content. Large single copy, small single copy, and inverted repeat are indicated with LSC, SSC, and IR (IRa and IRb), respectively
Fig. 2
Fig. 2
Comparison of the borders of the LSC, SSC, and IR regions among seventeen Begonia chloroplast genomes
Fig. 3
Fig. 3
The number of different types of SSRs in seventeen Begonia chloroplast genomes
Fig. 4
Fig. 4
The comparative analysis with LAGAN program of the whole-chloroplast genome of seventeen different species of Begonia. The x-axis represents the coordinate in the chloroplast genome
Fig. 5
Fig. 5
The nucleotide diversity (Pi) value in the seventeen Begonia chloroplast genomes. (A) The Pi value of LSC region. (B) The Pi value of IRb region. (C) The Pi value of SSC region. (D) The Pi value of Non-coding region
Fig. 6
Fig. 6
The ML phylogenetic tree of 42 species. Supporting values of > 50% for ML were shown on the branch. 25 species as the outgroup were colored blue, 17 Begonia species were colored purple ◆— newly sequenced species
Fig. 7
Fig. 7
Eight genes of positive selection of amino acid sequences in site model tests
Fig. 8
Fig. 8
Spatial location of the positively selected sites in proteins of B. cathayana. (A) Spatial location of the positively selected sites in the rpoC1 protein of B. cathayana. (B) Spatial location of the positively selected sites in the rpoB protein of B. cathayana. (C) Spatial location of the positively selected sites in the psbE protein of B. cathayana. (D) Spatial location of the positively selected sites in the psbK protein of B. cathayana. (E) Spatial location of the positively selected sites in the petA protein of B. cathayana. (F) Spatial location of the positively selected sites in the rps12 protein of B. cathayana. (G) Spatial location of the positively selected sites in the rpl2 protein of B. cathayana. (H) Spatial location of the positively selected sites in the rpl22 protein of B. cathayana
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