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Comparative Study
. 2024 Dec 26;24(1):1245.
doi: 10.1186/s12870-024-05974-w.

Comparative genomics and phylogenetic analysis of six Malvaceae species based on chloroplast genomes

Yiwang Zhong #  1   2 , Beibei Bai #  1 , Yangyang Sun  1   2 , Ke Wen  1   3 , Yang Qiao  2   4 , Lijun Guo  2   3 , Huidong Deng  2   3 , Yingjun Ye  2   4 , Liying Feng  5 , Xuejie Feng  6   7
Affiliations
Comparative Study

Comparative genomics and phylogenetic analysis of six Malvaceae species based on chloroplast genomes

Yiwang Zhong et al. BMC Plant Biol. .

Abstract

The Malvaceae family, comprising 9 subfamilies and 4,225 species, includes economically significant taxa, such as Ceiba pentandra, Gossypium ekmanianum, Gossypium stephensii, Kokia drynarioides, Talipariti hamabo, and Durio zibethinus. Chloroplast (cp) genome research is crucial for elucidating the evolutionary divergence and species identification within this family. In this study, we assembled and annotated cp genomes of six Malvaceae species, conducting comprehensive comparative genomic and phylogenomic analyses. The assembled genomes range from 160,495 to 163,970 bp in size, with 125-129 genes annotated. Notable differences were observed in the IR (inverted repeat) regions, and SSR analysis revealed that Durio zibethinus has the highest number of specific variation sites. Among the six species, Talipariti hamabo uniquely exhibits more palindromic repeats than forward repeats. Seven highly mutated regions were identified, offering potential markers for species identification. Phylogenetic reconstruction using the maximum likelihood method revealed two primary clades within Malvaceae: Byttneriina and Malvadendrina. Within Malvadendrina, the subfamily Helicteroideae represents the earliest divergence, followed by Sterculioideae. This study provides a robust phylogenetic framework and valuable insights into the classification and evolutionary history of Malvaceae species.

Keywords: Chloroplast genome; Comparative analysis; Malvaceae; Phylogeny; Sequence characteristic.

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Conflict of interest statement

Declarations. Ethical approval: The study was conducted the plant material that complies with relevant institutional, national, and international guidelines and legislation. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Cp genome maps of six Malvaceae. Genes shown outside of the outer layer circle are transcribed clockwise, while those insides are transcribed counterclockwise. The genes belonging to different functional groups are color-coded. The dark gray area of the inner circle denotes
Fig. 2
Fig. 2
Analysis of codon preferences in the cp genomes of six Malvaceae species. A. amino acid usage; B. codon usage
Fig. 3
Fig. 3
Analysis of sequence repeat in the six Malvaceae cp genomes. A. The type frequency of different SSR types. B. Frequency of identified long repeats types
Fig. 4
Fig. 4
Comparison of the borders of the LSC, SSC, and IR regions among six Malvaceae cp genomes
Fig. 5
Fig. 5
Phylogeny and gene loss in six Malvaceae species
Fig. 6
Fig. 6
Analysis of sequence alignment of six Malvaceae cp genomes
Fig. 7
Fig. 7
Nucleotide polymorphism of the cp genomes of six Malvaceae species
Fig. 8
Fig. 8
Phylogenetic relationships among subfamilies with complete cp sequence of Malvaceae. Species in genus assembled in this study are indicated in red text. The numbers within star symbols represent the number of species included
Fig. 9
Fig. 9
The phylogenetic relationships constructed based on homologous genes derived from the protein sequences of 25 nuclear genomes
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