Comparative genomic and phylogenetic analyses of the mitogenome of Graptopetalum Paraguayense (N. E. Br.) Walth. 1938

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Comparative genomic and phylogenetic analyses of the mitogenome of Graptopetalum Paraguayense (N. E. Br.) Walth. 1938

Scientific Reports , Article number:  (2026) Cite this article

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Abstract

Graptopetalum paraguayense is a perennial succulent plant with ornamental, ecological, and medicinal value. Here, we present the first complete mitogenome of G. paraguayense, assembled as a circular molecule of 242,059 bp with a GC content of 43.65%. The genome contains 50 genes, including 31 protein-coding genes (PCGs), 13 tRNAs, 3 rRNAs, and 3 pseudogenes. A total of 599 RNA editing sites were identified, with a predominant effect of altering amino acid hydrophobicity (47.41% were hydrophilic-to-hydrophobic conversions). Codon usage bias analysis revealed a preference for GCU (Ala), CGA (Arg), and UUA (Leu), with the stop codon UAA exhibiting the highest RSCU value (1.94). A total of 122 repetitive sequences were identified, comprising 59 simple sequence repeats (SSRs), 1 tandem repeat, and 62 dispersed repeats. Evolutionary analysis indicated positive selection on ccmB and nad7 genes, while the majority of PCGs were under purifying selection. The mitogenome of G. paraguayense shared 57.28% sequence similarity with that of Sedum plumbizincicola. We also found evidence of chloroplast-to-mitochondrial DNA transfer, involving genes such as psaC, ndhE, ndhG, ndhI, ndhA, and ndhH. Comparative analyses identified eleven divergent hotspot regions: atp9, atp8, rpl5, cox2, ccmFn, rps7, ccmC, ccmFc, mttB, nad6, and rps13. Phylogenetic analysis confirmed the placement of G. paraguayense within the Acre clade of Crassulaceae, showing a sister relationship with S. plumbizincicola. Our study not only provides the first mitochondrial genomic resource for G. paraguayense but also reveals potential adaptive evolution through positive selection and interorganellar gene transfer, offering new perspectives on mitogenome plasticity in succulent plants.

Data availability

The data is available at NCBI accession: PV256627.

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Funding

This work was supported by the Natural Science Foundation from Jiangsu Province (No. BK20211128) and the project of innovative entrepreneurship training for college students in Jiangsu province (No. 202313843019Y, No. 202313843009Y and No. S202513843029).

Author information

Authors and Affiliations

  1. School of Chemistry and Biological Engineering, NanJing Normal University TaiZhou College, TaiZhou, 225300, China

    Xue Zhou, Chuqi Lin, Zhirui Li, Lin Zhou & Xi Du

  2. Fisheries College, Jimei University, Xiamen, 361021, China

    Chuqi Lin

  3. College of Biological Science and Technology of Yangzhou University, Yangzhou, 225009, China

    Qingming Ren & Fei Xiong

Authors

  1. Xue Zhou
  2. Qingming Ren
  3. Chuqi Lin
  4. Zhirui Li
  5. Lin Zhou
  6. Fei Xiong
  7. Xi Du

Contributions

Xue Zhou: Data curation, Formal analysis, Funding acquisition, Investigation, Writing –original draft, Writing–review&editing. Qingming Ren: Data curation, Formal analysis, Investigation, Writing–review&editing. ChuQi Lin: Data curation, Formal analysis, Writing–original draft, Methodology. ZhiRui Li: Data curation, Writing–original draft, Methodology. Lin Zhou：Methodology. Fei Xiong: supervised the project and revised the manuscript. Xi Du: supervised the project and revised the manuscript.

Corresponding author

Correspondence to Xi Du.

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Zhou, X., Ren, Q., Lin, C. et al. Comparative genomic and phylogenetic analyses of the mitogenome of Graptopetalum Paraguayense (N. E. Br.) Walth. 1938. Sci Rep (2026). https://doi.org/10.1038/s41598-025-34236-4

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  • DOI: https://doi.org/10.1038/s41598-025-34236-4

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