Comparative genomic and phylogenetic analyses of mitochondrial genomes of Graptopetalum paraguayense (N. E. Br.) Walth.1938

Abstract Graptopetalum paraguayense is a perennial succulent plant with ornamental value, functional value and medicinal activity. This study presents the first complete mitochondrial genome of G. paraguayense. We assembled and annotated the complete mitochondrial genome of G. paraguayense. we characterized a 242,059bp circular mitogenome with 43.65% GC content, harboring 50 functional genes (31 PCGs, 13 tRNAs, 3 rRNAs) and 3 pseudogenes. Identification of 599 RNA editing sites, predominantly altering amino acid hydrophobicity (47.41% hydrophilic-to-hydrophobic conversions). Codon usage bias analysis revealing preferential use of GCU (Ala), CGA (Arg), and UUA (Leu), with UAA stop codon exhibiting highest RSCU (1.9355). A total of 122 repetitive sequences were identified, including 59 Simple sequence repeat, 1 tandem repeat, and 62 dispersed repeat. Ka/Ks analysis indicating positive selection on ccmB and nad7 genes. G. paraguayense shared 57.28% sequence similarity with Sedum plumbizincicola. Evidence of chloroplast-to-mitochondrial DNA transfer involving psaC, ndhE, ndhG, ndhI, ndhA, ndhH genes. Eleven divergent hotspot regions were identified by comparative analyses, were atp9, atp8, rpl5, cox2, ccmFn, rps7, ccmC, ccmFc, mttB, nad6 and rps13. Based on phylogenetic tree analysis, G. paraguayense is highly related to Sedum plumbizincicola. These results provide foundational insights into mitogenome evolution in Crassulaceae, highlighting adaptive genetic mechanisms and interorganellar gene transfer in succulent plants.