The mitochondrial and chloroplast genomes of Lagerstroemia suprareticulata revealed a convergent genome morphology in genetic material evolution

To investigate the mitochondrial genome characteristics and evolutionary dynamics of <i>Lagerstroemia suprareticulata</i>, we performed complete assembly and annotation of its mitochondrial genome, followed by comparative genomic analyses with related species. This research presents the initial comprehensive mitogenome of <i>L. suprareticulata</i>, a 364,645 bp independent single cyclic structure with a whole average GC content of 46.20%, twice the size of the chloroplast genome and an approximately similar tetrad structure. It comprised 62 functional genes and 386 open reading frames. Besides two long repeats above 800 bp, simple sequence repeat analysis revealed a predominance of mono-nucleotide and tetra-nucleotide repeats, which is consistent with patterns observed in most Lythraceae species. A total of 480 C-to-U RNA editing sites were predicted in 36 protein-coding genes, with the highest number in <i>nad4</i>. AUG and UGG had a relative synonymous codon usage value of 1, while GCU had the highest RSCU (1.62). <i>ccmB</i> and <i>rps4</i> may have undergone positive selection, whereas <i>atp8</i> and <i>cox1</i> experienced strong purifying selection. Phylogenetic analysis based on mitochondrial and chloroplast genomes confirmed a close relationship between <i>L. suprareticulata</i> and <i>L. indica</i>. Collinear segments decreased with increasing evolutionary distance, and gene rearrangement analysis revealed a lineage-specific gene arrangement pattern in <i>Lagerstroemia</i>. Homologous sequence analysis identified 34 mitochondrial-chloroplast homologous sequences (accounting for 4.63% of the mitochondrial genome) and 2182 mitochondrial-nuclear homologous sequences. These results provide a foundation for understanding the mitochondrial genome evolution of <i>Lagerstroemia</i> and Lythraceae, and may offer valuable genetic resources for horticultural and evolutionary studies.