Analysis of the Rhodomyrtus tomentosa mitochondrial genome: Insights into repeat-mediated recombination and intra-cellular DNA transfer

• Published in: Gene 2024-05, Vol.909, p.148288-148288, Article 148288
• Main Authors: Yu, Xiaoli, Ma, Zhengbing, Liu, Shu, Duan, Zhonggang
• Format: Article
• Language: English
• Subjects: Mitochondrial genome; MTPT; Myrtales; Recombination; Rhodomyrtus tomentosa; Topological incongruence
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2024.148288

•Complete Rhodomyrtus tomentosa mitochondrial genome (400,482 bp) unveiled.•Nanopore ONT reads and PCR reveal repeat-mediated recombination in the genome.•PCR amplification confirms existence of sequences from intracellular gene transfer.•R. tomentosa consistently clusters with Myrtaceae species in Myrtales phylogeny based on mitochondrial genome sequences. Plant mitochondrial genomes participate in encoding proteins crucial to the major producers of ATP in the cell and replication and heredity of their own DNA. The sequences and structure of the plant mitochondrial genomes profoundly impact these fundamental processes, and studies of plant mitochondrial genomes are needed. We reported the complete sequences of the Rhodomyrtus tomentosa mitochondrial genome here, totaling 400,482 bp. Nanopore ONT reads and PCR amplification provided evidence for recombination mediated by the eight repeat pairs for the R. tomentosa mitochondrial genome. Thirty-eight genes were identified in the R. tomentosa mitochondrial genome. Comparative analyses of the mitochondrial genome and plastome and PCR amplification suggest that five fragments of mitochondrial plastid DNA were unfunctional sequences resulting from intracellular gene transfer. Phylogenetic analysis based on each and all of the 27 mitochondrial protein-coding genes of nine Myrtales species revealed that R. tomentosa always clustered with other species of Myrtaceae. This study uncovered the enormous complexity of the R. tomentosa mitochondrial genome, the active repeat-mediated recombinations, the presence of mitochondrial plastid DNAs, and the topological incongruence of Myrtales among the single-gene trees.