Comparative analysis of mitochondrial genomes and evolutionary characteristics of five Alternaria species causing...

Mitochondria play a central role in fungal metabolism, adaptation, and pathogenesis, yet the evolutionary dynamics of mitochondrial genomes in plant-pathogenic Alternaria species remain poorly understood. In this study, we conducted a comprehensive comparative mitochondrial genomes analysis of five economically important Alternaria species-Alternaria burnsii, A. tenuissima, A. arborescens, A. alternata, and A. gossypina-to investigate structural architecture, genomic variation, selection pressures, repeat element dynamics, and phylogenetic relationships. The mitochondrial genomes exhibited a conserved gene content of 13-14 core genes, 30-33 tRNA and 2 rRNA, but varied in size due to differences in intron insertions, intergenic spacers, and repetitive sequences. Strong A/U-biased codon usage was observed across species, consistent with high AT-richness and translational optimization. Purifying selection dominated across essential respiratory complexes (cox1-3, atp6-9 and cob), indicating functional constraint, while signals of positive selection and pseudogenization (disrupted rps3 in A. burnsii YUN-Z1107) suggest lineage-specific adaptations. We identified evolutionary hotspots in both coding and non-coding regions enriched with InDeLs and repeat expansions. A total of 920 simple sequence repeats (SSRs) were annotated, with A. burnsii YUN-Z1107 showing the highest SSR density, particularly pentanucleotide motifs, implicating replication slippage in genome plasticity. Long repetitive elements were associated with intron mobility and possible recombination events, especially in A. arborescens YUN-Z0872. Phylogenomic analysis of 29 Ascomycota species confirmed a monophyletic Alternaria clade within Pleosporales, although limited resolution within the genus suggests complex evolutionary histories. Our findings support a "conserved core with flexible periphery" model of mitochondrial genomes evolution, where mitochondrial innovation contributes to host adaptation and pathogenicity. This study highlights the mitochondrial genomes as an active driver of fungal evolution and provides a foundation for exploring mitochondria-host coevolution in plant-pathogen interactions.