Characterization of the mitochondrial genome, cox1 intron dynamics and phylogenetic analysis of Fusarium species causing basal rot in onions

The Fusarium species complex causes basal rot in onions, impacting both crop yield and storage quality globally. While whole-genome sequencing of Fusarium species causing basal rot has identified many infection-related genes, there is limited research on their mitochondrial genomes, despite their crucial roles in virulence and disease development. In this study, we assembled and annotated the mitochondrial genomes of Fusarium acutatum , F. proliferatum , and F. oxysporum f. sp. cepae , which are 51,667 bp, 46,542 bp, and 47,302 bp long, respectively. All mitogenomes displayed high synteny, with their 15 core PCGs being highly conserved. Interestingly, the genomes contain highly variable regions that encode a large, unknown open reading frame (ORF) of 2,286 to 2488 amino acids. Most protein-coding genes exhibited a non-synonymous to synonymous substitution ratio (Ka/Ks) of less than 1, indicating they are under purifying selection. An intron landscape from 34 Fusarium species revealed size variation (46 kb to 110 kb) among mitogenomes, which was strongly correlated with the presence or absence of introns. We identified 19 intron positional classes in the cox1 gene across 27 species, with the highest number in F. pseudograminearum (16), including unique positions at P246, P1302, and P1313. The positional class P715 was widespread among the examined species. Phylogenetic analyses using maximum likelihood and Bayesian inference on combined mitochondrial gene datasets revealed a close relationship among the assembled mitogenomes and species within the Fusarium oxysporum and Fusarium fujikuroi species complex. Overall, these findings provide a foundation for future research into the evolutionary dynamics of emerging Fusarium species.