Phylogenetic and evolutionary insights from 30 newly-assembled Onygenales Mitochondrial Genomes: co-evolution of introns and HEGs shapes mitogenome size variation

Abstract

Mitochondrial genomes (mtDNA) provide valuable resources for investigating fungal evolution; however, comprehensive mitogenomic datasets for Onygenales are still scarce. Here, we assembled and annotated 30 new mitogenomes representing 18 species across five families, substantially expanding the available resources for this order. We tested two evolutionary hypotheses: (1) that structural features of mitochondrial genomes are phylogenetically conserved and (2) that introns and homing endonuclease genes (HEGs) have co-evolved and contributed to genome size variation. All mitogenomes exhibited conserved protein-coding content, but showed considerable variation in intron number and genome size. Phylogenetic signal was significant for multiple traits, including gene number and intron abundance. Furthermore, phylogenetic regression analyses revealed a strong correlation between intron content and HEG abundance, thereby substantiating the hypothesis of coordinated evolution. Our findings demonstrate that mitochondrial genome evolution in Onygenales reflects both structural conservation and lineage-specific expansion patterns, shaped in part by the distribution of introns and HEGs.