Large mitogenome of Gunnera prorepens reveals extensive structural expansion alongside ancestral gene retention

Gunnerales represent an early-diverging lineage sister to the Pentapetalae; however, mitochondrial genome evolution in this group remains uncharacterized. Characterizing the mitogenome structure and gene content in Gunnerales provides critical insights into early core eudicot evolution.

We assembled and annotated the complete mitogenome of Gunnera prorepens using PacBio HiFi sequencing. The 1,374,480 bp genome, larger than those of many basal angiosperms and early-diverging eudicots. The coding gene set remains largely conserved, including 39 protein-coding genes, 23 unique tRNA genes, and three rRNA genes. The sdh3 and sdh4, which are frequently lost in other early-diverging eudicots, are retained. Genome expansion is primarily associated with repeat accumulation, including 1,066 dispersed repeats and several large inverted repeats that may represent potential recombination sites in the mitogenome. In addition, plastid-derived sequences account for 6.33% of the genome. We predicted 380 RNA editing sites, including an editing event predicted to restore the start codon of nad1. Comparative analyses indicate extensive structural rearrangements and genome expansion while maintaining an ancestral like coding gene complement.

The mitogenome of G. prorepens provides additional evidence that mitochondrial genome expansion in angiosperms can occur without substantial loss of protein-coding genes. As a representative of Gunnerales, G. prorepens retains a largely ancestral mitochondrial gene complement despite its relatively large genome size. Our results underscore that significant mitogenomic expansion and ancestral gene retention can be uncoupled during the early divergence of core eudicots.