The First Five Mitochondrial Genomes for the Family <i>Nidulariaceae</i> Reveal Novel Gene Rearrangements, Intron Dynamics, and Phylogeny of <i>Agaricales</i>

The family <i>Nidulariaceae</i>, consisting of five genera including <i>Cyathus</i>, is a unique group of mushrooms commonly referred to as bird’s nest fungi due to their striking resemblance to bird’s nests. These mushrooms are considered medicinal mushrooms in Chinese medicine and have received attention in recent years for their anti-neurodegenerative properties. However, despite the interest in these mushrooms, very little is known about their mitochondrial genomes (mitogenomes). This study is the first comprehensive investigation of the mitogenomes of five <i>Nidulariaceae</i> species with circular genome structures ranging in size from 114,236 bp to 129,263 bp. Comparative analyses based on gene content, gene length, tRNA, and codon usage indicate convergence within the family <i>Nidulariaceae</i> and heterogeneity within the order <i>Agaricales</i>. Phylogenetic analysis based on a combined mitochondrial conserved protein dataset provides a well-supported phylogenetic tree for the Basidiomycetes, which clearly demonstrates the evolutionary relationships between <i>Nidulariaceae</i> and other members of <i>Agaricales</i>. Furthermore, phylogenetic inferences based on four different gene sets reveal the stability and proximity of evolutionary relationships within <i>Agaricales</i>. These results reveal the uniqueness of the family <i>Nidulariaceae</i> and its similarity to other members of <i>Agaricales</i>; provide valuable insights into the origin, evolution, and genetics of <i>Nidulariaceae</i> species; and enrich the fungal mitogenome resource. This study will help to expand the knowledge and understanding of the mitogenomes in mushrooms.