Evolution of mutualisms in the basidiomycete genus Termitomyces

Mutualisms are abundant in nature despite our common understanding that evolution by natural selection is driven by competition. To understand how mutualisms can arise and what maintains their long-term stability, in this thesis I explore mutualisms at three levels of selection in the basidiomycete genus Termitomyces: the domestication of the fungus itself by a termite host, the inheritance and genetic variation of mitochondria in the fungal cell following sexual reproduction, and the transfer of tRNA genes from mitochondria to linear plasmids that results in co-dependency. In addition, I reconstruct the mitochondrial genomes of several Termitomyces and related species to analyze mtDNA variation and evolution in this diverse group of fungi.

The mitochondrial genomes of Termitomyces are characterized by a large inverted repeat and a relatively high G4DNA motif content (Chapter 2). The significant enrichment of G4DNA in the repeats compared to the single copy regions suggests there may be reduced selection against G4DNA within the repeat regions, perhaps due to enhanced homologous recombination-driven repair of double-stranded breaks. G4DNA in fungal mtDNA is highly reduced in coding regions compared to human mtDNA, which may be the result of compensatory evolution in vertebrates to resolve G4DNA formation in transcribed RNA.

The common ancestor of Termitomyces was likely reliant on insect faeces as a growth substrate prior to its domestication by termites (Chapter 3). A phylogenomic reconstruction of Termitomyces and other Lyophyllaceae reveals that the free-living, insect-associated coprophiles Arthromyces and Blastosporella are close relatives of Termitomyces. Several key traits likely predate the fungus-termite mutualism, including conidiospores, a pseudorhiza, a perforatorium, and a repertoire of carbohydrate-active enzymes. The combination of these traits probably facilitated the transition of Termitomyces’ free-living ancestor to a termite-domesticated lifestyle.

The mitochondria of several Termitomyces species seem to be dependent on linear mitochondrial plasmids for their supply of an essential tRNA gene (Chapter 4). Phylogenetic reconstruction of plasmids, mostly derived from Termitomyces species, reveals that transfer of mitochondrial tRNA genes from mtDNA to plasmids occurred independently in several Termitomyces species. In two cases, the tRNA gene was subsequently lost from the mtDNA of Termitomyces, the only known occurrence of complete loss of a tRNA function from Termitomyces mtDNA. This suggests an abrupt emergence of genetic addiction of mtDNA to a plasmid.

The mtDNA of Termitomyces shows limited recombination near regions containing mobile homing endonucleases (Chapter 5). Experimental matings of two Termitomyces homokaryons, along with complete mtDNA sequence data for six wild populations, suggest the inheritance of mtDNA proceeds without extensive heteroplasmy or genome-wide recombination. Previous studies noted Termitomyces  appears to lack nuclear migration during mating, which would imply heterokaryon formation occurs in cells containing mixed cytoplasm. My results indicate that nuclear migration is either present but limited, or heteroplasmic cells quickly converge to a homoplasmic state. In either case, physical recombination of mtDNA is constrained but self-splicing endonucleases are able to transfer between different parental mitochondria during sex.