Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?

The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.

Automated summary

The genome of Saccharomyces cerevisiae was the first eukaryotic organism genome sequenced, reported in 1996, but it took over 10 years to sequence any of the zygomycete fungi, which belong to the phyla Mucoromycota and Zoopagomycota. Over 1000 zygomycete genomes have now been sequenced, revealing deep phylogenetic separation between plant-associated saprotrophic Mucoromycota and animal-associated parasites and commensals in the Zoopagomycota. Genomic studies have provided insights into fungal adaptations to living on land, including light and gravity sensing, hyphal growth, and co-existence with terrestrial plants. Genomic data has also facilitated research on genome architecture, pathogenicity genes, secondary metabolites, and endosymbiotic bacteria and viruses.