Chapter 3 Genome Evolution in Plant Pathogenic and Symbiotic Fungi

Approximately 100,000 species of fungi have been described so far, of which, a high percentage obtain nutrients by living in close association with other organisms (mainly plants), being pathogens or symbionts (i.e. commensalists or mutualists). At the genomic level, an association between broad-scale genetic changes and the emergences of the parasitic and symbiotic life style in fungi has been proposed. Although comparative genomic studies in fungi are still in the early stages, they have enormous potential to improve our understanding of how such life styles evolve. In this chapter, we review the main characteristics of genome evolution in fungi, particularly in species that are pathogenic or symbiotic with plants, by focusing on the mechanisms involved in host interactions. We address the following topics in relation to the pathogenic and symbiotic lifestyles in fungi: the evolution of genome organization, chromosomal rearrangements, evolution of gene families and clusters, suppression of recombination around mating type loci, rapidly evolving genes, horizontal transfer, hybridization, transposable elements, telomeres, introns, mitochondrial genomes, and we finally compare genome evolution between pathogenic bacteria and fungi.