Review The evolving fungal genome Eva H. STUKENBROCK a, *, Daniel CROLL b a Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany b Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC V6T 1Z4, Canada article info Article history: Received 18 June 2013 Received in revised form 26 January 2014 Accepted 3 February 2014 Keywords: Adaptive evolution Effective population size Genome evolution Mobile genetic elements Pathogens Ploidy abstract Fungal genomes vary considerably in size and organization. The genome of Microsporidium contains less than 3 Mb while the genomes of several Basidiomycetes and Ascomycetes greatly exceed 100 Mb. Likewise chromosome numbers and ploidy levels can differ even between closely related species. The differences in genome architecture among fungi reflect the interplay of different mutational processes as well as the population biology of the different species. Comparative genome studies have elucidated the underlying mechanisms of genome evolution in different groups of fungi and have provided insight into species-specific genomic traits. Mobile genetic elements have been instrumental in shaping the genome architecture and gene content in many fungal species. In many path- ogenic fungi the mobile genetic elements even play a crucial role in rapid adaptive evolu- tion by mediating high rates of sequence mutations, chromosomal rearrangements, and ploidy changes. But in many species mobile elements are efficiently restricted by defense mechanisms, which have evolved to suppress and regulate parasitic elements. Different rates of genome dynamic and adaptive evolution may reflect varying effective population sizes through which genetic drift and natural selection have differentially affected genome architecture in fungi over time. ª 2014 The British Mycological Society. Published by Elsevier Ltd. All rights reserved. 1. Introduction Since the first fungal (and eukaryotic) genome of Saccharo- myces cerevisiae was published in 1996 (Goffeau et al., 1996) several hundred fungal genomes have followed. Large-scale community sequencing programs such as the 1000 Fungal Ge- nomes Project (http://1000.fungalgenomes.org) and the Fungal Genome Initiative (http://www.broadinstitute.org/scientific- community/science/projects/fungal-genome-initiative) will provide an even broader representation of genome data from all major fungal groups. Beyond descriptive analyses of genome compositions, novel questions relating to mechanisms of genome evolution can be addressed. Most studies describing genome evolution in fungi have focused on pathogenic species except studies of model species such as species of Saccharomyces and Neurospora (see e.g. Ellison et al., 2011; Scannell et al., 2007; 2006). Host driven rapid evolu- tion in pathogenic species is reflected as high levels of genomic variation. A key question of interest is whether the rapid genome dynamic of pathogenic species is a particularity associated with parasitic life style. Below we will discuss and focus on aspects of genome evolution including the impor- tance of mobile genetic elements, genome defenses, and chro- mosomal plasticity in pathogenic species. The relative ease of * Corresponding author. Tel.: þ49 (0) 6421 178 630. E-mail address: eva.stukenbrock@mpi-marburg.mpg.de (E. H. Stukenbrock). journal homepage: www.elsevier.com/locate/fbr fungal biology reviews 28 (2014) 1 e12 1749-4613/$ e see front matter ª 2014 The British Mycological Society. Published by Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.fbr.2014.02.001