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Title: Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi

Author
item Ohm, Robin - Department Of Energy Joint Genome
item Feau, N - University Of British Columbia
item Henrissat, B - Aix-Marseille University
item Schoch, Conrad - National Institutes Of Health (NIH)
item Horwitz, B - University Of Haifa
item Barry, Kerrie - Department Of Energy Joint Genome
item Condon, B - Cornell University - New York
item Copeland, Alex - Department Of Energy Joint Genome
item Dhillon, B - University Of British Columbia
item Glaser, Fabian - University Of Haifa
item Goodwin, Stephen - Steve

Submitted to: PLoS Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/30/2012
Publication Date: 12/5/2012
Citation: Ohm, R., Feau, N., Henrissat, B., Schoch, C.L., Horwitz, B.A., Barry, K.W., Condon, B.J., Copeland, A.C., Dhillon, B., Glaser, F., Goodwin, S.B. et al. 2012. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathogens. 8(12): e1003037. DOI:10.1371/journal.ppat.1003037.

Interpretive Summary: The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Members of the Dothideomycetes infect almost every major crop whether for feed, fiber, food or fuel causing huge economic losses to growers and consumers. Controlling plant diseases caused by Dothideomycetes has been hampered due to limited understanding of their mechanisms of pathogenicity and relatively few tools for analysis. To rectify this deficiency, the Dothideomycetes research community came together to suggest species for genomic sequencing. Here for the first time we compare the sequenced genomes of 18 Dothideomycetes to analyze their evolution, genome organization, and functions as pathogens or saprotrophs. The 18 sequenced genomes have dramatically different sizes while gene counts are more consistent. Unlike other organisms, gene order in the Dothideomycetes was changed during evolution mostly within the boundaries of chromosomes by multiple inversions often surrounded by simple repeats. Several Dothideomycetes contain gene-poor, transposable element-rich, putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in the breakdown of plant cell walls and cellulose. This information will be useful to evolutionary biologists to better understand the genetics and evolution of host specificity and lifestyle type in fungi. Plant pathologists and breeders may be able to use this information to design better strategies for disease management. Fungal geneticists can use the results to identify potential genes involved in pathogenicity and other important biological processes for future analyses of gene function.

Technical Abstract: The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here for the first time we compare the sequenced genomes of 18 Dothideomycetes to analyze their evolution, genome organization, and functions as pathogens or saprotrophs. The 18 sequenced genomes from 17 species have dramatically different sizes due to variation in transposon expansions while gene counts are more consistent yielding a large set of core genes specific to Dothideomycetes. During evolution, gene order in these genomes was changed mostly within the boundaries of chromosomes by multiple inversions often surrounded by simple repeats, instead of the significant interchromosomal rearrangements observed in the genomes of other organisms. Several Dothideomycetes contain gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. In the current set of organisms, biotrophs and hemibiotrophs are separated from necrotrophs and saprobes phylogenetically, which is also reflected in differences between gene sets present in each group. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, cysteine-rich small secreted proteins and secondary metabolism, many of which are enriched in proximity to transposable elements and suggest faster evolution because of both TE mobility and effects of repeat-induced point mutation.