title: Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi.
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, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.
authors.affiliation: United States Department of Energy DOE Joint Genome Institute JGI, Walnut Creek, California, United States of America. raohm@lbl.gov
authors.forename: Robin A
authors.initials: RA
authors.lastname: Ohm
authors.forename: Nicolas
authors.initials: N
authors.lastname: Feau
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.forename: Conrad L
authors.initials: CL
authors.lastname: Schoch
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Horwitz
authors.forename: Kerrie W
authors.initials: KW
authors.lastname: Barry
authors.forename: Bradford J
authors.initials: BJ
authors.lastname: Condon
authors.forename: Alex C
authors.initials: AC
authors.lastname: Copeland
authors.forename: Braham
authors.initials: B
authors.lastname: Dhillon
authors.forename: Fabian
authors.initials: F
authors.lastname: Glaser
authors.forename: Cedar N
authors.initials: CN
authors.lastname: Hesse
authors.forename: Idit
authors.initials: I
authors.lastname: Kosti
authors.forename: Kurt
authors.initials: K
authors.lastname: LaButti
authors.forename: Erika A
authors.initials: EA
authors.lastname: Lindquist
authors.forename: Susan
authors.initials: S
authors.lastname: Lucas
authors.forename: Asaf A
authors.initials: AA
authors.lastname: Salamov
authors.forename: Rosie E
authors.initials: RE
authors.lastname: Bradshaw
authors.forename: Lynda
authors.initials: L
authors.lastname: Ciuffetti
authors.forename: Richard C
authors.initials: RC
authors.lastname: Hamelin
authors.forename: Gert H J
authors.initials: GH
authors.lastname: Kema
authors.forename: Christopher
authors.initials: C
authors.lastname: Lawrence
authors.forename: James A
authors.initials: JA
authors.lastname: Scott
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Spatafora
authors.forename: B Gillian
authors.initials: BG
authors.lastname: Turgeon
authors.forename: Pierre J G M
authors.initials: PJ
authors.lastname: de Wit
authors.forename: Shaobin
authors.initials: S
authors.lastname: Zhong
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Goodwin
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
mesh_terms: D001203:Ascomycota / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity*; D015825:Chromosomes, Fungal / Q000235:genetics* / Q000378:metabolism; D004251:DNA Transposable Elements / Q000502:physiology; D019143:Evolution, Molecular; D005800:Genes, Fungal / Q000502:physiology*; D018384:Oxidative Stress / Q000235:genetics; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D017354:Point Mutation
chemical_list: D004251:DNA Transposable Elements