title: Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence.
abstract: Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.
authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331-8530, USA.
authors: Viola A
authors: VA
authors: Manning
authors: Iovanna
authors: I
authors: Pandelova
authors: Braham
authors: B
authors: Dhillon
authors: Larry J
authors: LJ
authors: Wilhelm
authors: Stephen B
authors: SB
authors: Goodwin
authors: Aaron M
authors: AM
authors: Berlin
authors: Melania
authors: M
authors: Figueroa
authors: Michael
authors: M
authors: Freitag
authors: James K
authors: JK
authors: Hane
authors: Bernard
authors: B
authors: Henrissat
authors: Wade H
authors: WH
authors: Holman
authors: Chinnappa D
authors: CD
authors: Kodira
authors: Joel
authors: J
authors: Martin
authors: Richard P
authors: RP
authors: Oliver
authors: Barbara
authors: B
authors: Robbertse
authors: Wendy
authors: W
authors: Schackwitz
authors: David C
authors: DC
authors: Schwartz
authors: Joseph W
authors: JW
authors: Spatafora
authors: B Gillian
authors: BG
authors: Turgeon
authors: Chandri
authors: C
authors: Yandava
authors: Sarah
authors: S
authors: Young
authors: Shiguo
authors: S
authors: Zhou
authors: Qiandong
authors: Q
authors: Zeng
authors: Igor V
authors: IV
authors: Grigoriev
authors: Li-Jun
authors: LJ
authors: Ma
authors: Lynda M
authors: LM
authors: Ciuffetti
mesh_terms: D001203:Ascomycota / Q000235:genetics* / Q000472:pathogenicity*; D001483:Base Sequence; D002874:Chromosome Mapping; D020732:Cytogenetic Analysis; D017931:DNA Primers / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics; D014644:Genetic Variation; D016681:Genome, Fungal / Q000235:genetics*; D023281:Genomics; D016013:Likelihood Functions; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009183:Mycotoxins / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D014908:Triticum / Q000382:microbiology*
chemical_list: D017931:DNA Primers; D004251:DNA Transposable Elements; D009183:Mycotoxins
keywords: ToxA; ToxB; anastomosis; copy number variation; histone H3 transduplication; wheat (Triticum aestivum)