title: Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator.
abstract: BACKGROUND
  Powdery mildew, caused by the obligate biotrophic fungus Erysiphe necator, is an economically important disease of grapevines worldwide. Large quantities of fungicides are used for its control, accelerating the incidence of fungicide-resistance. Copy number variations (CNVs) are unbalanced changes in the structure of the genome that have been associated with complex traits. In addition to providing the first description of the large and highly repetitive genome of E. necator, this study describes the impact of genomic structural variation on fungicide resistance in Erysiphe necator.
  
  
  RESULTS
  A shotgun approach was applied to sequence and assemble the genome of five E. necator isolates, and RNA-seq and comparative genomics were used to predict and annotate protein-coding genes. Our results show that the E. necator genome is exceptionally large and repetitive and suggest that transposable elements are responsible for genome expansion. Frequent structural variations were found between isolates and included copy number variation in EnCYP51, the target of the commonly used sterol demethylase inhibitor (DMI) fungicides. A panel of 89 additional E. necator isolates collected from diverse vineyard sites was screened for copy number variation in the EnCYP51 gene and for presence/absence of a point mutation (Y136F) known to result in higher fungicide tolerance. We show that an increase in EnCYP51 copy number is significantly more likely to be detected in isolates collected from fungicide-treated vineyards. Increased EnCYP51 copy numbers were detected with the Y136F allele, suggesting that an increase in copy number becomes advantageous only after the fungicide-tolerant allele is acquired. We also show that EnCYP51 copy number influences expression in a gene-dose dependent manner and correlates with fungal growth in the presence of a DMI fungicide.
  
  
  CONCLUSIONS
  Taken together our results show that CNV can be adaptive in the development of resistance to fungicides by providing increasing quantitative protection in a gene-dosage dependent manner. The results of this work not only demonstrate the effectiveness of using genomics to dissect complex traits in organisms with very limited molecular information, but also may have broader implications for understanding genomic dynamics in response to strong selective pressure in other pathogens with similar genome architectures.
authors.forename: Laura
authors.initials: L
authors.lastname: Jones
authors.forename: Summaira
authors.initials: S
authors.lastname: Riaz
authors.forename: Abraham
authors.initials: A
authors.lastname: Morales-Cruz
authors.forename: Katherine C H
authors.initials: KC
authors.lastname: Amrine
authors.forename: Brianna
authors.initials: B
authors.lastname: McGuire
authors.forename: W Douglas
authors.initials: WD
authors.lastname: Gubler
authors.forename: M Andrew
authors.initials: MA
authors.lastname: Walker
authors.affiliation: Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616, USA. dacantu@ucdavis.edu.
authors.forename: Dario
authors.initials: D
authors.lastname: Cantu
mesh_terms: D001203:Ascomycota / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D056915:DNA Copy Number Variations; D025141:Drug Resistance, Fungal / Q000235:genetics; D005659:Fungicides, Industrial / Q000494:pharmacology; D015870:Gene Expression; D023061:Gene Order; D056426:Genetic Loci; D016681:Genome, Fungal; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010641:Phenotype; D010935:Plant Diseases / Q000382:microbiology*; D020543:Proteome; D027843:Vitis / Q000382:microbiology*
chemical_list: D005659:Fungicides, Industrial; D020543:Proteome