Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

The genome of the grape powdery mildew pathogen

ABSTRACT: Powdery mildew (Erysiphe necator) is a widespread and economically important disease of grapevines. Large quantities of fungicides are used for its control, accelerating the incidence of fungicide-resistance. A shotgun approach was applied to sequence and assemble the E. necator genome of five isolates, and RNA-seq and comparative genomics were used to predict and annotate protein-coding genes. In addition, a collection of 98 E. necator isolates collected from diverse locations was used for SSR profiling and was screened for copy number variation and presence/absence of a single point mutation (Y136F) in the CYP51 gene, a key target for DMI fungicides. Our results show that the E. necator genome is exceptionally large and repetitive and suggests that transposable elements are responsible for genome expansion. Frequent structural variations were found between isolates and included copy number variant (CNV) in CYP51. We show that CYP51 copy number correlates with expression level and that an increase in copy number is detected in isolates collected from fungicide-treated vineyards. This copy number variation was usually detected with the CYP51 mutant allele (Y136F), suggesting that an increase in copy number becomes advantageous only when the allele is mutated. We also show that CYP51 copy number correlates with fungal growth in the presence of DMI fungicide in vitro. These results suggest that copy number variation can be adaptive in the development of resistance to DMI fungicides in E. necator. Detach Carignan leaves were sprayed with a Erysiphe necator C-strain conida suspension, leaves were collected in 4 time points (12 hours, 24 hours, 3 days, and 6 days) post inoculation. For each time point, two leaves from the same seedling were pooled and frozen in liquid nitrogen, and each time point was performed in triplicate.

ORGANISM(S): Vitis vinifera

SUBMITTER: Dario Cantu

PROVIDER: E-GEOD-58958 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator.

Jones Laura L Riaz Summaira S Morales-Cruz Abraham A Amrine Katherine C H KC McGuire Brianna B Gubler W Douglas WD Walker M Andrew MA Cantu Dario D

BMC genomics 20141209

<h4>Background</h4>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, ...[more]

PMID: 25487071

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Project description:Grape powdery mildew (PM), caused by the biotrophic ascomycete Erysiphe necator, is a devastating fungal disease that affects most Vitis vinifera cultivars. We have previously identified a panel of V. vinifera accessions from Central Asia with partial resistance to PM that possess a Ren1-like local haplotype. In this study we show that in addition to the typical Ren1-associated late post-penetration resistance, these accessions display a range of different levels of disease development suggesting that alternative alleles or additional genes contribute to determining the outcome of the interaction with the pathogen. To identify potential Ren1-dependent transcriptional responses and functions associated with the different levels of resistance, we sequenced and analyzed the transcriptomes of these Central Asian accessions at two time-points of PM infection. Transcriptomes were compared to identify constitutive differences and PM-inducible responses that may underlie their disease resistant phenotype. Responses to E. necator in all resistant accessions were characterized by an early up-regulation of 13 genes, most encoding putative defense functions, and a late down-regulation of 32 genes, enriched in transcriptional regulators and protein kinases. Potential Ren1-dependent responses included a hotspot of co-regulated genes on chromosome 18. We also identified 81 genes whose expression levels and dynamics correlated with the phenotypic differences between the most resistant accessions ?Karadzhandahal?, DVIT3351.27, and O34-16 and the other genotypes. This study provides a first exploration of the functions associated with varying levels of partial resistance to PM in V. vinifera accessions that can be exploited as sources of genetic resistance in grape breeding programs. Eight varieties (7 resistant to powdery mildew, 2 of which are V. vinifera spp. sylvestris, 5 of which are V. vinifera spp. sativa) are infected with powdery mildew (E. necator) at two timepoints (1 dpi and 5 dpi) with three replicates for each timepoint for each condition (uninfected vs. infected), for a total of 96 samples

Dataset Information

The genome of the grape powdery mildew pathogen

Publications

Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator.

Similar Datasets

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