Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of C. necator H16 ΔmmsA123 ΔphaCAB cells grown with and without supplementation of aspartate

ABSTRACT: C. necator H16 can grow on aspartate as the sole carbon source. Using RNA-seq analysis here, we tried to identify genes that are overexpressed when the culture medium is supplemented with aspartate.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Cupriavidus necator H16

SUBMITTER: Alejandro Salinas

PROVIDER: E-MTAB-11897 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

RNA-seq of C. necator H16 ΔmmsA123 ΔphaCAB cells grown with and without supplementation of aspartate

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