Dataset Information

RNA-seq data of control and powdery mildew pathogen (Golovinomyces orontii) treated transcriptomes of Helianthus niveus.

ABSTRACT: Identification of genes expressed during the Golovinomyces orontii infection process in Helianthus niveus assumes importance for incorporation of resistance to powdery mildew in cultivated sunflower (H. annuus L.) from this donor species. RNA-seq analysis of control (uninfected) and infected samples of H. niveus resulted in identification of 231,754 transcripts. A total of 3726 transcripts were differentially expressed of which 205 were specifically expressed in control and 1961 in infected samples. Functional annotation of the differentially expressed transcripts showed significant upregulation of GRAS type transcription factor (TF) and plant specific GATA-type zinc finger TF in infected samples and the K-box, MADS box TF and WRKY family TF in control tissues. Gene ontology classification showed that genes involved in cell and cell part functioning, catalytic and metabolic processes were significantly and highly expressed. This is the first application of RNA-Seq for identification of key genes and pathways involved in powdery mildew infection process in a Helianthus species conferring resistance to the pathogen.

SUBMITTER: Sujatha M

PROVIDER: S-EPMC5988023 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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RNA-seq data of control and powdery mildew pathogen (Golovinomyces orontii) treated transcriptomes of Helianthus niveus.

Sujatha Mulpuri M Ulaganathan Kandasamy K Bhanu Bhupatipalli Divya BD Soni Prashant Kumar PK

Data in brief 20180104

Identification of genes expressed during the Golovinomyces orontii infection process in Helianthus niveus assumes importance for incorporation of resistance to powdery mildew in cultivated sunflower (H. annuus L.) from this donor species. RNA-seq analysis of control (uninfected) and infected samples of H. niveus resulted in identification of 231,754 transcripts. A total of 3726 transcripts were differentially expressed of which 205 were specifically expressed in contr ...[more]

PMID: 29876388

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Project description: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.

Project description:BACKGROUND:Plants encounter pathogenic and non-pathogenic microorganisms on a nearly constant basis. Small RNAs such as siRNAs and miRNAs/milRNAs influence pathogen virulence and host defense responses. We exploited the biotrophic interaction between the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh), and its diploid host plant, barley (Hordeum vulgare) to explore fungal and plant sRNAs expressed during Bgh infection of barley leaf epidermal cells. RESULTS:RNA was isolated from four fast-neutron immune-signaling mutants and their progenitor over a time course representing key stages of Bgh infection, including appressorium formation, penetration of epidermal cells, and development of haustorial feeding structures. The Cereal Introduction (CI) 16151 progenitor carries the resistance allele Mla6, while Bgh isolate 5874 harbors the AVRa6 avirulence effector, resulting in an incompatible interaction. Parallel Analysis of RNA Ends (PARE) was used to verify sRNAs with likely transcript targets in both barley and Bgh. Bgh sRNAs are predicted to regulate effectors, metabolic genes, and translation-related genes. Barley sRNAs are predicted to influence the accumulation of transcripts that encode auxin response factors, NAC transcription factors, homeodomain transcription factors, and several splicing factors. We also identified phasing small interfering RNAs (phasiRNAs) in barley that overlap transcripts that encode receptor-like kinases (RLKs) and nucleotide-binding, leucine-rich domain proteins (NLRs). CONCLUSIONS:These data suggest that Bgh sRNAs regulate gene expression in metabolism, translation-related, and pathogen effectors. PARE-validated targets of predicted Bgh milRNAs include both EKA (effectors homologous to AVRk1 and AVRa10) and CSEP (candidate secreted effector protein) families. We also identified barley phasiRNAs and miRNAs in response to Bgh infection. These include phasiRNA loci that overlap with a significant proportion of receptor-like kinases, suggesting an additional sRNA control mechanism may be active in barley leaves as opposed to predominant R-gene phasiRNA overlap in many eudicots. In addition, we identified conserved miRNAs, novel miRNA candidates, and barley genome mapped sRNAs that have PARE validated transcript targets in barley. The miRNA target transcripts are enriched in transcription factors, signaling-related proteins, and photosynthesis-related proteins. Together these results suggest both barley and Bgh control metabolism and infection-related responses via the specific accumulation and targeting of genes via sRNAs.

Dataset Information

RNA-seq data of control and powdery mildew pathogen (Golovinomyces orontii) treated transcriptomes of Helianthus niveus.

Publications

RNA-seq data of control and powdery mildew pathogen (<i>Golovinomyces orontii)</i> treated transcriptomes of <i>Helianthus niveus</i>.

Similar Datasets

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