Characterization of microRNAs of Beta macrocarpa and their responses to Beet necrotic yellow vein virus infection
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ABSTRACT:
PROVIDER: PRJNA397432 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5830082.fastq.gz | Fastqsanger.gz | |||
| SRR5830083.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Plant microRNAs (miRNAs) are a class of non-coding RNAs that play important regulatory roles in plant development, defense and abnormal disease symptom formation. Here, 547 known miRNAs, representing 129 miRNA families, and 282 potential novel miRNAs were identified in Beta macrocarpa using small RNA deep sequencing. Through a differential expression analysis, miRNAs responding to Beet necrotic yellow vein virus (BNYVV) infection were identified and confirmed using a microarray analysis. In total, 103 known miRNAs, representing 38 miRNA families, and 45 potential novel miRNAs were differentially regulated, with at least a two-fold change, in BNYVV-infected plants compared with the mock-inoculated control. These differentially expressed miRNAs were involved in hormone biosynthesis and signal transduction pathways, and enhanced axillary bud development and plant defenses. This work is the first to describe miRNAs of the plant genus Beta and may offer a reference for miRNA research in other species in the genus. It provides valuable information on the pathogenicity mechanisms of BNYVV.
2017-08-07 | GSE102330 | GEO
Project description:Plant microRNAs (miRNAs) are a class of non-coding RNAs that play important regulatory roles in plant development, defense and abnormal disease symptom formation. Here, 547 known miRNAs, representing 129 miRNA families, and 282 potential novel miRNAs were identified in Beta macrocarpa using small RNA deep sequencing. Through a differential expression analysis, miRNAs responding to Beet necrotic yellow vein virus (BNYVV) infection were identified and confirmed using a microarray analysis. In total, 103 known miRNAs, representing 38 miRNA families, and 45 potential novel miRNAs were differentially regulated, with at least a two-fold change, in BNYVV-infected plants compared with the mock-inoculated control. These differentially expressed miRNAs were involved in hormone biosynthesis and signal transduction pathways, and enhanced axillary bud development and plant defenses. This work is the first to describe miRNAs of the plant genus Beta and may offer a reference for miRNA research in other species in the genus. It provides valuable information on the pathogenicity mechanisms of BNYVV.
2017-07-17 | GSE101436 | GEO
Project description:Beet necrotic yellow vein virus (BNYVV) and Beet soil-borne mosaic virus (BSBMV) belong to the genus Benyvirus. Both viruses share a similar genome organization, but disease development induced in their major host plant sugar beet displays striking differences. BNYVV induces excessive lateral root (LR) formation by hijacking auxin-regulated pathways; whereas BSBMV infected roots appear asymptomatic. To elucidate transcriptomic changes associated with the virus-specific disease development of BNYVV and BSBMV, we performed a comparative transcriptome analysis of a virus infected susceptible sugar beet genotype.
2019-11-06 | E-MTAB-8187 | biostudies-arrayexpress
Project description:Title : Characterization of genes differentially expressed in roots of transgenic arabidopsis lines expressing the p25 protein of beet necrotic yellow vein virus.<br> <br> Biological question : <br> Rhizomania ("crazy root") is a severe disease of sugar beet caused by beet necrotic yellow vein virus (BNYVV), which is transmitted by the soil-inhabiting fungus Polymyxa betae. Symptoms of virus infection are characterized by a constricted tap root and a massive proliferation of fine rootlets that often undergo necrosis. BNYVV RNA-3 encodes a 25 kDa (p25) which is an important determinant of leaf symptom phenotype. It also governs BNYVV invasion of the plant root system and induction of rootlet proliferation in sugar beet.<br> In order to obtain a better understanding of molecular aspects of disease development in roots and to characterize specific host genes involved in response to viral infection, transgenic Arabidopsis overexpressors of p25 viral protein was obtained and better characterized. It was shown that transgenic plants that efficiently expressed p25 protein produced more lateral roots. <br> Comparative analysis (microarray) was performed between wild type Arabidopsis roots and transgenic Arabidopsis roots expressing p25 protein, in order to identify Arabidopsis genes differentially expressed in response to p25 viral protein.<br> <br> Experiment description: <br> Seeds were surface sterilized, chilled at 4C for 4 days, and then germinated and grown on square Petri plates containing sterilized Murashige and Skoog (MS) medium with 1% sucrose. Such stock plates were arranged vertically in plastic racks and placed into growth chamber. After 5 days, plants were transferred carefully onto fresh MS medium big round plates. On each plate, 60 Wild Type (WT) plantlets were transferred on the half right of the plate, and 60 transgenic plantlets (B, E or T lines) were transferred on the half left of the plate. Plates were arranged horizontally and placed into growth chamber. <br> <br>Experiment 1 : 5 plates containing WT0A control plants and B0A transgenic plants. <br> <br>Experiment 2 : 5 plates containing WT1 control plants and B transgenic plants. <br>5 plates containing WT2 control plants and E transgenic plants. <br>5 plates containing WT3 control plants and T transgenic plants. <br> <br>Plants were harvested after 7 days (experiment 1) or 12 days (experiment 2), and WT roots or transgenic roots were pooled and conserved at -80C.
2007-12-08 | E-MEXP-404 | biostudies-arrayexpress
Project description:Plant microRNAs (miRNAs) are a class of non-coding RNAs that play important roles in plant development, defense, and symptom development. Here, 547 known miRNAs representing 129 miRNA families, and 282 potential novel miRNAs were identified in Beta macrocarpa using small RNA deep sequencing. A phylogenetic analysis was performed, and 8 Beta lineage-specific miRNAs were identified. Through a differential expression analysis, miRNAs associated with Beet necrotic yellow vein virus (BNYVV) infection were identified and confirmed using a microarray analysis and stem-loop RT-qPCR. In total, 103 known miRNAs representing 38 miRNA families, and 45 potential novel miRNAs were differentially regulated, with at least a two-fold change, in BNYVV-infected plants compared with that of the mock-inoculated control. Targets of these differentially expressed miRNAs were also predicted by degradome sequencing. These differentially expressed miRNAs were involved in hormone biosynthesis and signal transduction pathways, and enhanced axillary bud development and plant defenses. This work is the first to describe miRNAs of the plant genus Beta and may offer a reference for miRNA research in other species in the genus. It provides valuable information on the pathogenicity mechanisms of BNYVV.
| S-EPMC5643120 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2017-08-07 | GSE102331 | GEO
Project description:Herein, proteomic profiling was conducted on susceptible sugarbeet infected with BNYVV to clarify the types of proteins prevalent during compatible virus-host plant interactions. Total protein was extracted from sugarbeet leaf tissue infected with BNYVV (beet necrotic yellow vein virus), quantified, and analyzed by mass spectrometry. A proprietary sugarbeet variety, KWS-rzNI, susceptible to all forms of BNYVV, was provided by KWS (Einbeck, Germany). To enable detection of a broad range of proteins associated with compatible interactions, two sources of BNYVV were used; standard BNYVV pathotype A, originally collected from Spence Field at the USDA-ARS in Salinas, CA, and resistance-breaking BNYVV-IV originating from the field, Rockwood 158, Imperial County, CA. Pooled leaf tissue from each cup was ground in liquid nitrogen and lyophilized. Total protein was extracted from 100 mg (dry weight) of lyophilized leaf tissue of each sample using the Plant Total Protein Extraction Kit (Sigma, St. Louis, MO) according to manufacturer’s recommendations. Protease inhibitors were added to liquid protein extracts (Pierce, Rockford, IL), and samples were stored at -80oC prior to analysis. Protein concentrations were determined via Bradford Assay [10] (Thermo Scientific, Rockford, IL) and 30 g of each sample underwent in-solution proteolytic digestion as previously described [11]. Briefly, samples were solubilized in 8 M urea, 0.2% Protease Max (Promega, Madision, WI), then reduced with dithiothreitol, alkylated with iodoacetamide, and digested with 1% Protease Max and trypsin at 37oC for 3 hours. Samples were dried in a Speed Vac® vacuum centrifuge, desalted using Pierce PepClean C18 spin columns (Pierce, Rockford, IL), dried and resuspended in 30 ull 3% ACN, 0.1% formic acid. All solvents, water, and acid were LC-MS/MS grade from Sigma (St. Louis, MO). 1 l of each sample (three replicates from each soil type) was analyzed in duplicate injections via LC-MS/MS . Peptides were purified and concentrated using an on-line enrichment column (Thermo Scientific 5m, 100 m ID x 2 cm C18 columns). Subsequent chromatographic separation was performed on a reverse phase nanospray column (Thermo Scientific EASYnano-LC, 3m, 75 m ID x 100 mm C18 column) using a 90 minute linear gradient from 10%-30% buffer B (100% ACN, 0.1% formic acid) at a flow rate of 400 nanoliters/min. Peptides were eluted directly into the mass spectrometer (Thermo Scientific Orbitrap Velos Pro) and spectra collected over a m/z range of 400-2000 Da using a dynamic exclusion limit of 2 MS/MS spectra of a given peptide mass for 30 s (exclusion duration of 90 s). Compound lists of the resulting spectra were generated using Xcalibur 2.2 software (Thermo Scientific) with a S/N threshold of 1.5 and 1 scan/group. MS/MS spectra were searched against a Uniprot Amaranthacae database (3,645 entries, version 03/06/13) concatenated to a reverse database and the Uniprot Mus musculus database (50,665 entries, version 03/06/13) using the Mascot database search engine (Matrix Science, version 2.3.02) and SEQUEST (version v.27, rev. 11, Sorcerer, Sage-N Research). Due to the limited size of the Amaranthaceae database, the Mus musculus sequences were added to ensure adequate database size for statistical scoring and calculation of false discovery rates. The following search parameters were used in Mascot: monoisotopic mass, parent mass tolerance of 20 ppm, fragment ion mass tolerance of 0.8 Da , complete tryptic digestion allowing two missed cleavages, variable modification of methionine oxidation, and a fixed modification of cysteine carbamidomethylation. SEQUEST search parameters were the same except for a fragment ion mass tolerance of 1.0 Da and a parent ion tolerance of 0.0120 Da. Peptide identifications from both of the search engines were combined using probabilistic protein identification algorithms in Scaffold 4 [13, 14] (Version 4.0.3, Proteome Software, Portland, OR) with protein clustering enabled. All data files were then combined using the “mudpit” option in Scaffold 4 generating a composite listing for all proteins identified. Thresholds were set to 99% protein probability, 95% peptide probability, and a 2 unique peptide minimum was required. The peptide FDR was 0% after manual validation of all proteins identified by 2 unique peptides [15]. Criteria for manual validation included the following: 1) a minimum of at least 5 theoretical y or b ions in consecutive order that are peaks greater than 5% of the maximum intensity; 2) an absence of prominent unassigned peaks greater than 5% of the maximum intensity; and 3) indicative residue specific fragmentation, such as intense ions N-terminal to proline and immediately C-terminal to aspartate and glutamate.
2014-05-20 | PXD000237 | Pride
Project description:Characterization of microRNAs of Beta macrocarpa and their responses to Beet necrotic yellow vein virus infection [miRNA-seq]
| PRJNA394607 | ENA
Project description:Characterization of microRNAs of Beta macrocarpa and their responses to Beet necrotic yellow vein virus infection [miRNA array]
| PRJNA397433 | ENA
Project description:Comparative transcriptome analysis provides molecular insights into the interaction of Beet necrotic yellow vein virus and Beet soil-borne mosaic virus with their host sugar beet
| PRJEB33674 | ENA