Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

53 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Three potato cultivars infected by Phytophthora infestans

ABSTRACT: RNA-sequencing data of three potato cultivars (Deisree, Sarpo Mira and SW92-1015) with different susceptibility to Phytopthora infestans causing late blight 24 hours post P. infestans infection

INSTRUMENT(S): Illumina Genome Analyzer II

ORGANISM(S): Solanum tuberosum

SUBMITTER: Erik Alexandersson

PROVIDER: E-MTAB-1712 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions.

Ali Ashfaq A Alexandersson Erik E Sandin Marianne M Resjö Svante S Lenman Marit M Hedley Pete P Levander Fredrik F Andreasson Erik E

BMC genomics 20140619

<h4>Background</h4>In order to get global molecular understanding of one of the most important crop diseases worldwide, we investigated compatible and incompatible interactions between Phytophthora infestans and potato (Solanum tuberosum). We used the two most field-resistant potato clones under Swedish growing conditions, which have the greatest known local diversity of P. infestans populations, and a reference compatible cultivar.<h4>Results</h4>Quantitative label-free proteomics of 51 apoplas ...[more]

PMID: 24947944

Similar Datasets

RNA-seq of mRNA in three wild Solanum species (S. physalifolium, S. dulcamara, S. nigrum) during Phytopthora infestans interaction

Project description:Leaves were collected before infection and at 24 and 48 hours after infection by P. infestans (isolate SE-03058). Samples were pooled for each species.

2015-09-21 | E-MTAB-2953 | biostudies-arrayexpress

Phytophthora infestans infection of three potato cultivars

Project description:Time course study of potato leaves from three cultivars (cv. Desiree, Sarpo Mira, SW-1015) 6, 24 and 72 hours after P. infestans infection

2014-06-23 | E-MTAB-1515 | biostudies-arrayexpress

RNA-seq of a P. infestans resistance segregating population with parents Desiree (cv) and breeding line SW93-1015

Project description:A segregating population was produced by crossing the tetraploid parents, the cultivar Desire and the breeding line SW93-1015. In all, 34 progeny lines were further characterized by phenotyping for multiple traits both in the field and controlled climate settings. For example the late blight resistance screening was done for the lines. Leaf transcriptomes of each line and the two parents were sequenced by Illumina HiSeq 2000 to produce RNA-seq data.

2019-04-02 | E-MTAB-5996 | biostudies-arrayexpress

Expression analysis of Phytophthora infestans isolates 06_3928A and NL07434 during potato infection 2-4 days post-inoculation

Project description:The expression of genes in P. infestans isolates 06_3928A and NL07434 was monitored from 2 to 4 days time course of a potato infection. Genes encoding known and putative effector proteins were found induced at two and/or three days post-inoculation. We used a custom chip GPL8093 from Roche Nimblegen’s proprietary Maskless Array Synthesis (MAS) technology uses digital light processing and rapid, high-yield photochemistry to synthesize long oligo, high-density DNA microarrays with extreme flexibility. Each GPL8093 chip measures the expression level of 18155 genes from Phytophthora infestans with 60-mer probe pairs (PM/MM) per gene. Total RNA samples recovered from mycelia in two medias (rye sucrose agar and V8 agar) and infected potato leaves from a time couse infection (2, 3 and 4 days post incoulation). Experiments included two biological repllicates from each sample. We carried out total RNA extractions (mycelia and potato infected material) for two P. infestans isolates 06_3928A and NL07434. cDNA synthesis was performed Nimblegen.

2012-09-01 | E-GEOD-33240 | biostudies-arrayexpress

phytophthora infestans LC/MS/MS

Project description:The oomycete potato blight pathogen Phytophthora infestans secretes a diverse set of proteins to manipulate host plant immunity. However, there is limited knowledge about the role(s) of majority of these secreted proteins. Here we subjected extracellular proteins from in vitro cultured hyphae to LC/MS/MS to investigate the cargo of protein secretion pathways in P. infestans, in particular the conventional secretory pathway. Like the apoplastic effector EPIC1 (a cysteine protease inhibitor), we show that secretion of cell wall degrading enzymes and pathogen associated molecular pattern (PAMP)-like proteins is inhibited by brefeldin A (BFA) in vitro and in planta, demonstrating that these proteins are secreted by the conventional, Golgi-mediated pathway. For comparison, an RXLR (Arg-any amino acid-Leu-Arg) effector, Pi22926, was shown to be unconventionally secreted at haustoria, pathogen structures that penetrate host plant cells, and delivered into infected cells to suppress host defences, consistent with previous findings. We further characterised a pectinesterase (PE), a cell wall degrading enzyme, and INF4, a PAMP-like protein. Both were highly expressed early in infection, enhanced P. infestans colonization, and secreted at haustoria. Notably, in P. infestans transformed lines, PE-mRFP accumulated around the base of haustoria while INF4-mRFP was found to envelop the whole haustorium. We propose that the haustorium is a major site for both non-conventional and conventional secretion, and cell wall degrading enzymes and PAMP proteins are secreted at these sites to facilitate pathogenicity in P. infestans.

2018-09-03 | PXD009802 | Pride

Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection [host plant infection]

Project description:Background: The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. Results: To identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19-40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line. Conclusions: Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs with elevated levels during infection of potato by P. infestans. Small RNA sequence data from Phytophthora infestans-infected potato leaf tissue and P. infestans mycelium tissue. Three infection stage time-points. Two P. infestans lines: 88089 (wild-type) and PiDcl1 (transformant PiDcl1 knock-down). No replicates. Total number of samples: 8.

2014-12-12 | E-GEOD-63292 | biostudies-arrayexpress

Metabolic and transcriptional response of Arabidopsis thaliana wildtype and mutants to Phytophtora infestans

Project description:The oomycete P. infestans is the causal agent of late blight, the most devastating potato disease. In contrast to potato, A. thaliana is able to successfully prevent colonization of the pathogen due to a multi-layered nonhost resistance. Several mutants have been isolated which are impaired in penetration resistance. A mutation in the gene PEN2, which encodes for an enzyme involved in indole glucosinolate metabolism (Bednarek et al. (2009)), results in the loss of penetration resistance against P. infestans (Lipka et al. (2005)). Despite its ability to penetrate epidermal cells of pen2 mutant plants, P. infestans is still not able to colonize these plants. Additional mutants were isolated by Kopischke et al. (2013) which show enhanced defense responses upon infection with P. infestans: pen2erp1 and pen2erp2, and backcrossed mutants erp140 and erp2D. We used six different plant lines, the wildtype-like gl1, and the five different mutants (pen2, pen2erp1, pen2erp2, erp2D, erp140). The plants were either infected with P. infestans spores or treated with water as control, and harvested 6h and 12h after treatment. The experiment was repeated three times with different P. infestans cultures, resulting in biological triplicates, for an overall of 6 x 2 x 2 x 3 = 72 samples. A metabolomics data set from the same set of samples has been submitted to MetaboLights database at EMBL-EBI (http://www.ebi.ac.uk/metabolights/index) under accession number MTBLS18 .

2019-01-25 | E-MTAB-3287 | biostudies-arrayexpress

Compatible and incompatible infection of potato by nematode Globodera rostochiensis

Project description:The cultivar Desirée and the breeding line SW93-1015 were challenged with potato cyst nematodes and transcriptomes analysed after 8h and 48 h.

2018-04-02 | E-MTAB-5215 | biostudies-arrayexpress

Microarray analysis of gene expression induced by Phytophthora infestans in tomato leaves

Project description:Phytophthora infestans is most notorious oomycete causing a devastating disease on tomato called late blight. The molecular mechanisms involved in host-parasite interaction is still unexplored well. Investigation of changes in gene expression profile after pathogen infection to find out the mechanisms involved in infection process Second full expanded leaves from both healthy tomato plants (non-inoculated) and diseased tomato plants inoculated with Phytophthora infestans inoculum were used to extract total RNA for microarry analysis 12 hours post inoculation time.

2011-10-24 | E-GEOD-33177 | biostudies-arrayexpress

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora infestans small RNA

Project description:Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. In contrast, 21-nucleotide small RNAs are associated with inverted repeats, including a novel microRNA family, and may function at the post-transcriptional level. Phytophthora infestans mycelium small RNAs were sequenced and aligned to the P. infestans genome for analysis.

2013-10-21 | E-GEOD-50030 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data