Phytophthora
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA542680 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Lima bean is an important vegetable processing crop to the Mid-Atlantic U.S. and is highly susceptible to the oomycete pathogen Phytophthora phaseoli, which causes downy mildew. P. phaseoli resides in the same clade with the late blight pathogen, Phytophthora infestans. Genetic resistance and fungicides are used to manage P. phaseoli and often fail. Currently there are no molecular data on this pathosystem. To rectify this situation and determine virulence mechanisms in P. phaseoli we performed a whole-transcriptome analysis using Illumina mRNA-Seq. Six libraries were generated and compared, plate-grown and plant-grown. Our data were normalized and were matched to the P. infestans gene models to obtain the abundance of the sequence reads. This resulted in 10,427 P. phaseoli genes with homology to P. infestans and with expression in either one of the libraries. Upon closer examination, 318 P. phaseoli-homologs matched either known or putative virulence genes in P. infestans. We present data from the whole transcriptome as well as specifically chosen genes from this set of 318. Interestingly, in six libraries from P. phaseoli we found a commonly expressed gene set of 66 out of 563 predicted RXLR genes in P. infestans. The majority of the differentially expressed RxLR and elicitin-like were up-regulated in planta, while the reverse was true for crinkler homologs. These results are discussed with respect to possible pathogenicity mechanisms in P. phaseoli and how they compare to P. infestans. Examination of 3 different conditions of Phytophthora phaseoli
2011-08-01 | E-GEOD-23453 | biostudies-arrayexpress
Project description:Phytophthora infestans Raw sequence reads
| PRJNA323952 | ENA
Project description:Phytophthora infestans Raw sequence reads
| PRJNA623165 | ENA
Project description:Phytophthora infestans Raw sequence reads
| PRJNA722136 | ENA
Project description:Lima bean is an important vegetable processing crop to the Mid-Atlantic U.S. and is highly susceptible to the oomycete pathogen Phytophthora phaseoli, which causes downy mildew. P. phaseoli resides in the same clade with the late blight pathogen, Phytophthora infestans. Genetic resistance and fungicides are used to manage P. phaseoli and often fail. Currently there are no molecular data on this pathosystem. To rectify this situation and determine virulence mechanisms in P. phaseoli we performed a whole-transcriptome analysis using Illumina mRNA-Seq. Six libraries were generated and compared, plate-grown and plant-grown. Our data were normalized and were matched to the P. infestans gene models to obtain the abundance of the sequence reads. This resulted in 10,427 P. phaseoli genes with homology to P. infestans and with expression in either one of the libraries. Upon closer examination, 318 P. phaseoli-homologs matched either known or putative virulence genes in P. infestans. We present data from the whole transcriptome as well as specifically chosen genes from this set of 318. Interestingly, in six libraries from P. phaseoli we found a commonly expressed gene set of 66 out of 563 predicted RXLR genes in P. infestans. The majority of the differentially expressed RxLR and elicitin-like were up-regulated in planta, while the reverse was true for crinkler homologs. These results are discussed with respect to possible pathogenicity mechanisms in P. phaseoli and how they compare to P. infestans.
2011-08-01 | GSE23453 | GEO
Project description:Phytophthora spp. encode large sets of effector proteins and distinct populations of small RNAs (sRNAs). Reports suggest that pathogen-derived sRNAs can modulate the expression of plant defense genes. The experiments reported here were designed to shed light on impact of sRNAs in the potato-P. infestans interaction. We used the Argonaute or Ago1 from P. infestans tagged with GFP transformed into the 88069 strain to infect potato cv. Bintje plants. Collected leaf materials were used in co-immunoprecipitation experiments together with P. infestans harboring GFP (control GFP) and P. infestans mycelia grown on media (control mycelia). These three materials were sequenced at a Ion Proton platform. The reads length of 8-38 nt were adaptor-trimmed and mapped to the P. infestans genome and the Solanom tuberosum genome v4.04. Both P. infestans-associated and potato derived sRNAs were identified.
2021-06-30 | GSE119230 | GEO
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
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 sojae mycelium small RNAs were sequenced and aligned to the P. sojae genome for analysis. *Raw data files (fastq) are unavailable for this study.
2013-10-21 | E-GEOD-50032 | biostudies-arrayexpress
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 ramorum mycelium small RNAs were sequenced and aligned to the P. ramorum genome for analysis. *Raw data files (fastq) are unavailable for this study.
2013-10-21 | E-GEOD-50031 | biostudies-arrayexpress
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