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

ABSTRACT: 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.

ORGANISM(S): Phytophthora ramorum

SUBMITTER: James Carrington

PROVIDER: E-GEOD-50031 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

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

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

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-10-21 | E-GEOD-50033 | biostudies-arrayexpress

Gene expression in Phytophthora sojae mycelia, germinating zoospores, and during infection of soybean hypocotyls

Project description:Total RNA extracted from Phytophthora sojae (strain P6497) and infected soybean hypocotyls (cultivar Harosoy) provided template for synthesis of cDNA probes used in the microarray hybridizations. Infected plant hypocotyls were sampled 6 h, 12 h, 24 h, and 48 h after inoculation. Mycelia were grown on synthetic media (H&S) or vegetable juice media (V8). Zoospores were sampled at 0 h, 2 h and 6 h after inducing encystment and germination by agitation. We used microarrays to characterize gene expression patterns in the root rot pathogen Phytophthora sojae and its host Glycine max. Keywords: infection time course, zoospore germination time course, media formulation response 28 samples from 9 treatments; 2 to 5 biological replicates per treatment.

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

2013-10-21 | GSE50032 | GEO

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

2013-10-21 | GSE50031 | GEO

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

2013-10-21 | GSE50030 | GEO

JHI Sl Pc JJ timecourse

Project description:Phytophthora species are a destructive group of filamentous plant pathogens, which have a global distribution and devastating effect on a wide range of plants important to agriculture and natural ecosystems. Throughout the infection cycle, Phytophthora secrete an effector repertoire into its host to inhibit or counter defence associated compounds, lytic enzymes and intracellular processes required for immunity. Despite the advent of genome sequences of both host and microbe however, little is known about the signal interplay between host and pathogen during infection. Here we explore and report on the association between the hemi-biotrophic broad host range pathogen Phytophthora capsici and tomato. Infection assays reveal a distinct hemi-biotrophic infection cycle, featuring haustoria formation early in infection, followed by necrotrophy in the lateinfection stages. We assessed gene expression changes during infection in both P. capsici and tomato and unveil distinct changes in both host and pathogen transcriptomes, associated with biotrophy and the subsequent switch to necrotrophy. These results suggest dynamic but highly regulated transcriptional programmes that underpin P. capsici hemi-biotrophy. Our results provide new detail on coordinate transcriptional reprogramming during infection and sheds light on the basic processes that accompany hemibiotrophy. Please note the timepoint is hours post inoculation (hpi) of P capsici zoospores on detached tomato leaves. Where it is na (not applicable), these are in vitro cultures of P capsici only.

2013-03-24 | E-MTAB-1295 | biostudies-arrayexpress

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

Digital gene expression profiling of the Phytophthora sojae transcriptome

Project description:This experiment contains Phytophthora sojae samples and RNA-seq data from experiment E-GEOD-29561 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29651/) to understand gene expression during the P. sojae life cycle. The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at 5 different developmental stages: mycelia (MY), zoosporangia (SP), zoospores (ZO), cysts (CY) and germinating cysts (GC); based on a 3'-tag digital gene expression (DGE) protocol. More than 90 million clean sequence tags were generated and compared to the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A web-based server named the Phytophthora Transcriptional Database (PTD) has been established.

2011-09-01 | E-MTAB-4039 | biostudies-arrayexpress

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