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Characterisation of the role of ABP19 during Phytophthora rubi infection and resistance to Raspberry root rot

ABSTRACT: Raspberry root transcriptomic response to Phytophthora root rot

PROVIDER: PRJEB73351 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12723512_1.fastq.gz	Fastqsanger.gz
	ERR12723512_2.fastq.gz	Fastqsanger.gz
	ERR12723513_1.fastq.gz	Fastqsanger.gz
	ERR12723513_2.fastq.gz	Fastqsanger.gz
	ERR12723514_1.fastq.gz	Fastqsanger.gz

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Studying the effect of TIBA on raspberry root-Phytophthora rubi interactions

Project description:Raspberry root transcriptomic response to Phytophthora root rot infections and TIBA treatment

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Functional genomics identifies a small secreted protein that plays a role during the biotrophic to necrotrophic shift in the root rot pathogen Phytophthora medicaginis

Project description:Introduction: Hemibiotrophic Phytophthora are a group of agriculturally and ecologically important pathogenic oomycetes causing severe decline in plant growth and fitness. The lifestyle of these pathogens consists of an initial biotrophic phase followed by a switch to a necrotrophic phase in the latter stages of infection. Between these two phases is the biotrophic to necrotrophic switch (BNS) phase, the timing and controls of which are not well understood particularly in Phytophthora spp. where host resistance has a purely quantitative genetic basis. Methods: To investigate this we sequenced and annotated the genome of Phytophthora medicaginis, causal agent of root rot and substantial yield losses to Fabaceae hosts. We analysed the transcriptome of P. medicaginis across three phases of colonisation of a susceptible chickpea host (Cicer arietinum) and performed co-regulatory analysis to identify putative small secreted protein (SSP) effectors that influence timing of the BNS in a quantitative pathosystem. Results: The genome of P. medicaginis is ~78 Mb, comparable to P. fragariae and P. rubi which also cause root rot. Despite this, it encodes the second smallest number of RxLR (arginine-any amino acid-leucine-arginine) containing proteins of currently sequenced Phytophthora species. Only quantitative resistance is known in chickpea to P. medicaginis, however, we found that many RxLR, Crinkler (CRN), and Nep1-like protein (NLP) proteins and carbohydrate active enzymes (CAZymes) were regulated during infection. Characterisation of one of these, Phytmed_10271, which encodes an RxLR effector demonstrates that it plays a role in the timing of the BNS phase and root cell death. Discussion: These findings provide an important framework and resource for understanding the role of pathogenicity factors in purely quantitative Phytophthora pathosystems and their implications to the timing of the BNS phase.

2024-08-05 | GSE183604 | GEO

Phytophthora fragariae and rubi

Project description:Isolates of two closely related phytophthora species causing either red core disease on Strawberry (P.fragariae) or Raspberry root rot (P.rubi). Genome sequencing and assembly

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Genetic Variation of Phytophthora rubi Isolates from Red Raspberry

Project description:Genome Resources and Whole Genome Resequencing of Phytophthora rubi Isolates from Red Raspberry

2023-06-05 | PRJEB62133 | EVA

Systemic suppression of the rice shoot metabolism upon root rot nematode infection

Project description:Rice (Oryza sativa L.) is one of the most important staple foods in the world, feeding more than 50% of the human population. One of its most damaging pathogens, with major impact on rice yield, is the migratory root rot nematode Hirschmanniella oryzae. In comparison with the existing knowledge on the infection process of dicots by sedentary nematodes, far less is known about the interaction between monocot plants and nematodes or plant interactions with migratory nematode species. Therefore, to gain deeper insight into the systemic transcriptional changes in rice after migratory root rot nematode infection we have performed mRNA-Seq on the shoots of root rot nematode infected rice plants. The observations were independently validated using qRT-PCR and biochemical analyses. This research reveals significant modifications in the metabolism of the plant, with a general suppression of chlorophyll biosynthesis, and primary metabolic processes involved in plant growth . Differential expression analysis between controls rice shoots and shoots from root rot nematode (H. oryzae) infected rice at two time points.

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Phytophthora rubi

Project description:Phytophthora rubi and Phytophthora fragariae Genotyping-by-sequencing

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Phytophthora rubi

Project description:Phytophthora rubi overview

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Transcriptome profile of Carrizo citrange roots in response to Phytophthora parasitica infection

Project description:Phytophthora parasitica is one of the most widespread Phytophthora species, which is known to cause root rot, foot rot/gummosis and brown rot of fruits in citrus. In this study, we have analyzed the transcriptome of a commonly used citrus rootstock Carrizo citrange in response to P. parasitica infection using the RNA-seq technology. In total, we have identified 6692 differentially expressed transcripts (DETs) among P. parasitica-inoculated and mock-treated roots. Of these, 3960 genes were differentially expressed at 24 hours post inoculation and 5521 genes were differentially expressed at 48 hours post inoculation. Gene ontology analysis of DETs suggested substantial transcriptional reprogramming of diverse cellular processes particularly the biotic stress response pathways in Carrizo citrange roots. Many R genes, transcription factors, and several other genes putatively involved in plant immunity were differentially modulated in citrus roots in response to P. parasitica infection. Analysis reported here lays out a strong foundation for future studies aimed at improving resistance of citrus rootstocks to P. parasitica.

2019-04-13 | GSE129758 | GEO

protemomics of wolfberry under root rot stress

Project description:Root rot is one of the most severe diseases affecting agricultural productivity worldwide, particularly wolfberry. However, the mechanisms underlying wolfberry resistance to root rot pathogens remain unclear. In this study, we selected Chinese wolfberry (Lycium chinense Mill., LC) and Ningxia wolfberry ‘Ningqi No.5’ (Lycium barbarum L., N5) as research materials, which have been reported to show different tolerances to root rot.

2023-06-26 | PXD043279 |

Systemic suppression of the rice shoot metabolism upon root rot nematode infection

2015-05-18 | GSE57707 | GEO