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Non-coding RNAs in the interaction between rice and Meloidogyne graminicola

ABSTRACT: Non-coding RNAs in the interaction between rice and Meloidogyne graminicola

PROVIDER: PRJNA657181 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12453568.fastq.gz	Fastqsanger.gz
	SRR12453569.fastq.gz	Fastqsanger.gz
	SRR12453570.fastq.gz	Fastqsanger.gz
	SRR12453571.fastq.gz	Fastqsanger.gz
	SRR12453572.fastq.gz	Fastqsanger.gz

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Non-coding RNAs in the interaction between rice and Meloidogyne graminicola

Project description:In this study we generated small RNA libraries from tissues rice plants infected with Meloidogyne graminicola (Mg)3 days postinoculation as well as from uninfected rice plants. The goal was to study the behaviour of small RNA (miRNA and siRNAs) in response to Mg infection. We combine the expression data gathered from this experiment together with degradome sequencing to predict the targets of differentially expressed miRNAs. Expression was validated using RT-qPCR. The small RNA sequencing datasets were also used with literature annotated siRNA loci for differential expression analysis. DNA methylation data and total RNA sequencing data were used to find siRNAs that were candidates to regulate gene expression through DNA methylation of promoter regions.

2021-07-28 | GSE156244 | GEO

Meloidogyne graminicola

Project description:Meloidogyne graminicola overview

| PRJNA170695 | ENA

Non-coding RNAs in the interaction between rice and Meloidogyne graminicola.

Project description:BackgroundRoot knot nematodes (RKN) are plant parasitic nematodes causing major yield losses of widely consumed food crops such as rice (Oryza sativa). Because non-coding RNAs, including small interfering RNAs (siRNA), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are key regulators of various plant processes, elucidating their regulation during this interaction may lead to new strategies to improve crop protection. In this study, we aimed to identify and characterize rice siRNAs, miRNAs and lncRNAs responsive to early infection with RKN Meloidogyne graminicola (Mg), based on sequencing of small RNA, degradome and total RNA libraries from rice gall tissues compared with uninfected root tissues.ResultsWe found 425 lncRNAs, 3739 siRNAs and 16 miRNAs to be differentially expressed between both tissues, of which a subset was independently validated with RT-qPCR. Functional prediction of the lncRNAs indicates that a large part of their potential target genes code for serine/threonine protein kinases and transcription factors. Differentially expressed siRNAs have a predominant size of 24 nts, suggesting a role in DNA methylation. Differentially expressed miRNAs are generally downregulated and target transcription factors, which show reduced degradation according to the degradome data.ConclusionsTo our knowledge, this work is the first to focus on small and long non-coding RNAs in the interaction between rice and Mg, and provides an overview of rice non-coding RNAs with the potential to be used as a resource for the development of new crop protection strategies.

| S-EPMC8293575 | biostudies-literature

Below ground attack by root knot nematode Meloidogyne graminicola predisposes rice to blast disease

Project description:Magnaporthe oryzae (rice blast) and the root-knot nematode Meloidogyne graminicola are causing two of the most important pathogenic diseases jeopardizing rice production. Here, we show that root-knot nematode infestation on rice roots leads to important above-ground changes in plant immunity gene expression, which is correlated with significantly enhanced susceptibility to blast disease.

2018-11-02 | GSE89449 | GEO

Meloidogyne graminicola

Project description:Meloidogyne graminicola Genome sequencing

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Proteomic profiling of rice (Oryza sativa Nipponbare) roots during compatible interaction with the root-knot nematode Meloidogyne graminicola

Project description:This study employed label-free quantitative mass spectrometry to investigate the proteomic changes in roots of the susceptible rice cultivar Nipponbare during a compatible interaction with the root-knot nematode Meloidogyne graminicola. Root samples were collected at four time points: before inoculation (0 dpi), and at 1, 3, and 7 days post-inoculation (dpi). For time points where galls were visible (3 and 7 dpi), root sections containing galls were specifically collected. Three biological replicates were analyzed for each condition. In total, 6,072 proteins were identified. Comparative analysis between infected and uninfected roots identified 513 proteins uniquely regulated in response to nematode infection. Bioinformatic analyses (GO, KEGG) of these proteins highlighted significant enrichment in defense-related pathways, including phenylpropanoid biosynthesis, glutathione metabolism, and alpha-linolenic acid metabolism. Key downregulated defense-related proteins were further validated, and their corresponding gene expression was analyzed in a resistant rice accession.

2025-12-08 | PXD071707 | Pride

Meloidogyne graminicola

Project description:Meloidogyne graminicola Raw sequence reads

| PRJNA355912 | ENA

Meloidogyne graminicola

Project description:Meloidogyne graminicola Transcriptome or Gene expression

| PRJNA170484 | ENA

Meloidogyne graminicola isolate:root

Project description:Meloidogyne graminicola isolate:root Genome sequencing

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Meloidogyne graminicola isolate:MG1

Project description:Meloidogyne graminicola isolate:MG1 Genome sequencing