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Characterization of small RNAs expressed in roots and galls from Arabidopsis thaliana induced by the plant parasitic nematodes Meloidogyne incognita

ABSTRACT: Characterization of small RNAs expressed in roots and galls from Arabidopsis thaliana induced by the plant parasitic nematodes Meloidogyne incognita

OTHER RELATED OMICS DATASETS IN: GSE100498

PROVIDER: PRJNA391955 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5758310.fastq.gz	Fastqsanger.gz
	SRR5758320.fastq.gz	Fastqsanger.gz
	SRR5758311.fastq.gz	Fastqsanger.gz
	SRR5758321.fastq.gz	Fastqsanger.gz
	SRR5758312.fastq.gz	Fastqsanger.gz

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Characterization of small RNAs expressed in roots and galls from Arabidopsis thaliana induced by the plant parasitic nematodes Meloidogyne incognita

Project description:By sequencing small RNAs from uninfected Arabidopsis roots and from galls seven and 14 days post infection with Meloidogyne incognita, we sequenced by SOLiD technology the RNA fraction below 50nt. We identified 24 miRNAs differentially expressed in gall as putative regulators of gall development.

2017-10-04 | GSE100498 | GEO

RNA-seq of roots of ten genotypes of Solanum lycopersicum infected with Meloidogyne incognita over six time-points

Project description:In this experiment we measured the transcriptional response of ten tomato cultivars when infected by the plant-parasitic nematode M. incognita. The ten cultivars showed differential levels of susceptibility to M. incognita infection. Ten-days old plants were exposed to nematodes and harvested 1, 2, 3, 4, 7, or 10 days post infection. Galls or representative uninfected tissues were harvested and used for RNA sequencing. The data was used to investigate the link between susceptibility to M. incognita infection and gene expression in tomato.

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Local and systemic transcriptome and spliceome changes induced by Meloidigyne incognita in tomato roots.

Project description:The aim of study is to investigate DEGs, long non-coding RNAs and alternative splicing events in the development of galls and neighboring region compared to the non-infected whole root induced by root-knot nematode (RKN, Meloidogyne incognita). Total RNA was extracted, ribosomal depleted libraries were prepared, and then high throughput RNA sequencing was performed using the Illumina NovaSeq 6000. High quality, paired-end reads were then aligned to the tomato reference genome (Heinz1706 assembly SL4.0) and uniquely mapped reads were counted using Htseq. Finally, differentially expressed genes (DEGs) between whole roots-galls and whole roots-neighboring region were identified using DESeq package and downstream analyses were performed.

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MELOHOSTRACE: Whole genome polymorphism across Meloidogyne incognita isolates showing different biological traits

Project description:High-coverage whole genome sequencing of 11 Brazilian isolates of the root-knot nematode Meloidogyne incognita, presenting different host plant preferences and different geographical origins. Four M. incognita host races had been proposed in the past, based on host (in)compatibility on four different plant strains. The objective was to assess whether genomic variations (SNP) correlate with host range compatibility, geographical origin and host plant of origin.

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Project description:Meloidogyne incognita Transcriptome or Gene expression

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