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Title: Small RNA mediated immune responses: insights from analyses of nine soybean R-gene near-isogenic lines and their susceptible parent      
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available
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instance of dataset
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not applicable
refinement:
curated
dateReleased:
08-19-2015
ID:
E-GEOD-56859
description:
Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are negative regulators to target endogenous genes and repetitive sequences in plants. Although miRNAs and trans-acting or phased siRNAs (tasiRNAs or phasiRNAs) were found to target hundreds of disease related genes in Medicago, their role in plant-pathogen interactions in the legumes, particularly the R genes mediated interaction of soybean and the pathogen Phytophthora sojae is poorly understood. A deep sequencing was performed on nine soybean near isogenic lines (NILs) each carrying an Rps (Resistance to Phytophthora sojae) gene and their recurrent parent “Williams”, with sampling performed both pre- and post-inoculation with P. sojae. From these data, 44 known MIRNA loci with new miRNA variants, 78 novel miRNAs corresponding to 108 precursors, and 208 phasiRNA-producing (PHAS) loci were identified. Our data showed that overall the expression levels of miRNAs, phasiRNAs and siRNAs were extensively down-regulated after pathogen-inoculation. Moreover, the down-regulation levels in the nine resistant NILs were significantly higher than that detected in the susceptible Williams, and variations of small RNA expression within the resistant NILs were also observed, suggesting the molecular responses of different Rps lines are distinct. Surprisingly, the expression level changes of 21-nt phasiRNAs were significantly positively correlated with that of the corresponding mRNA level of the PHAS genes, suggesting the cascade effects of miRNA triggers on the downstream PHAS genes and phasiRNAs. Our data provided a comprehensive picture regarding small RNA based regulation of target genes, particularly NB-LRRs, involved in the responses to the pathogen. 20 samples were sequenced, 10 inoculated with P. sojae, the other 10 were mock-inoculated
keywords:
RNA-seq of non coding RNA
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Array Express
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accessURL: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-56859
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JSON
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OmicsDI
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accessType:
download
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false
accessURL: www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-56859.json
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XML
storedIn:
OmicsDI
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not compressed
accessType:
download
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none
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accessURL: http://www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-56859.xml
ID:
SCR:014747
name:
Omics Discovery Index
abbreviation:
OmicsDI
homePage: http://www.omicsdi.org/