Integrative Analysis of the microRNAome and Transcriptome Illuminates the Response of Susceptible Rice Plants to Rice Stripe Virus

PloS One
Jian YangHeng-Mu Zhang

Abstract

Rice stripe virus (RSV) is one of the most serious rice viruses in East Asia. To investigate how rice responds to RSV infection, we integrated miRNA expression with parallel mRNA transcription profiling by deep sequencing. A total of 570 miRNAs were identified of which 69 miRNAs (56 up-regulated and 13 down-regulated) were significantly modified by RSV infection. Digital gene expression (DGE) analysis showed that 1274 mRNAs (431 up-regulated and 843 down-regulated genes) were differentially expressed as a result of RSV infection. The differential expression of selected miRNAs and mRNAs was confirmed by qRT-PCR. Gene ontology (GO) and pathway enrichment analysis showed that a complex set of miRNA and mRNA networks were selectively regulated by RSV infection. In particular, 63 differentially expressed miRNAs were found to be significantly and negatively correlated with 160 target mRNAs. Interestingly, 22 up-regulated miRNAs were negatively correlated with 24 down-regulated mRNAs encoding disease resistance-related proteins, indicating that the host defense responses were selectively suppressed by RSV infection. The suppression of both osa-miR1423-5p- and osa-miR1870-5p-mediated resistance pathways was further confirmed by qRT-PCR...Continue Reading

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Citations

Mar 15, 2020·Animals : an Open Access Journal From MDPI·Xiangfei MaGuirong Sun
Oct 21, 2016·Frontiers in Microbiology·Jinping ZhaoYule Liu
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Nov 19, 2020·Genes·Marek MarzecAgnieszka Brąszewska

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Datasets Mentioned

BETA
GSM1921841-
GSM1921846
GSM1921835-
GSM1921840

Methods Mentioned

BETA
ELISA
PCR
chip
electrophoresis

Software Mentioned

custom Perl script
Digital Gene Expression Tag Profiling ( DGE )
psRNA Target
SOAP2
Solexa
Rotor
DEGseq
miRDeep
Gene
FASTX Toolkit

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