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Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [RNA-Seq]

ABSTRACT: Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [RNA-Seq]

PROVIDER: PRJNA451497 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7058090_1.fastq.gz	Fastqsanger.gz
	SRR7058090_2.fastq.gz	Fastqsanger.gz
	SRR7058091_1.fastq.gz	Fastqsanger.gz
	SRR7058091_2.fastq.gz	Fastqsanger.gz
	SRR7058092_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect

Project description:Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect

| PRJNA451502 | ENA

Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [sRNA-Seq]

Project description:Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [sRNA-Seq]

| PRJNA451503 | ENA

Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [sRNA-Seq]

Project description:research was focus on the virus-derived sRNAs expression pattern in rice host or planthopper vector and host/vector gene expression pattern when infected with RSV

2018-12-26 | GSE113554 | GEO

Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [RNA-Seq]

Project description:research was focus on the virus-derived sRNAs expression pattern in rice host or planthopper vector and host/vector gene expression pattern when infected with RSV

2018-12-26 | GSE113553 | GEO

Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-12-26 | GSE113555 | GEO

Rice stripe virus-derived siRNAs play different regulatory roles in rice and in the insect vector Laodelphax striatellus.

Project description:BACKGROUND:Most plant viruses depend on vector insects for transmission. Upon viral infection, virus-derived small interfering RNAs (vsiRNAs) can target both viral and host transcripts. Rice stripe virus (RSV) is a persistent-propagative virus transmitted by the small brown planthopper (Laodelphax striatellus, Fallen) and can cause a severe disease on rice. RESULTS:To investigate how vsiRNAs regulate gene expressions in the host plant and the insect vector, we analyzed the expression profiles of small RNAs (sRNAs) and mRNAs in RSV-infected rice and RSV-infected planthopper. We obtained 88,247 vsiRNAs in rice that were predominantly derived from the terminal regions of the RSV RNA segments, and 351,655 vsiRNAs in planthopper that displayed relatively even distributions on RSV RNA segments. 38,112 and 80,698 unique vsiRNAs were found only in rice and planthopper, respectively, while 14,006 unique vsiRNAs were found in both of them. Compared to mock-inoculated rice, 273 genes were significantly down-regulated genes (DRGs) in RSV-infected rice, among which 192 (70.3%) were potential targets of vsiRNAs based on sequence complementarity. Gene ontology (GO) analysis revealed that these 192 DRGs were enriched in genes involved in kinase activity, carbohydrate binding and protein binding. Similarly, 265 DRGs were identified in RSV-infected planthoppers, among which 126 (47.5%) were potential targets of vsiRNAs. These planthopper target genes were enriched in genes that are involved in structural constituent of cuticle, serine-type endopeptidase activity, and oxidoreductase activity. CONCLUSIONS:Taken together, our results reveal that infection by the same virus can generate distinct vsiRNAs in different hosts to potentially regulate different biological processes, thus reflecting distinct virus-host interactions.

| S-EPMC6172784 | biostudies-literature

Characterization of rice black-streaked dwarf virus- and rice stripe virus-derived siRNAs in singly and doubly infected insect vector Laodelphax striatellus.

Project description:Replication of RNA viruses in insect cells triggers an antiviral defense that is mediated by RNA interference (RNAi) which generates viral-derived small interfering RNAs (siRNAs). However, it is not known whether an antiviral RNAi response is also induced in insects by reoviruses, whose double-stranded RNA genome replication is thought to occur within core particles. Deep sequencing of small RNAs showed that when the small brown planthopper (Laodelphax striatellus) was infected by Rice black-streaked dwarf virus (RBSDV) (Reoviridae; Fijivirus), more viral-derived siRNAs accumulated than when the vector insect was infected by Rice stripe virus (RSV), a negative single-stranded RNA virus. RBSDV siRNAs were predominantly 21 and 22 nucleotides long and there were almost equal numbers of positive and negative sense. RBSDV siRNAs were frequently generated from hotspots in the 5'- and 3'-terminal regions of viral genome segments but these hotspots were not associated with any predicted RNA secondary structures. Under laboratory condition, L. striatellus can be infected simultaneously with RBSDV and RSV. Double infection enhanced the accumulation of particular genome segments but not viral coat protein of RBSDV and correlated with an increase in the abundance of siRNAs derived from RBSDV. The results of this study suggest that reovirus replication in its insect vector potentially induces an RNAi-mediated antiviral response.

| S-EPMC3679040 | biostudies-literature

Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq

Project description:Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5’-ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and SPRI bead cleanups, a STRIPE-seq library can be constructed in approximately four hours. We demonstrate application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for measuring transcript levels and for differential gene expression analysis. In conjunction with our ready-to-use computational analysis workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.

2020-01-13 | GSE142524 | GEO

RNA sequencing of stripe rust infected wheat leaves and isolated haustoria

Project description:The fungus Puccinia striiformis f.sp. tritici (PST) is the causal pathogen of stripe rust in wheat. New highly virulent PST races appeared at the beginning of this century and spread rapidly causing significant yield losses in wheat production worldwide. Race PST-08/21 was isolated in the UK in 2008 Yr1, Yr2, Yr3, Yr4, Yr6, Yr9, Yr17, Yr27, Yr32, YrRob, YrSol. We applied the RNAseq approach to refine the gene prediction in de novo assembled PST 08/21 contigs and to determine which genes are expressed during wheat infections. Total RNA was extracted from a pool of stripe rust infected wheat leaves and from two biological replicates of haustoria isolates.

2013-08-19 | E-GEOD-42496 | biostudies-arrayexpress

Rice stripe virus hitchhikes the vector insect vitellogenin ligand-receptor pathway for ovary entry.

Project description:It is known that plant arboviruses infect insect vector cells by endocytosis; however, the cellular receptors that mediate endocytosis have not been well defined. In our recently published work and this study, by clarifying the vertical transmission mechanism of Rice stripe virus (RSV) in Laodelphax striatellus, we provide a novel paradigm for how arboviruses enter insect germ-line cells. Instead of direct interaction with a viral receptor, the virus binds to a secreted ligand protein, hitchhiking the ligand-receptor pathway to achieve cell entry. Vitellogenin (Vg) is an indispensable protein for embryo development that is synthesized extra-ovarially and taken up by germ-line cells through Vg receptor (VgR)-mediated endocytosis. After revealing that RSV invades L. striatellus ovary by a specific molecular interaction with the insect Vg in haemolymph, this study addressed VgR's function in mediating the RSV invasion of the germarium nurse cells, further confirming the ligand's receptor-mediated viral cell-invasion mechanism. Understanding the viral ovary-entry pathways in vectors will help to find suitable measures to block the trans-generation transmission of the viruses. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.

| S-EPMC6367155 | biostudies-literature

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