Cargando…

Genome-Wide Investigation Using sRNA-Seq, Degradome-Seq and Transcriptome-Seq Reveals Regulatory Networks of microRNAs and Their Target Genes in Soybean during Soybean mosaic virus Infection

MicroRNAs (miRNAs) play key roles in a variety of cellular processes through regulation of their target gene expression. Accumulated experimental evidence has demonstrated that infections by viruses are associated with the altered expression profile of miRNAs and their mRNA targets in the host. Howe...

Descripción completa

Detalles Bibliográficos
Autores principales: Chen, Hui, Arsovski, Andrej Adam, Yu, Kangfu, Wang, Aiming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4786119/
https://www.ncbi.nlm.nih.gov/pubmed/26963095
http://dx.doi.org/10.1371/journal.pone.0150582
_version_ 1782420499938148352
author Chen, Hui
Arsovski, Andrej Adam
Yu, Kangfu
Wang, Aiming
author_facet Chen, Hui
Arsovski, Andrej Adam
Yu, Kangfu
Wang, Aiming
author_sort Chen, Hui
collection PubMed
description MicroRNAs (miRNAs) play key roles in a variety of cellular processes through regulation of their target gene expression. Accumulated experimental evidence has demonstrated that infections by viruses are associated with the altered expression profile of miRNAs and their mRNA targets in the host. However, the regulatory network of miRNA-mRNA interactions during viral infection remains largely unknown. In this study, we performed small RNA (sRNA)-seq, degradome-seq and as well as a genome-wide transcriptome analysis to profile the global gene and miRNA expression in soybean following infections by three different Soybean mosaic virus (SMV) isolates, L (G2 strain), LRB (G2 strain) and G7 (G7 strain). sRNA-seq analyses revealed a total of 253 soybean miRNAs with a two-fold or greater change in abundance compared with the mock-inoculated control. 125 transcripts were identified as the potential cleavage targets of 105 miRNAs and validated by degradome-seq analyses. Genome-wide transcriptome analysis showed that total 2679 genes are differentially expressed in response to SMV infection including 71 genes predicted as involved in defense response. Finally, complex miRNA-mRNA regulatory networks were derived using the RNAseq, small RNAseq and degradome data. This work represents a comprehensive, global approach to examining virus-host interactions. Genes responsive to SMV infection are identified as are their potential miRNA regulators. Additionally, regulatory changes of the miRNAs themselves are described and the regulatory relationships were supported with degradome data. Taken together these data provide new insights into molecular SMV-soybean interactions and offer candidate miRNAs and their targets for further elucidation of the SMV infection process.
format Online
Article
Text
id pubmed-4786119
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-47861192016-03-23 Genome-Wide Investigation Using sRNA-Seq, Degradome-Seq and Transcriptome-Seq Reveals Regulatory Networks of microRNAs and Their Target Genes in Soybean during Soybean mosaic virus Infection Chen, Hui Arsovski, Andrej Adam Yu, Kangfu Wang, Aiming PLoS One Research Article MicroRNAs (miRNAs) play key roles in a variety of cellular processes through regulation of their target gene expression. Accumulated experimental evidence has demonstrated that infections by viruses are associated with the altered expression profile of miRNAs and their mRNA targets in the host. However, the regulatory network of miRNA-mRNA interactions during viral infection remains largely unknown. In this study, we performed small RNA (sRNA)-seq, degradome-seq and as well as a genome-wide transcriptome analysis to profile the global gene and miRNA expression in soybean following infections by three different Soybean mosaic virus (SMV) isolates, L (G2 strain), LRB (G2 strain) and G7 (G7 strain). sRNA-seq analyses revealed a total of 253 soybean miRNAs with a two-fold or greater change in abundance compared with the mock-inoculated control. 125 transcripts were identified as the potential cleavage targets of 105 miRNAs and validated by degradome-seq analyses. Genome-wide transcriptome analysis showed that total 2679 genes are differentially expressed in response to SMV infection including 71 genes predicted as involved in defense response. Finally, complex miRNA-mRNA regulatory networks were derived using the RNAseq, small RNAseq and degradome data. This work represents a comprehensive, global approach to examining virus-host interactions. Genes responsive to SMV infection are identified as are their potential miRNA regulators. Additionally, regulatory changes of the miRNAs themselves are described and the regulatory relationships were supported with degradome data. Taken together these data provide new insights into molecular SMV-soybean interactions and offer candidate miRNAs and their targets for further elucidation of the SMV infection process. Public Library of Science 2016-03-10 /pmc/articles/PMC4786119/ /pubmed/26963095 http://dx.doi.org/10.1371/journal.pone.0150582 Text en © 2016 Chen et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Chen, Hui
Arsovski, Andrej Adam
Yu, Kangfu
Wang, Aiming
Genome-Wide Investigation Using sRNA-Seq, Degradome-Seq and Transcriptome-Seq Reveals Regulatory Networks of microRNAs and Their Target Genes in Soybean during Soybean mosaic virus Infection
title Genome-Wide Investigation Using sRNA-Seq, Degradome-Seq and Transcriptome-Seq Reveals Regulatory Networks of microRNAs and Their Target Genes in Soybean during Soybean mosaic virus Infection
title_full Genome-Wide Investigation Using sRNA-Seq, Degradome-Seq and Transcriptome-Seq Reveals Regulatory Networks of microRNAs and Their Target Genes in Soybean during Soybean mosaic virus Infection
title_fullStr Genome-Wide Investigation Using sRNA-Seq, Degradome-Seq and Transcriptome-Seq Reveals Regulatory Networks of microRNAs and Their Target Genes in Soybean during Soybean mosaic virus Infection
title_full_unstemmed Genome-Wide Investigation Using sRNA-Seq, Degradome-Seq and Transcriptome-Seq Reveals Regulatory Networks of microRNAs and Their Target Genes in Soybean during Soybean mosaic virus Infection
title_short Genome-Wide Investigation Using sRNA-Seq, Degradome-Seq and Transcriptome-Seq Reveals Regulatory Networks of microRNAs and Their Target Genes in Soybean during Soybean mosaic virus Infection
title_sort genome-wide investigation using srna-seq, degradome-seq and transcriptome-seq reveals regulatory networks of micrornas and their target genes in soybean during soybean mosaic virus infection
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4786119/
https://www.ncbi.nlm.nih.gov/pubmed/26963095
http://dx.doi.org/10.1371/journal.pone.0150582
work_keys_str_mv AT chenhui genomewideinvestigationusingsrnaseqdegradomeseqandtranscriptomeseqrevealsregulatorynetworksofmicrornasandtheirtargetgenesinsoybeanduringsoybeanmosaicvirusinfection
AT arsovskiandrejadam genomewideinvestigationusingsrnaseqdegradomeseqandtranscriptomeseqrevealsregulatorynetworksofmicrornasandtheirtargetgenesinsoybeanduringsoybeanmosaicvirusinfection
AT yukangfu genomewideinvestigationusingsrnaseqdegradomeseqandtranscriptomeseqrevealsregulatorynetworksofmicrornasandtheirtargetgenesinsoybeanduringsoybeanmosaicvirusinfection
AT wangaiming genomewideinvestigationusingsrnaseqdegradomeseqandtranscriptomeseqrevealsregulatorynetworksofmicrornasandtheirtargetgenesinsoybeanduringsoybeanmosaicvirusinfection