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Deep Illumina sequencing reveals conserved and novel microRNAs in grass carp in response to grass carp reovirus infection
BACKGROUND: The grass carp hemorrhagic disease caused by the grass carp reovirus (GCRV) is a major disease that hampers the development of grass carp aquaculture. The mechanism underlying GCRV pathogenesis and hemorrhagic symptoms is still unknown. MicroRNAs (miRNAs) are key regulators involved in v...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319172/ https://www.ncbi.nlm.nih.gov/pubmed/28219339 http://dx.doi.org/10.1186/s12864-017-3562-4 |
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author | He, Libo Zhang, Aidi Chu, Pengfei Li, Yongming Huang, Rong Liao, Lanjie Zhu, Zuoyan Wang, Yaping |
author_facet | He, Libo Zhang, Aidi Chu, Pengfei Li, Yongming Huang, Rong Liao, Lanjie Zhu, Zuoyan Wang, Yaping |
author_sort | He, Libo |
collection | PubMed |
description | BACKGROUND: The grass carp hemorrhagic disease caused by the grass carp reovirus (GCRV) is a major disease that hampers the development of grass carp aquaculture. The mechanism underlying GCRV pathogenesis and hemorrhagic symptoms is still unknown. MicroRNAs (miRNAs) are key regulators involved in various biological processes. The aim of this study was to identify conserved and novel miRNAs in grass carp in response to GCRV infection, as well as attempt to reveal the mechanism underlying GCRV pathogenesis and hemorrhagic symptoms. RESULTS: Grass carp were infected with GCRV, and spleen samples were collected at 0 (control), 1, 3, 5, 7, and 9 days post-infection (dpi). These samples were used to construct and sequence small RNA libraries. A total of 1208 miRNAs were identified, of which 278 were known miRNAs and 930 were novel miRNAs. Thirty-six miRNAs were identified to exhibit differential expression when compared with the control, and 536 target genes were predicted for the 36 miRNAs. GO and KEGG enrichment analyses of these target genes showed that many of the significantly enriched terms were associated with immune response, blood coagulation, hemostasis, and complement and coagulation cascades, especially the GO term “blood coagulation” and pathway “complement and coagulation cascades.” Ten representative target genes involved in “complement and coagulation cascades” were selected for qPCR analysis, and the results showed that the expression patterns of these target genes were significantly upregulated at 7 dpi, suggesting that the pathway “complement and coagulation cascades” was strongly activated. CONCLUSION: Conserved and novel miRNAs in response to GCRV infection were identified in grass carp, of which 278 were known miRNAs and 930 were novel miRNAs. Many of the target genes involved in immune response, blood coagulation, hemostasis, and complement and coagulation cascades. Strong activation of the pathway “complement and coagulation cascades” may have led to endothelial-cell and blood-cell damage and hemorrhagic symptoms. The present study provides a new insight into understanding the mechanism underlying GCRV pathogenesis and hemorrhagic symptoms. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3562-4) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5319172 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-53191722017-02-24 Deep Illumina sequencing reveals conserved and novel microRNAs in grass carp in response to grass carp reovirus infection He, Libo Zhang, Aidi Chu, Pengfei Li, Yongming Huang, Rong Liao, Lanjie Zhu, Zuoyan Wang, Yaping BMC Genomics Research Article BACKGROUND: The grass carp hemorrhagic disease caused by the grass carp reovirus (GCRV) is a major disease that hampers the development of grass carp aquaculture. The mechanism underlying GCRV pathogenesis and hemorrhagic symptoms is still unknown. MicroRNAs (miRNAs) are key regulators involved in various biological processes. The aim of this study was to identify conserved and novel miRNAs in grass carp in response to GCRV infection, as well as attempt to reveal the mechanism underlying GCRV pathogenesis and hemorrhagic symptoms. RESULTS: Grass carp were infected with GCRV, and spleen samples were collected at 0 (control), 1, 3, 5, 7, and 9 days post-infection (dpi). These samples were used to construct and sequence small RNA libraries. A total of 1208 miRNAs were identified, of which 278 were known miRNAs and 930 were novel miRNAs. Thirty-six miRNAs were identified to exhibit differential expression when compared with the control, and 536 target genes were predicted for the 36 miRNAs. GO and KEGG enrichment analyses of these target genes showed that many of the significantly enriched terms were associated with immune response, blood coagulation, hemostasis, and complement and coagulation cascades, especially the GO term “blood coagulation” and pathway “complement and coagulation cascades.” Ten representative target genes involved in “complement and coagulation cascades” were selected for qPCR analysis, and the results showed that the expression patterns of these target genes were significantly upregulated at 7 dpi, suggesting that the pathway “complement and coagulation cascades” was strongly activated. CONCLUSION: Conserved and novel miRNAs in response to GCRV infection were identified in grass carp, of which 278 were known miRNAs and 930 were novel miRNAs. Many of the target genes involved in immune response, blood coagulation, hemostasis, and complement and coagulation cascades. Strong activation of the pathway “complement and coagulation cascades” may have led to endothelial-cell and blood-cell damage and hemorrhagic symptoms. The present study provides a new insight into understanding the mechanism underlying GCRV pathogenesis and hemorrhagic symptoms. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3562-4) contains supplementary material, which is available to authorized users. BioMed Central 2017-02-20 /pmc/articles/PMC5319172/ /pubmed/28219339 http://dx.doi.org/10.1186/s12864-017-3562-4 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article He, Libo Zhang, Aidi Chu, Pengfei Li, Yongming Huang, Rong Liao, Lanjie Zhu, Zuoyan Wang, Yaping Deep Illumina sequencing reveals conserved and novel microRNAs in grass carp in response to grass carp reovirus infection |
title | Deep Illumina sequencing reveals conserved and novel microRNAs in grass carp in response to grass carp reovirus infection |
title_full | Deep Illumina sequencing reveals conserved and novel microRNAs in grass carp in response to grass carp reovirus infection |
title_fullStr | Deep Illumina sequencing reveals conserved and novel microRNAs in grass carp in response to grass carp reovirus infection |
title_full_unstemmed | Deep Illumina sequencing reveals conserved and novel microRNAs in grass carp in response to grass carp reovirus infection |
title_short | Deep Illumina sequencing reveals conserved and novel microRNAs in grass carp in response to grass carp reovirus infection |
title_sort | deep illumina sequencing reveals conserved and novel micrornas in grass carp in response to grass carp reovirus infection |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319172/ https://www.ncbi.nlm.nih.gov/pubmed/28219339 http://dx.doi.org/10.1186/s12864-017-3562-4 |
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