Transcriptome Analysis of Epithelioma Papulosum Cyprini Cells Infected by Reovirus Isolated from Allogynogenetic Silver Crucian Carp
The present study aimed to identify differentially expressed genes (DEGs) and major signal transduction pathways that were related to the immune response of epithelioma papulosum cyprinid (EPC) cells to reoviruses isolated from allogynogenetic silver crucian carp. The study also lays a theoretical f...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2018-03-01
|
| Series: | Viruses |
| Subjects: | |
| Online Access: | http://www.mdpi.com/1999-4915/10/3/135 |
| _version_ | 1828496120635981824 |
|---|---|
| author | Cui-Yu Ba Xiao-Yan Du Pei-Jun Zhang Ping Chen Ya-Nan Cai Yue-Hong Li |
| author_facet | Cui-Yu Ba Xiao-Yan Du Pei-Jun Zhang Ping Chen Ya-Nan Cai Yue-Hong Li |
| author_sort | Cui-Yu Ba |
| collection | DOAJ |
| description | The present study aimed to identify differentially expressed genes (DEGs) and major signal transduction pathways that were related to the immune response of epithelioma papulosum cyprinid (EPC) cells to reoviruses isolated from allogynogenetic silver crucian carp. The study also lays a theoretical foundation for the pathogenesis and immunity of the reovirus, which is helpful to the breeding of cyprinids fish. Reovirus infected and uninfected EPC cells were analyzed by using a new-generation high-throughput sequencing technology. DEGs were identified, annotated, and classified, and the signal pathways involved in the response to reovirus infection were identified by using bioinformatics tool. The data were assembled into 92,101 contigs with an average length of 835.24 bp and an N50 value of 1432 nt. Differential expression analysis of all the genes identified 3316 DEGs at a false discovery rate (FDR) of <0.01 and a fold-change of ≥3, of which 1691 were upregulated genes, 1625 were downregulated, and about 305 were immune-related genes. Gene Ontology (GO) enrichment analysis resulted in the annotation of 3941 GO terms, including 2719 biological processes (37,810 unigenes), 376 cell components (7943 unigenes), and 846 molecular functions (11,750 unigenes). KEGG metabolic pathway analysis matched the DEGs from pre-and post-infection EPC cells to 193 pathways, of which 35 were immune-related, including the Toll-like receptor, cytokine-cytokine receptor interaction, and the JAK-STAT signaling pathways. |
| first_indexed | 2024-12-11T12:24:18Z |
| format | Article |
| id | doaj.art-6003b7763ba344c0840f62d7903358a7 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-12-11T12:24:18Z |
| publishDate | 2018-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-6003b7763ba344c0840f62d7903358a72022-12-22T01:07:27ZengMDPI AGViruses1999-49152018-03-0110313510.3390/v10030135v10030135Transcriptome Analysis of Epithelioma Papulosum Cyprini Cells Infected by Reovirus Isolated from Allogynogenetic Silver Crucian CarpCui-Yu Ba0Xiao-Yan Du1Pei-Jun Zhang2Ping Chen3Ya-Nan Cai4Yue-Hong Li5Animal Science and Technology, Jilin Agriculture University, Changchun 130118, ChinaFreshwater Fisheries Research Institute of Jilin Province, Changchun 130000, ChinaHealth Monitoring and Inspection Center of Jilin Province, Changchun 130062, ChinaCollege of Food Science and Engineering, Jilin Agriculture University, Changchun 130118, ChinaAnimal Science and Technology, Jilin Agriculture University, Changchun 130118, ChinaAnimal Science and Technology, Jilin Agriculture University, Changchun 130118, ChinaThe present study aimed to identify differentially expressed genes (DEGs) and major signal transduction pathways that were related to the immune response of epithelioma papulosum cyprinid (EPC) cells to reoviruses isolated from allogynogenetic silver crucian carp. The study also lays a theoretical foundation for the pathogenesis and immunity of the reovirus, which is helpful to the breeding of cyprinids fish. Reovirus infected and uninfected EPC cells were analyzed by using a new-generation high-throughput sequencing technology. DEGs were identified, annotated, and classified, and the signal pathways involved in the response to reovirus infection were identified by using bioinformatics tool. The data were assembled into 92,101 contigs with an average length of 835.24 bp and an N50 value of 1432 nt. Differential expression analysis of all the genes identified 3316 DEGs at a false discovery rate (FDR) of <0.01 and a fold-change of ≥3, of which 1691 were upregulated genes, 1625 were downregulated, and about 305 were immune-related genes. Gene Ontology (GO) enrichment analysis resulted in the annotation of 3941 GO terms, including 2719 biological processes (37,810 unigenes), 376 cell components (7943 unigenes), and 846 molecular functions (11,750 unigenes). KEGG metabolic pathway analysis matched the DEGs from pre-and post-infection EPC cells to 193 pathways, of which 35 were immune-related, including the Toll-like receptor, cytokine-cytokine receptor interaction, and the JAK-STAT signaling pathways.http://www.mdpi.com/1999-4915/10/3/135transcriptomeEPCreovirusallogynogenetic silver crucian carp |
| spellingShingle | Cui-Yu Ba Xiao-Yan Du Pei-Jun Zhang Ping Chen Ya-Nan Cai Yue-Hong Li Transcriptome Analysis of Epithelioma Papulosum Cyprini Cells Infected by Reovirus Isolated from Allogynogenetic Silver Crucian Carp Viruses transcriptome EPC reovirus allogynogenetic silver crucian carp |
| title | Transcriptome Analysis of Epithelioma Papulosum Cyprini Cells Infected by Reovirus Isolated from Allogynogenetic Silver Crucian Carp |
| title_full | Transcriptome Analysis of Epithelioma Papulosum Cyprini Cells Infected by Reovirus Isolated from Allogynogenetic Silver Crucian Carp |
| title_fullStr | Transcriptome Analysis of Epithelioma Papulosum Cyprini Cells Infected by Reovirus Isolated from Allogynogenetic Silver Crucian Carp |
| title_full_unstemmed | Transcriptome Analysis of Epithelioma Papulosum Cyprini Cells Infected by Reovirus Isolated from Allogynogenetic Silver Crucian Carp |
| title_short | Transcriptome Analysis of Epithelioma Papulosum Cyprini Cells Infected by Reovirus Isolated from Allogynogenetic Silver Crucian Carp |
| title_sort | transcriptome analysis of epithelioma papulosum cyprini cells infected by reovirus isolated from allogynogenetic silver crucian carp |
| topic | transcriptome EPC reovirus allogynogenetic silver crucian carp |
| url | http://www.mdpi.com/1999-4915/10/3/135 |
| work_keys_str_mv | AT cuiyuba transcriptomeanalysisofepitheliomapapulosumcyprinicellsinfectedbyreovirusisolatedfromallogynogeneticsilvercruciancarp AT xiaoyandu transcriptomeanalysisofepitheliomapapulosumcyprinicellsinfectedbyreovirusisolatedfromallogynogeneticsilvercruciancarp AT peijunzhang transcriptomeanalysisofepitheliomapapulosumcyprinicellsinfectedbyreovirusisolatedfromallogynogeneticsilvercruciancarp AT pingchen transcriptomeanalysisofepitheliomapapulosumcyprinicellsinfectedbyreovirusisolatedfromallogynogeneticsilvercruciancarp AT yanancai transcriptomeanalysisofepitheliomapapulosumcyprinicellsinfectedbyreovirusisolatedfromallogynogeneticsilvercruciancarp AT yuehongli transcriptomeanalysisofepitheliomapapulosumcyprinicellsinfectedbyreovirusisolatedfromallogynogeneticsilvercruciancarp |