Limits...
Transcriptome analysis of epithelioma papulosum cyprini cells after SVCV infection.

Yuan J, Yang Y, Nie H, Li L, Gu W, Lin L, Zou M, Liu X, Wang M, Gu Z - BMC Genomics (2014)

Bottom Line: At 24 h post SVCV infection (1.0 MOI), a total of 623 genes were differentially expressed in EPC cells compared to non-infected cells, including 288 up-regulated genes and 335 down-regulated genes.Our findings demonstrate previously unrecognised changes in gene transcription that are associated with SVCV infection in vitro, and many potential cascades identified in the study clearly warrant further experimental investigation.Our data provide new clues to the mechanism of viral susceptibility in EPC cells.

View Article: PubMed Central - PubMed

Affiliation: Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, People's Republic of China. guzemao@mail.hzau.edu.cn.

ABSTRACT

Background: Spring viraemia of carp virus (SVCV) has been identified as the causative agent of spring viraemia of carp (SVC) and it has caused significant losses in the cultured common carp (Cyprinus carpio) industry. The molecular mechanisms that underlie the pathogenesis of the disease remain poorly understood. In this study, deep RNA sequencing was used to analyse the transcriptome and gene expression profile of EPC cells at progressive times after SVCV infection. This study addressed the complexity of virus-cell interactions and added knowledge that may help to understand SVCV.

Results: A total of 33,849,764 clean data from 36,000,000 sequence reads, with a mean read length 100 bp, were obtained. These raw data were assembled into 88,772 contigs. Of these contigs, 19,642 and 25,966 had significant hits to the NR and Uniprot databases where they matched 17,642 and 13,351 unique protein accessions, respectively. At 24 h post SVCV infection (1.0 MOI), a total of 623 genes were differentially expressed in EPC cells compared to non-infected cells, including 288 up-regulated genes and 335 down-regulated genes. These regulated genes were primarily involved in pathways of apoptosis, oxidative stress and the interferon system, all of which may be involved in viral pathogenesis. In addition, 8 differentially expressed genes (DEGs) were validated by quantitative PCR.

Conclusions: Our findings demonstrate previously unrecognised changes in gene transcription that are associated with SVCV infection in vitro, and many potential cascades identified in the study clearly warrant further experimental investigation. Our data provide new clues to the mechanism of viral susceptibility in EPC cells.

Show MeSH

Related in: MedlinePlus

Gene ontology assignments forP. promelas. The annotated contigs from P. promelas sequencing that matched the three major categories, including biological process, cellular component, and molecular function were shown. The x-axis indicates the GO terms and the y-axis indicates the number of genes mapped to the indicated GO term.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4221675&req=5

Fig2: Gene ontology assignments forP. promelas. The annotated contigs from P. promelas sequencing that matched the three major categories, including biological process, cellular component, and molecular function were shown. The x-axis indicates the GO terms and the y-axis indicates the number of genes mapped to the indicated GO term.

Mentions: BLASTX searches for all contigs from EPC cells were performed against several protein databases, including the GenBank non-redundant (NR) and Uniprot databases with an E- value cut-off of 10−5. Of the 88,772 contigs, 19,642 and 25,966 had significant hits to the NR and Uniprot databases respectively, and they respectively matched 17,642 and 13,351 unique protein accessions.Further gene ontology (GO) analysis was performed with these contigs. A total of 16,994 unique proteins mapped to 114,154 GO terms: 48,270 unigenes mapped to biological processes, 40,247 unigenes mapped to molecular functions, and 48,151 unigenes mapped to cellular components (Figure 2).EuKaryotic Orthologous Groups (KOG) classification of the unigenes is important for functional annotation and evolutionary studies. As shown in Figure 3, a total of 12,896 unigenes were finally mapped onto 25 different KOG categories. The largest KOG group was “Signal transduction mechanisms” (2,604 unigenes), followed by “General function prediction only” (1,531 unigenes) and “Posttranslational modification, protein turnover, chaperones” (937 unigenes).To obtain more information for predicted functions of the unigenes, the genes from the EPC cells were categorised in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 7,349 unigenes was obtained the KO number (Figure 4).Figure 2


Transcriptome analysis of epithelioma papulosum cyprini cells after SVCV infection.

Yuan J, Yang Y, Nie H, Li L, Gu W, Lin L, Zou M, Liu X, Wang M, Gu Z - BMC Genomics (2014)

Gene ontology assignments forP. promelas. The annotated contigs from P. promelas sequencing that matched the three major categories, including biological process, cellular component, and molecular function were shown. The x-axis indicates the GO terms and the y-axis indicates the number of genes mapped to the indicated GO term.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4221675&req=5

Fig2: Gene ontology assignments forP. promelas. The annotated contigs from P. promelas sequencing that matched the three major categories, including biological process, cellular component, and molecular function were shown. The x-axis indicates the GO terms and the y-axis indicates the number of genes mapped to the indicated GO term.
Mentions: BLASTX searches for all contigs from EPC cells were performed against several protein databases, including the GenBank non-redundant (NR) and Uniprot databases with an E- value cut-off of 10−5. Of the 88,772 contigs, 19,642 and 25,966 had significant hits to the NR and Uniprot databases respectively, and they respectively matched 17,642 and 13,351 unique protein accessions.Further gene ontology (GO) analysis was performed with these contigs. A total of 16,994 unique proteins mapped to 114,154 GO terms: 48,270 unigenes mapped to biological processes, 40,247 unigenes mapped to molecular functions, and 48,151 unigenes mapped to cellular components (Figure 2).EuKaryotic Orthologous Groups (KOG) classification of the unigenes is important for functional annotation and evolutionary studies. As shown in Figure 3, a total of 12,896 unigenes were finally mapped onto 25 different KOG categories. The largest KOG group was “Signal transduction mechanisms” (2,604 unigenes), followed by “General function prediction only” (1,531 unigenes) and “Posttranslational modification, protein turnover, chaperones” (937 unigenes).To obtain more information for predicted functions of the unigenes, the genes from the EPC cells were categorised in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 7,349 unigenes was obtained the KO number (Figure 4).Figure 2

Bottom Line: At 24 h post SVCV infection (1.0 MOI), a total of 623 genes were differentially expressed in EPC cells compared to non-infected cells, including 288 up-regulated genes and 335 down-regulated genes.Our findings demonstrate previously unrecognised changes in gene transcription that are associated with SVCV infection in vitro, and many potential cascades identified in the study clearly warrant further experimental investigation.Our data provide new clues to the mechanism of viral susceptibility in EPC cells.

View Article: PubMed Central - PubMed

Affiliation: Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, People's Republic of China. guzemao@mail.hzau.edu.cn.

ABSTRACT

Background: Spring viraemia of carp virus (SVCV) has been identified as the causative agent of spring viraemia of carp (SVC) and it has caused significant losses in the cultured common carp (Cyprinus carpio) industry. The molecular mechanisms that underlie the pathogenesis of the disease remain poorly understood. In this study, deep RNA sequencing was used to analyse the transcriptome and gene expression profile of EPC cells at progressive times after SVCV infection. This study addressed the complexity of virus-cell interactions and added knowledge that may help to understand SVCV.

Results: A total of 33,849,764 clean data from 36,000,000 sequence reads, with a mean read length 100 bp, were obtained. These raw data were assembled into 88,772 contigs. Of these contigs, 19,642 and 25,966 had significant hits to the NR and Uniprot databases where they matched 17,642 and 13,351 unique protein accessions, respectively. At 24 h post SVCV infection (1.0 MOI), a total of 623 genes were differentially expressed in EPC cells compared to non-infected cells, including 288 up-regulated genes and 335 down-regulated genes. These regulated genes were primarily involved in pathways of apoptosis, oxidative stress and the interferon system, all of which may be involved in viral pathogenesis. In addition, 8 differentially expressed genes (DEGs) were validated by quantitative PCR.

Conclusions: Our findings demonstrate previously unrecognised changes in gene transcription that are associated with SVCV infection in vitro, and many potential cascades identified in the study clearly warrant further experimental investigation. Our data provide new clues to the mechanism of viral susceptibility in EPC cells.

Show MeSH
Related in: MedlinePlus