Transcriptome Analysis on Chinese Shrimp Fenneropenaeus chinensis during WSSV Acute Infection

Previous studies have discovered a lot of immune-related genes responding to white spot syndrome virus (WSSV) infection in crustacean. However, little information is available in relation to underlying mechanisms of host responses during the WSSV acute infection stage in naturally infected shrimp. I...

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Published inPloS one Vol. 8; no. 3; p. e58627
Main Authors Li, Shihao, Zhang, Xiaojun, Sun, Zheng, Li, Fuhua, Xiang, Jianhai
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 19.03.2013
Public Library of Science (PLoS)
Subjects
Agriculture
Amino Acid Sequence
Analysis
Animals
Antimicrobial Cationic Peptides - genetics
Antimicrobial Cationic Peptides - immunology
Antiviral agents
Aquaculture
Arthropod Proteins - genetics
Arthropod Proteins - immunology
Biology
Cloning
Computational Biology
Crustaceans
Deoxyribonucleic acid
DNA
Endocytosis
Fenneropenaeus chinensis
Gene expression
Gene Expression Profiling
Gene mapping
Genes
Genomics
Health aspects
Homology
Host-Pathogen Interactions - genetics
Host-Pathogen Interactions - immunology
Infection
Infections
Kinases
Laboratories
Latent infection
Lipopolysaccharides
Litopenaeus vannamei
Marine biology
Marsupenaeus japonicus
Medical research
Molecular Sequence Data
Pathogenesis
Penaeidae - genetics
Penaeidae - immunology
Penaeidae - virology
Penaeus monodon
Peptide mapping
Peptides
Phylogeny
Proteins
Ribonucleic acid
RNA
RNA-mediated interference
Sequence Homology, Amino Acid
Shellfish
Toll-Like Receptors - genetics
Toll-Like Receptors - immunology
Viral infections
Viruses
White spot syndrome
White spot syndrome virus
White spot syndrome virus 1 - immunology
White spot syndrome virus 1 - pathogenicity
China
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Abstract Previous studies have discovered a lot of immune-related genes responding to white spot syndrome virus (WSSV) infection in crustacean. However, little information is available in relation to underlying mechanisms of host responses during the WSSV acute infection stage in naturally infected shrimp. In this study, we employed next-generation sequencing and bioinformatic techniques to observe the transcriptome differences of the shrimp between latent infection stage and acute infection stage. A total of 64,188,426 Illumina reads, including 31,685,758 reads from the latent infection group and 32,502,668 reads from the acute infection group, were generated and assembled into 46,676 unigenes (mean length: 676 bp; range: 200-15,094 bp). Approximately 24,000 peptides were predicted and classified based on homology searches, gene ontology, clusters of orthologous groups of proteins, and biological pathway mapping. Among which, 805 differentially expressed genes were identified and categorized into 11 groups based on their possible function. Genes in the Toll and IMD pathways, the Ras-activated endocytosis process, the RNA interference pathway, anti-lipopolysaccharide factors and many other genes, were found to be activated in shrimp from latent infection stage to acute infection stage. The anti-bacterially proPO-activating cascade was firstly uncovered to be probably participated in antiviral process. These genes contain not only members playing function in host defense against WSSV, but also genes utilized by WSSV for its rapid proliferation. In addition, the transcriptome data provides detail information for identifying novel genes in absence of the genome database of shrimp.
AbstractList Previous studies have discovered a lot of immune-related genes responding to white spot syndrome virus (WSSV) infection in crustacean. However, little information is available in relation to underlying mechanisms of host responses during the WSSV acute infection stage in naturally infected shrimp. In this study, we employed next-generation sequencing and bioinformatic techniques to observe the transcriptome differences of the shrimp between latent infection stage and acute infection stage. A total of 64,188,426 Illumina reads, including 31,685,758 reads from the latent infection group and 32,502,668 reads from the acute infection group, were generated and assembled into 46,676 unigenes (mean length: 676 bp; range: 200-15,094 bp). Approximately 24,000 peptides were predicted and classified based on homology searches, gene ontology, clusters of orthologous groups of proteins, and biological pathway mapping. Among which, 805 differentially expressed genes were identified and categorized into 11 groups based on their possible function. Genes in the Toll and IMD pathways, the Ras-activated endocytosis process, the RNA interference pathway, anti-lipopolysaccharide factors and many other genes, were found to be activated in shrimp from latent infection stage to acute infection stage. The anti-bacterially proPO-activating cascade was firstly uncovered to be probably participated in antiviral process. These genes contain not only members playing function in host defense against WSSV, but also genes utilized by WSSV for its rapid proliferation. In addition, the transcriptome data provides detail information for identifying novel genes in absence of the genome database of shrimp.
Previous studies have discovered a lot of immune-related genes responding to white spot syndrome virus (WSSV) infection in crustacean. However, little information is available in relation to underlying mechanisms of host responses during the WSSV acute infection stage in naturally infected shrimp. In this study, we employed next-generation sequencing and bioinformatic techniques to observe the transcriptome differences of the shrimp between latent infection stage and acute infection stage. A total of 64,188,426 Illumina reads, including 31,685,758 reads from the latent infection group and 32,502,668 reads from the acute infection group, were generated and assembled into 46,676 unigenes (mean length: 676 bp; range: 200-15,094 bp). Approximately 24,000 peptides were predicted and classified based on homology searches, gene ontology, clusters of orthologous groups of proteins, and biological pathway mapping. Among which, 805 differentially expressed genes were identified and categorized into 11 groups based on their possible function. Genes in the Toll and IMD pathways, the Ras-activated endocytosis process, the RNA interference pathway, anti-lipopolysaccharide factors and many other genes, were found to be activated in shrimp from latent infection stage to acute infection stage. The anti-bacterially proPO-activating cascade was firstly uncovered to be probably participated in antiviral process. These genes contain not only members playing function in host defense against WSSV, but also genes utilized by WSSV for its rapid proliferation. In addition, the transcriptome data provides detail information for identifying novel genes in absence of the genome database of shrimp.Previous studies have discovered a lot of immune-related genes responding to white spot syndrome virus (WSSV) infection in crustacean. However, little information is available in relation to underlying mechanisms of host responses during the WSSV acute infection stage in naturally infected shrimp. In this study, we employed next-generation sequencing and bioinformatic techniques to observe the transcriptome differences of the shrimp between latent infection stage and acute infection stage. A total of 64,188,426 Illumina reads, including 31,685,758 reads from the latent infection group and 32,502,668 reads from the acute infection group, were generated and assembled into 46,676 unigenes (mean length: 676 bp; range: 200-15,094 bp). Approximately 24,000 peptides were predicted and classified based on homology searches, gene ontology, clusters of orthologous groups of proteins, and biological pathway mapping. Among which, 805 differentially expressed genes were identified and categorized into 11 groups based on their possible function. Genes in the Toll and IMD pathways, the Ras-activated endocytosis process, the RNA interference pathway, anti-lipopolysaccharide factors and many other genes, were found to be activated in shrimp from latent infection stage to acute infection stage. The anti-bacterially proPO-activating cascade was firstly uncovered to be probably participated in antiviral process. These genes contain not only members playing function in host defense against WSSV, but also genes utilized by WSSV for its rapid proliferation. In addition, the transcriptome data provides detail information for identifying novel genes in absence of the genome database of shrimp.
Audience Academic
Author Sun, Zheng
Li, Shihao
Zhang, Xiaojun
Li, Fuhua
Xiang, Jianhai
AuthorAffiliation Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
Uppsala University, Sweden
AuthorAffiliation_xml – name: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
– name: Uppsala University, Sweden
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  givenname: Shihao
  surname: Li
  fullname: Li, Shihao
– sequence: 2
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  surname: Zhang
  fullname: Zhang, Xiaojun
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  givenname: Zheng
  surname: Sun
  fullname: Sun, Zheng
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  givenname: Fuhua
  surname: Li
  fullname: Li, Fuhua
– sequence: 5
  givenname: Jianhai
  surname: Xiang
  fullname: Xiang, Jianhai
BackLink https://www.ncbi.nlm.nih.gov/pubmed/23527000$$D View this record in MEDLINE/PubMed
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2013 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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– notice: 2013 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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Competing Interests: The authors have declared that no competing interests exist.
Conceived and designed the experiments: FL JX. Performed the experiments: SL XZ. Analyzed the data: SL ZS. Contributed reagents/materials/analysis tools: XZ ZS. Wrote the paper: SL FL JX.
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SSID ssj0053866
Score 2.467321
Snippet Previous studies have discovered a lot of immune-related genes responding to white spot syndrome virus (WSSV) infection in crustacean. However, little...
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StartPage e58627
SubjectTerms Agriculture
Amino Acid Sequence
Analysis
Animals
Antimicrobial Cationic Peptides - genetics
Antimicrobial Cationic Peptides - immunology
Antiviral agents
Aquaculture
Arthropod Proteins - genetics
Arthropod Proteins - immunology
Biology
Cloning
Computational Biology
Crustaceans
Deoxyribonucleic acid
DNA
Endocytosis
Fenneropenaeus chinensis
Gene expression
Gene Expression Profiling
Gene mapping
Genes
Genomics
Health aspects
Homology
Host-Pathogen Interactions - genetics
Host-Pathogen Interactions - immunology
Infection
Infections
Kinases
Laboratories
Latent infection
Lipopolysaccharides
Litopenaeus vannamei
Marine biology
Marsupenaeus japonicus
Medical research
Molecular Sequence Data
Pathogenesis
Penaeidae - genetics
Penaeidae - immunology
Penaeidae - virology
Penaeus monodon
Peptide mapping
Peptides
Phylogeny
Proteins
Ribonucleic acid
RNA
RNA-mediated interference
Sequence Homology, Amino Acid
Shellfish
Toll-Like Receptors - genetics
Toll-Like Receptors - immunology
Viral infections
Viruses
White spot syndrome
White spot syndrome virus
White spot syndrome virus 1 - immunology
White spot syndrome virus 1 - pathogenicity
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Title Transcriptome Analysis on Chinese Shrimp Fenneropenaeus chinensis during WSSV Acute Infection
URI https://www.ncbi.nlm.nih.gov/pubmed/23527000
https://www.proquest.com/docview/1330889372
https://www.proquest.com/docview/1319621828
https://www.proquest.com/docview/1458524671
https://pubmed.ncbi.nlm.nih.gov/PMC3602427
https://doaj.org/article/3e5e7e846f0a41b6bc9af2be66603ab0
http://dx.doi.org/10.1371/journal.pone.0058627
Volume 8
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