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Genome-wide analysis of long noncoding RNA profiles in Vero cells infected with porcine epidemic diarrhea virus

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Abstract

Porcine epidemic diarrhea (PED) is an acute enteric disease caused by porcine epidemic diarrhea virus (PEDV). In China, variant PEDV causes severe watery diarrhea, vomiting, and dehydration in piglets, leading to very high morbidity and mortality. However, the pathogenesis of PEDV is still not fully understood. In our study, we analyzed the long noncoding RNA (lncRNA) and mRNA expression profiles of PEDV GDgh16 in infected Vero cells at 60 h postinfection. A total of 61,790 annotated mRNAs, 14,247 annotated lncRNAs and 1290 novel lncRNAs were identified. A total of 227 annotated lncRNAs and 13 novel lncRNAs were significantly and differentially expressed after viral infection. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases were used to identify genes adjacent to the lncRNAs, and it was found that these lncRNAs were enriched in pathways related to immune and antiviral responses. Next, we selected candidate lncRNAs and their predicted target genes for study. RT-qPCR demonstrated that these lncRNAs and genes were differentially expressed after PEDV infection. Our study investigated the function of lncRNAs involved in PEDV infection, providing new insight into the pathogenic mechanisms of PEDV.

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Availability of data and materials

The genetic data presented in this paper are publicly available in the GenBank database under accession no. MG983755.

Abbreviations

PED:

Porcine epidemic diarrhea

PEDV:

Porcine epidemic diarrhea virus

GO:

Gene Ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

RT-qPCR:

Real-time quantitative PCR

RNA-Seq:

RNA sequencing

CPC:

Coding Potential Calculator

MOI:

Multiplicity of infection

PLA2G4C:

Cytosolic phospholipase A2 gamma

TIRAP:

Toll/interleukin 1 receptor domain-containing adaptor protein

CLIP170:

Cytoplasmic linker protein 170

IL6R:

Interleukin-6 receptor

IL6:

Interleukin-6

STAT3:

Signal transducer and activator of transcription 3

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Funding

This work was supported by the National Key Research and Development Program of China (2018YFD0501102), Guangdong Rural Revitalization Strategy Program (201817SY0002), National Key Technologies R&D Program (2015BAD12B02-5), Henan Scale Pig Farm Major Disease Purification and Innovative Technology Team, the Henan Science and Technology Project (182102110037), and Key and Cultivation Discipline of Xinyang Agriculture and Forestry University (ZDXK201702).

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Author notes

  1. Linyang Yu, Jianguo Dong and Yanling Liu contributed equally to this work.

Authors and Affiliations

  1. College of Animal Science and National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou, 510642, China

    Linyang Yu, Yanling Liu, Leyi Zhang, Pengshuai Liang, Lei Wang, Zheng Xu & Changxu Song

  2. School of Animal Husbandry and Medical Engineering, Xinyang Agriculture and Forestry University, Xinyang, 464000, China

    Jianguo Dong & Li Huang

Authors
  1. Linyang Yu
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Contributions

LY, JD, and YL contributed equally to the work; LY and YL performed the assays and data analysis; LZ, PL, and LW performed the sequence alignment; LH contributed to the experimental design and revision of manuscript; and JD and CS wrote the manuscript. All authors reviewed and approved the final form of the manuscript.

Corresponding authors

Correspondence to Zheng Xu or Changxu Song.

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Conflict of interest

The authors declare no conflict of interest.

Ethics approval and consent to participate

All of the samples were collected according to the animal ethics regulations of the National Engineering Center for Swine Breeding Industry (NECSBI 2015-16).

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Handling Editor: Sheela Ramamoorthy.

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Yu, L., Dong, J., Liu, Y. et al. Genome-wide analysis of long noncoding RNA profiles in Vero cells infected with porcine epidemic diarrhea virus. Arch Virol 165, 1969–1977 (2020). https://doi.org/10.1007/s00705-020-04694-4

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  • DOI: https://doi.org/10.1007/s00705-020-04694-4

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