Comparative genomic analysis reveals an 'open' pan-genome of African swine fever virus

Wang, Liang1; Luo, Yuzi2; Zhao, Yuhui1; Gao, George F.1,3,4,5; Bi, Yuhai1,3; Qiu, Hua-Ji2

2020-02-06

10.1111/tbed.13489

Transboundary and Emerging Diseases   影响因子和分区

1865-1674

1865-1682

The worldwide transmission of African swine fever virus (ASFV) drastically affects the pig industry and global trade. Development of vaccines is hindered by the lack of knowledge of the genomic characteristics of ASFV. In this study, we developed a pipeline for the de novo assembly of ASFV genome without virus isolation and purification. We then used a comparative genomics approach to systematically study 46 genomes of ASFVs to reveal the genomic characteristics. The analysis revealed that ASFV has an 'open' pan-genome based on both protein-coding genes and intergenic regions. Of the 151-174 genes found in the ASFV strains, only 86 were identified as core genes; the remainder were flexible accessory genes. Notably, 44 of the 86 core genes and 155 of the 324 accessory genes have been functionally annotated according to the known proteins. Interestingly, a dynamic number of taxis-related genes were identified in the accessory genes, and two potential virulence genes were identified in all ASFV isolates. The 'open' pan-genome of ASFV based on gene and intergenic regions reveals its pronounced natural diversity concerning genomic composition and regulation.

accessory genes African swine fever virus core genes evolution open pan-genome taxis-related genes

SCI

英语

通讯

Youth Innovation Promotion Association of CAS[2017122]

Infectious Diseases ; Veterinary Sciences

Infectious Diseases ; Veterinary Sciences

WOS:000511268800001

WILEY

Web of Science

1.Chinese Acad Sci, CAS Key Lab Pathogen Microbiol & Immunol, Inst Microbiol, Ctr Influenza Res & Early Warning CASCIRE, Beijing 100101, Peoples R China
2.Chinese Acad Agr Sci, Harbin Vet Res Inst, State Key Lab Vet Biotechnol, Harbin 150069, Peoples R China
3.Southern Univ Sci & Technol, Guangdong Key Lab Diag & Treatment Emerging Infec, State Key Discipline Infect Dis,Hosp Affiliated 2, Shenzhen Key Lab Pathogen & Immun,Shenzhen People, Shenzhen, Peoples R China
4.Chinese Ctr Dis Control & Prevent China CDC, Natl Inst Viral Dis Control & Prevent, Beijing, Peoples R China
5.Univ Chinese Acad Sci, Savaid Med Sch, Beijing, Peoples R China

Wang, Liang,Luo, Yuzi,Zhao, Yuhui,et al. Comparative genomic analysis reveals an 'open' pan-genome of African swine fever virus[J]. Transboundary and Emerging Diseases,2020,67(4):1553-1562.

Wang, Liang,Luo, Yuzi,Zhao, Yuhui,Gao, George F.,Bi, Yuhai,&Qiu, Hua-Ji.(2020).Comparative genomic analysis reveals an 'open' pan-genome of African swine fever virus.Transboundary and Emerging Diseases,67(4),1553-1562.

Wang, Liang,et al."Comparative genomic analysis reveals an 'open' pan-genome of African swine fever virus".Transboundary and Emerging Diseases 67.4(2020):1553-1562.