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Codon usage bias of goose circovirus and its adaptation to host

文献类型： 外文期刊

作者： Xu, Quanming 1 ; Cao, Jie 1 ; Rai, Kul Raj 3 ; Zhu, Binling 4 ; Liu, Dan 5 ; Wan, Chunhe 2 ;

作者机构： 1.Fujian Police Coll, Sci Res & Expt Ctr, Fuzhou 350007, Peoples R China

2.Fujian Acad Agr Sci, Inst Anim Husb & Vet Med, Fujian Anim Dis Control Technol Dev Ctr, Fujian Key Lab Avian Dis Control & Prevent, Fuzhou 350013, Peoples R China

3.Fujian Agr & Forestry Univ, Coll Anim Sci, Fuzhou 350002, Peoples R China

4.Fujian Police Coll, Dept Forens Sci, Fuzhou 350007, Peoples R China

5.China Inst Vet Drug Control, Beijing 100081, Peoples R China

关键词： goose circovirus; codon usage bias; natural selection; mutation; host adaptability

期刊名称：POULTRY SCIENCE （ 影响因子：4.4； 五年影响因子：4.4 ）

ISSN： 0032-5791

年卷期： 2024 年 103 卷 7 期

页码：

收录情况： SCI

摘要： Goose circovirus ( GoCV ), a potential immunosuppressive virus possessing a circular singlestranded DNA genome, is widely distributed in both domesticated and wild geese. This virus infection causes signi ficant economic losses in the waterfowl industry. The codon usage patterns of viruses re flect the evolutionary history and genetic architecture, allowing them to adapt quickly to changes in the external environment, particularly to their hosts. In this study, we retrieved the coding sequences (Rep and Cap) and the genome of GoCV from GenBank, conducting comprehensive research to explore the codon usage patterns in 144 GoCV strains. The overall codon usage of the GoCV strains was relatively similar and exhibited a slight bias. The effective number of codons ( ENC ) indicated a low overall extent of codon usage bias ( CUB ) in GoCV. Combined with the base composition and relative synonymous codon usage ( RSCU ) analysis, the results revealed a bias toward Aand G-ending codons in the overall codon usage. Analysis of the ENC-GC 3s plot and neutrality plot suggested that natural selection plays an important role in shaping the codon usage pattern of GoCV, with mutation pressure having a minor in fluence. Furthermore, the correlations between ENC and relative indices, as well as correspondence analysis ( COA ), showed that hydrophobicity and geographical distribution also contribute to codon usage variation in GoCV, suggesting the possible involvement of natural selection. In conclusion, GoCV exhibits comparatively slight CUB, with natural selection being the major factor shaping the codon usage pattern of GoCV. Our research contributes to a deeper understanding of GoCV evolution and its host adaptation, providing valuable insights for future basic studies and vaccine design related to GoCV.

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