Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences
Feng, Hua (Henan Provincial Key Laboratory of Animal Immunology)
Segalés Coma, Joaquim (Universitat Autònoma de Barcelona. Departament de Sanitat i d'Anatomia Animals)
Wang, Fangyu (Henan Provincial Key Laboratory of Animal Immunology)
Jin, Qianyue (Henan Provincial Key Laboratory of Animal Immunology)
Wang, Aiping (Zhengzhou University. School of Life Sciences)
Zhang, Gaiping (Zhengzhou University. School of Life Sciences)
Franzo, Giovanni (University of Padua. Department of Animal Medicine)

Data:	2022
Resum:	Porcine circoviruses (PCVs) are distributed in swine herds worldwide and represent a threat to the health of domestic pigs and the profits of the swine industry. Currently, four PCV species, including PCV-1, PCV-2, PCV-3 and PCV-4, have been identified in China. Considering the ubiquitous characteristic of PCVs, the new emerged PCV-4 and the large scale of swine breeding in China, an overall analysis on codon usage bias for Chinese PCV sequences was performed by using the major proteins coding sequences (ORF1 and ORF2) to better understand the relationship of these viruses with their host. The data from genome nucleotide frequency composition and relative synonymous codon usage (RSCU) analysis revealed an overrepresentation of AT pair and the existence of a certain codon usage bias in all PCVs. However, the values of an effective number of codons (ENC) revealed that the bias was of low magnitude. Principal component analysis, ENC-plot, parity rule two analysis and correlation analysis suggested that natural selection and mutation pressure were both involved in the shaping of the codon usage patterns of PCVs. However, a neutrality plot revealed a stronger effect of natural selection than mutation pressure on codon usage patterns. Good host adaptation was also shown by the codon adaptation index analysis for all these viruses. Interestingly, obtained data suggest that PCV-4 might be more adapted to its host compared to other PCVs. The present study obtained insights into the codon usage pattern of PCVs based on ORF1 and ORF2, which further helps the understanding the molecular evolution of these swine viruses.
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Porcine circovirus ; Codon usage pattern ; Natural selection ; Mutation pressure ; Viral host adaptability
Publicat a:	Viruses, Vol. 14 (january 2022) , ISSN 1999-4915

Adreça alternativa: https://www.mdpi.com/1999-4915/14/1/81
DOI: 10.3390/v14010081
PMID: 35062285

15 p, 1.6 MB

El registre apareix a les col·leccions:
Articles > Articles de recerca
Articles > Articles publicats