Bioinformatics analysis of codon usage patterns and influencing factors in Penaeus monodon nudivirus

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• 作者：Anuj Tyagi ; Niraj K. Singh ; Volker Gurtler ; Indrani Karunasagar
• 关键词：Codon usage bias ; Codon adaptation index ; Correspondence analysis ; Penaeus monodon nudivirus ; Shrimp
• 刊名：Archives of Virology
• 出版年：2016
• 出版时间：February 2016
• 年：2016
• 卷：161
• 期：2
• 页码：459-464
• 全文大小：480 KB
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• 作者单位：Anuj Tyagi (1)
  Niraj K. Singh (2)
  Volker Gurtler (3)
  Indrani Karunasagar (4)
  
  1. College of Fisheries, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, 141004, Punjab, India
  2. School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, 141004, Punjab, India
  3. School of Applied Sciences, Building 223, Level 1, Bundoora Campus RMIT University, PO Box 71, Bundoora, 3083, Australia
  4. UNESCO MIRCEN for Medical and Marine Biotechnology, Nitte University Center for Science Education and Research, Deralakatte, Mangalore, 575018, Karnataka, India
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Biomedicine
  Virology
  Medical Microbiology
  Infectious Diseases
  
• 出版者：Springer Wien
• ISSN：1432-8798

文摘

Penaeus monodon nudivirus (PmNV) is one of the most important and most commonly reported shrimp viruses. In the present study, codon usage of PmNV was studied in detail. Based on effective number of codons (ENC) values, strong to low codon usage bias was observed in PmNV genes. Nucleotide composition–ENC correlation analysis and the GC3 versus ENC relationship indicated that compositional constraint has a major effect on codon usage of PmNV. At the whole-genome level, relative synonymous codon usage (RSCU) analysis showed almost complete antagonism between the codon usage pattern of PmNV and its host P. monodon. However, codon adaptive index (CAI) values indicated that forces of selective/translational constraints have been able to overcome this antagonism in some genes. Keywords Codon usage bias Codon adaptation index Correspondence analysis Penaeus monodon nudivirus Shrimp