Analysis of synonymous codon usage bias and phylogeny of coat protein gene in banana bract mosaic virus isolates

被引：10
作者：
Patil A.B. [1 ]
Dalvi V.S. [1 ]
Mishra A.A. [1 ]
Krishna B. [2 ]
Azeez A. [2 ]
机构：
[1] Plant Virology Lab, Jain R&D, Jain Hills, Jain Irrigation Systems Limited, Jalgaon
[2] Plant Molecular Biology Lab, Jain R&D, Jain Hills, Jain Irrigation Systems Limited, Jalgaon
来源：
VirusDisease | 2017年 / 28卷 / 2期
关键词：
Codon usage; Correspondence analysis; Mutational bias; Translational selection;
D O I：
10.1007/s13337-017-0380-x
中图分类号：
学科分类号：
摘要：
The banana is one of the world’s most important livelihood crops. Banana plants are principally infected by four virus species, Banana bunchy top virus (genus Babuvirus), Cucumber mosaic virus (genus Cucumovirus), Banana streak virus (genus Badnavirus) and Banana bract mosaic virus (genus Potyvirus). The objective of this study is to understand the codon usage pattern and phylogeny of coat protein gene in different banana bract mosaic virus (BBrMV) isolates. The BBrMV Coat Protein (CP) gene was amplified from BBrMV infected banana plant samples collected from different districts of Tamil Nadu and Karnataka, India. Six new BBrMV isolates were submitted to National Center for Biotechnology Information. Phylogenetic analysis and codon usage indices were studied along with other isolates of BBrMV. Phylogenetic analysis of CP genes shows that most of BBrMV isolates are closely related to each other except KF385484.1 and KF385478.1. Relative codon usage patterns among different BBrMV isolates were calculated by software CodonW version 1.4.2. In BBrMV, codons with A-ended or U ended are the most preferential except the Leu and Gln whose optimized codons are CAG and UUG ending by G. The codon usage patterns of BBrMV isolates are principally influenced by mutational bias; however, compositional constraints along with mutational bias also play a major role. © 2017, Indian Virological Society.
引用
收藏
页码：156 / 163
页数：7
相关论文
共 36 条
  • [1] Adams M.J., Antoniw J.F., Codon usage bias amongst plant viruses, Arch Virol, 149, 1, pp. 113-135, (2003)
  • [2] Balasubramanian V., Selvarajan R., Complete genome sequence of a banana bract mosaic virus isolate infecting the French plantain cv. Nendran in India, Arch Virol, 157, 2, pp. 397-400, (2012)
  • [3] Balasubramanian V., Selvarajan R., Genetic diversity and recombination analysis in the coat protein gene of Banana bract mosaic virus, Virus Genes, 48, 3, pp. 509-517, (2014)
  • [4] Bateson M.F., Dale J.L., Banana bract mosaic virus: characterisation using potyvirus specific degenerate PCR primers, Arch Virol, 140, 3, pp. 515-527, (1995)
  • [5] Belalov I.S., Lukashev A.N., Causes and implications of codon usage bias in RNA viruses, PLoS ONE, 8, 2, (2013)
  • [6] Benzecri J.P., Correspondence analysis handbook, (1992)
  • [7] Bernardi G., Bernardi G., Compositional constraints and genome evolution, J Mol Evol, 24, 1-2, pp. 1-11, (1986)
  • [8] Campanella J.J., Bitincka L., Smalley J., MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences, BMC Bioinform, 4, 1, (2003)
  • [9] Cardinale D.J., DeRosa K., Duffy S., Base composition and translational selection are insufficient to explain codon usage bias in plant viruses, Viruses, 5, 1, pp. 162-181, (2013)
  • [10] Chiapello H., Lisacek F., Caboche M., Henaut A., Codon usage and gene function are related in sequences of Arabidopsis thaliana, Gene., 209, 1, pp. GC1-GC38, (1998)
1234