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Codon Usage Bias Analysis of Citrus tristeza virus: Higher Codon Adaptation to Citrus reticulata Host

Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 11012, India
ICAR-Central Citrus Research Institute, Nagpur 440033, India
Department of Plant Pathology, Assam Agricultural University, Jorhat 785013, India
Department of Botany and Plant Sciences, University of California, Riverside, CA 92507, USA
National Clonal Germplasm Repository for Citrus & Dates, United States Department of Agriculture-Agricultural Research Service, Riverside, CA 92507, USA
Asia-Pacific Association of Agricultural Research Institutions, Bangkok 10100, Thailand
Author to whom correspondence should be addressed.
Viruses 2019, 11(4), 331;
Received: 18 February 2019 / Revised: 25 March 2019 / Accepted: 3 April 2019 / Published: 8 April 2019
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
PDF [2384 KB, uploaded 10 April 2019]


Citrus tristeza virus (CTV), a member of the aphid-transmitted closterovirus group, is the causal agent of the notorious tristeza disease in several citrus species worldwide. The codon usage patterns of viruses reflect the evolutionary changes for optimization of their survival and adaptation in their fitness to the external environment and the hosts. The codon usage adaptation of CTV to specific citrus hosts remains to be studied; thus, its role in CTV evolution is not clearly comprehended. Therefore, to better explain the host–virus interaction and evolutionary history of CTV, the codon usage patterns of the coat protein (CP) genes of 122 CTV isolates originating from three economically important citrus hosts (55 isolate from Citrus sinensis, 38 from C. reticulata, and 29 from C. aurantifolia) were studied using several codon usage indices and multivariate statistical methods. The present study shows that CTV displays low codon usage bias (CUB) and higher genomic stability. Neutrality plot and relative synonymous codon usage analyses revealed that the overall influence of natural selection was more profound than that of mutation pressure in shaping the CUB of CTV. The contribution of high-frequency codon analysis and codon adaptation index value show that CTV has host-specific codon usage patterns, resulting in higheradaptability of CTV isolates originating from C. reticulata (Cr-CTV), and low adaptability in the isolates originating from C. aurantifolia (Ca-CTV) and C. sinensis (Cs-CTV). The combination of codon analysis of CTV with citrus genealogy suggests that CTV evolved in C. reticulata or other Citrus progenitors. The outcome of the study enhances the understanding of the factors involved in viral adaptation, evolution, and fitness toward their hosts. This information will definitely help devise better management strategies of CTV. View Full-Text
Keywords: Citrus tristeza virus; codon usage bias; citrus host; high-frequency codons; natural selection; codon usage adaptation Citrus tristeza virus; codon usage bias; citrus host; high-frequency codons; natural selection; codon usage adaptation

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Biswas, K.K.; Palchoudhury, S.; Chakraborty, P.; Bhattacharyya, U.K.; Ghosh, D.K.; Debnath, P.; Ramadugu, C.; Keremane, M.L.; Khetarpal, R.K.; Lee, R.F. Codon Usage Bias Analysis of Citrus tristeza virus: Higher Codon Adaptation to Citrus reticulata Host. Viruses 2019, 11, 331.

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