Codon Usage Bias Analysis of : Higher Codon Adaptation to Host.

Authors:
Kajal Kumar Biswas
Kajal Kumar Biswas
Indian Agricultural Research Institute
New Delhi | India
Dilip K Ghosh
Dilip K Ghosh
University of Kalyani
India
Palash Debnath
Palash Debnath
Assam Agricultural University
Chandrika Ramadugu
Chandrika Ramadugu
University of California
United States
Manjunath L Keremane
Manjunath L Keremane
900 University Ave.
United States

Viruses 2019 Apr 8;11(4). Epub 2019 Apr 8.

National Clonal Germplasm Repository for Citrus & Dates, United States Department of Agriculture-Agricultural Research Service, Riverside, CA 92507, USA.

(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 () genes of 122 CTV isolates originating from three economically important citrus hosts (55 isolate from , 38 from , and 29 from ) 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 (Cr-CTV), and low adaptability in the isolates originating from (Ca-CTV) and (Cs-CTV). The combination of codon analysis of CTV with citrus genealogy suggests that CTV evolved in or other 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.

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Source
https://www.mdpi.com/1999-4915/11/4/331
Publisher Site
http://dx.doi.org/10.3390/v11040331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6521185PMC
April 2019
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References

(Supplied by CrossRef)
Viruses, greening bacterium and viroids associated with citrus (Citrus species) decline in India
Ahlawat et al.
Indian J. Agric. Sci. 1997
Molecular diagnosis of Citrus tristeza virus in mandarin (Citrus reticulata) orchards of hills of West Bengal
Biswas et al.
Indian J. Virol. 2008
Characterization of Citrus tristeza virus and determination of genetic variability in North-east and South India
Tarafdar et al.
Indian Phytopath. 2013

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