Analysis of codon usage patterns and influencing factors in rice tungro bacilliform virus.

Autor: Nguyen TH; College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China; Department of Genetic Engineering, Agricultural Genetics Institute, Tuliem, Hanoi 100000, Viet Nam., Wang D; China animal health and epidemiology center, Qingdao, Shandong, China., Rahman SU; College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China; Department of Computer Science and Bioinformatics, Khushal Khan Khattak university, Karak, Khyber Pakhtunkhwa 27200, Pakistan., Bai H; College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China., Yao X; College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China., Chen D; College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China. Electronic address: chendekun163@163.com., Tao S; College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China. Electronic address: shihengt@nwsuaf.edu.cn.
Jazyk: angličtina
Zdroj: Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases [Infect Genet Evol] 2021 Jun; Vol. 90, pp. 104750. Date of Electronic Publication: 2021 Feb 04.
DOI: 10.1016/j.meegid.2021.104750
Abstrakt: Rice tungro bacilliform virus (RTBV) belongs to genus Tungrovirus within the family Caulimoviridae harbors circular double-stranded DNA (dsDNA). Rice tungro disease (RTD) caused by RTBV, responsible for severe rice yield losses in South and Southeast Asia. Here, we performed a systematic evolutionary and codon usage bias (CUB) analysis of RTBV genome sequences. We analysed different bioinformatics techniques to calculate the nucleotide compositions, the relative synonymous codon usage (RSCU), and other indices. The results indicated slightly or low codon usage bias in RTBV isolates. Mutation and natural selection pressures have equally contributed to this low codon usage bias. Additionally, multiple factors such as host, geographical distribution also affect codon usage patterns in RTBV genomes. RSCU analysis revealed that RTBV shows mutation bias and prefers A and U ended codons to code amino acids. Codon usage patterns of RTBV were also found to be influenced by its host. This indicates that RTBV have evolved codon usage patterns that are specific to its host. The findings from this study are expected to increase our understanding of factors leading to viral evolution and fitness with respect to hosts and the environment.
(Copyright © 2021 Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
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