Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock Infection
Bluetongue virus (BTV) is a double-stranded RNA virus with multiple segments and belongs to the genus Orbivirus within the family Reoviridae. BTV is spread to livestock through its dominant vector, biting midges of genus Culicoides. Although great progress has been made in genomic analyses, it is no...
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doaj-1ad838ff3c46451dbda134c80161b90e2020-11-25T02:37:13ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-05-011110.3389/fmicb.2020.00655523397Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock InfectionXiaoting Yao0Xiaoting Yao1Qinlei Fan2Bo Yao3Ping Lu4Siddiq Ur Rahman5Siddiq Ur Rahman6Dekun Chen7Shiheng Tao8State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, ChinaCollege of Veterinary Medicine, Northwest A&F University, Yangling, ChinaChina Animal Health and Epidemiology Center, Qingdao, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, ChinaChina Animal Health and Epidemiology Center, Qingdao, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, ChinaDepartment of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, PakistanCollege of Veterinary Medicine, Northwest A&F University, Yangling, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, ChinaBluetongue virus (BTV) is a double-stranded RNA virus with multiple segments and belongs to the genus Orbivirus within the family Reoviridae. BTV is spread to livestock through its dominant vector, biting midges of genus Culicoides. Although great progress has been made in genomic analyses, it is not fully understood how BTVs adapt to their hosts and evade the host’s immune systems. In this study, we retrieved BTV genome sequences from the National Center for Biotechnology Information (NCBI) database and performed a comprehensive research to explore the codon usage patterns in 50 BTV strains. We used bioinformatic approaches to calculate the relative synonymous codon usage (RSCU), codon adaptation index (CAI), effective number of codons (ENC), and other indices. The results indicated that most of the overpreferred codons had A-endings, which revealed that mutational pressure was the major force shaping codon usage patterns in BTV. However, the influence of natural selection and geographical factors cannot be ignored on viral codon usage bias. Based on the RSCU values, we performed a comparative analysis between BTVs and their hosts, suggesting that BTVs were inclined to evolve their codon usage patterns that were comparable to those of their hosts. Such findings will be conducive to understanding the elements that contribute to viral evolution and adaptation to hosts.https://www.frontiersin.org/article/10.3389/fmicb.2020.00655/fullbluetongue virusReoviridaeCulicoidesnucleotide compositioncodon usage biasevolution |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Xiaoting Yao Xiaoting Yao Qinlei Fan Bo Yao Ping Lu Siddiq Ur Rahman Siddiq Ur Rahman Dekun Chen Shiheng Tao |
spellingShingle |
Xiaoting Yao Xiaoting Yao Qinlei Fan Bo Yao Ping Lu Siddiq Ur Rahman Siddiq Ur Rahman Dekun Chen Shiheng Tao Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock Infection Frontiers in Microbiology bluetongue virus Reoviridae Culicoides nucleotide composition codon usage bias evolution |
author_facet |
Xiaoting Yao Xiaoting Yao Qinlei Fan Bo Yao Ping Lu Siddiq Ur Rahman Siddiq Ur Rahman Dekun Chen Shiheng Tao |
author_sort |
Xiaoting Yao |
title |
Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock Infection |
title_short |
Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock Infection |
title_full |
Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock Infection |
title_fullStr |
Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock Infection |
title_full_unstemmed |
Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock Infection |
title_sort |
codon usage bias analysis of bluetongue virus causing livestock infection |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2020-05-01 |
description |
Bluetongue virus (BTV) is a double-stranded RNA virus with multiple segments and belongs to the genus Orbivirus within the family Reoviridae. BTV is spread to livestock through its dominant vector, biting midges of genus Culicoides. Although great progress has been made in genomic analyses, it is not fully understood how BTVs adapt to their hosts and evade the host’s immune systems. In this study, we retrieved BTV genome sequences from the National Center for Biotechnology Information (NCBI) database and performed a comprehensive research to explore the codon usage patterns in 50 BTV strains. We used bioinformatic approaches to calculate the relative synonymous codon usage (RSCU), codon adaptation index (CAI), effective number of codons (ENC), and other indices. The results indicated that most of the overpreferred codons had A-endings, which revealed that mutational pressure was the major force shaping codon usage patterns in BTV. However, the influence of natural selection and geographical factors cannot be ignored on viral codon usage bias. Based on the RSCU values, we performed a comparative analysis between BTVs and their hosts, suggesting that BTVs were inclined to evolve their codon usage patterns that were comparable to those of their hosts. Such findings will be conducive to understanding the elements that contribute to viral evolution and adaptation to hosts. |
topic |
bluetongue virus Reoviridae Culicoides nucleotide composition codon usage bias evolution |
url |
https://www.frontiersin.org/article/10.3389/fmicb.2020.00655/full |
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