Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts

Potato virus M (PVM) is a member of the genus Carlavirus of the family Betaflexviridae and causes large economic losses of nightshade crops. Several previous studies have elucidated the population structure, evolutionary timescale and adaptive evolution of PVM. However, the synonymous codon usage pattern of PVM remains unclear. In this study, we performed comprehensive analyses of the codon usage and composition of PVM based on 152 nucleotide sequences of the coat protein (CP) gene and 125 sequences of the cysteine-rich nucleic acid binding protein (NABP) gene. We observed that the PVM CP and NABP coding sequences were GC-and AU-rich, respectively, whereas U- and G-ending codons were preferred in the PVM CP and NABP coding sequences. The lower codon usage of the PVM CP and NABP coding sequences indicated a relatively stable and conserved genomic composition. Natural selection and mutation pressure shaped the codon usage patterns of PVM, with natural selection being the most important factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analysis revealed that the greatest adaption of PVM was to pepino, followed by tomato and potato. Moreover, similarity Index (SiD) analysis showed that pepino had a greater impact on PVM than tomato and potato. Our study is the first attempt to evaluate the codon usage pattern of the PVM CP and NABP genes to better understand the evolutionary changes of a carlavirus.

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The characteristics of the synonymous codon usage in hepatitis B virus and the effects of host on the virus in codon usage pattern

Virology Journal ◽

10.1186/1743-422x-8-544 ◽

2011 ◽

Vol 8 (1) ◽

Cited By ~ 13

Author(s):

Ming-ren Ma ◽

Xiao-qin Ha ◽

Hui Ling ◽

Mei-liang Wang ◽

Fang-xin Zhang ◽

...

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Codon Usage ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Codon Usage Pattern ◽

Usage Pattern ◽

B Virus

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P1063 THE CHARACTERISTICS OF THE SYNONYMOUS CODON USAGE PATTERN OF rtN236T MUTATION IN CHRONIC HEPATITIS B PATIENTS TREATED WITH ADEFOVIR DIPIVOXIL: PYROSEQUENCING ANALYSIS OF 1418 CASES

Journal of Hepatology ◽

10.1016/s0168-8278(14)61223-x ◽

2014 ◽

Vol 60 (1) ◽

pp. S431

Author(s):

W. Hou ◽

W. Lu

Keyword(s):

Chronic Hepatitis ◽

Hepatitis B ◽

Codon Usage ◽

Chronic Hepatitis B ◽

Adefovir Dipivoxil ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Codon Usage Pattern ◽

Usage Pattern ◽

Pyrosequencing Analysis

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Synonymous codon usage pattern analysis of Hepatitis D virus

Virus Research ◽

10.1016/j.virusres.2013.01.007 ◽

2013 ◽

Vol 173 (2) ◽

pp. 350-353 ◽

Cited By ~ 5

Author(s):

Arghya Kamal Bishal ◽

Rashmi Mukherjee ◽

Chandan Chakraborty

Keyword(s):

Codon Usage ◽

Pattern Analysis ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Codon Usage Pattern ◽

Usage Pattern ◽

Hepatitis D ◽

Hepatitis D Virus

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Characterization of Codon Usage Bias in the UL55 Gene of Duck Enteritis Virus

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.204-210.649 ◽

2011 ◽

Vol 204-210 ◽

pp. 649-662 ◽

Cited By ~ 1

Author(s):

Ying Wu ◽

An Chun Cheng ◽

Ming Shu Wang ◽

De Kang Zhu ◽

Xiao Yue Chen

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Duck Enteritis Virus ◽

Codon Usage Pattern ◽

Usage Pattern ◽

E Coli ◽

Usage Patterns ◽

Enteritis Virus

The analysis of codon usage may improve our understanding of the evolution and pathogenesis of DEV（Duck enteritis virus） and allow reengineering of target gene to improve their expression for gene therapy.In this study,we calculated the codon usage bias in DEV UL55 gene and performed a comparative analysis of synonymous codon usage patterns in other 26 related viruses by EMBOSS CUSP program and Codon W on line.Moreover,statistical methods were used to investigate the correlations of these related parameters. By comparing synonymous codon usage patterns in different viruses,we observed that synonymous codon usage pattern in these virus is virus speciﬁc and phylogenetically conserved, with a strong bias towards the codons with A and T at the third codon position. Phylogenetic analysis based on codon usage pattern suggested that DEV UL55 gene was clustered with the avian Alphaherpesvirus but diverged to form a single branch. The Neutrality-plot suggested GC12 and GC3s adopt the same mutation pattern,meanwhile,the ENC-plot revealed that the genetic heterogeneity in UL55 genes is constrained by the G+C content, while translational selection and gene length have no or micro effect on the variations of synonymous codon usage in these virus genes.Furthermore, we compared the codon preferences of DEV with those of E. coli, yeast and Homo sapiens.Data suggested the eukaryotes system such as human system may be more suitable for the expression of DEV UL55 gene in vitro. If the yeast and E. coli expression system are wanted for the expression of DEV UL55 gene ,codon optimization of the DEV UL55 gene may be required.

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Comprehensive Analysis of Codon Usage on Porcine Astrovirus

Viruses ◽

10.3390/v12090991 ◽

2020 ◽

Vol 12 (9) ◽

pp. 991

Author(s):

Huiguang Wu ◽

Zhengyu Bao ◽

Chunxiao Mou ◽

Zhenhai Chen ◽

Jingwen Zhao

Keyword(s):

Natural Selection ◽

Codon Usage ◽

Synonymous Codon ◽

Similarity Index ◽

Synonymous Codon Usage ◽

Codon Usage Pattern ◽

Broad Host Range ◽

Mutation Pressure ◽

Porcine Astrovirus ◽

Usage Patterns

Porcine astrovirus (PAstV), associated with mild diarrhea and neurological disease, is transmitted in pig farms worldwide. The purpose of this study is to elucidate the main factors affecting codon usage to PAstVs. Phylogenetic analysis showed that the subtype PAstV-5 sat at the bottom of phylogenetic tree, followed by PAstV-3, PAstV-1, PAstV-2, and PAstV-4, indicating that the five existing subtypes (PAstV1-PAstV5) may be formed by multiple differentiations of PAstV ancestors. A codon usage bias was found in the PAstVs-2,3,4,5 from the analyses of effective number of codons (ENC) and relative synonymous codon usage (RSCU). Nucleotides A/U are more frequently used than nucleotides C/G in the genome CDSs of the PAstVs-3,4,5. Codon usage patterns of PAstV-5 are dominated by mutation pressure and natural selection, while natural selection is the main evolutionary force that affects the codon usage pattern of PAstVs-2,3,4. The analyses of codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) showed the codon usage similarities between the PAstV and animals might contribute to the broad host range and the cross-species transmission of astrovirus. Our results provide insight into understanding the PAstV evolution and codon usage patterns.

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Synonymous codon usage pattern in mitochondrial CYB gene in pisces, aves, and mammals

Mitochondrial DNA Part A ◽

10.3109/19401736.2015.1115842 ◽

2015 ◽

Vol 28 (2) ◽

pp. 187-196 ◽

Cited By ~ 15

Author(s):

Arif Uddin ◽

Supriyo Chakraborty

Keyword(s):

Codon Usage ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Codon Usage Pattern ◽

Usage Pattern

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Phylogenetic and Codon Usage Analysis for Capsid and Replicase Genes of Porcine Circovirus 3

10.21203/rs.3.rs-527349/v1 ◽

2021 ◽

Author(s):

Xianglong Yu ◽

Kuipeng Gao ◽

Molin Pi ◽

Huizi Li ◽

Wenxia Zhong ◽

...

Keyword(s):

Codon Usage ◽

Synonymous Codon ◽

Economic Loss ◽

Porcine Circovirus Type ◽

Synonymous Codon Usage ◽

Porcine Circovirus ◽

Codon Usage Pattern ◽

Usage Pattern ◽

Swine Industry ◽

Usage Analysis

Abstract Porcine circovirus type 3 (PCV3) is a highly contagious virus belonging to the family Circoviridae that causes the severe dermatitis and nephropathy syndrome. To date, PCV3 has a worldwide distribution and bring huge economic loss in swine industry. Replicase protein (Rep) and capsid protein (Cap) are two major proteins of PCV3. Considering that the large number of new PCV3 isolates were reported in the past few years and the research for the codon usage pattern of Rep and Cap genes was still a gap, phylogenetic and codon usage analysis of these two genes was performed. Phylogenetic analysis with all strains showed no clear clusters were displayed, but almost all strains of one genotype were separated into same clade. Relative synonymous codon usage (RSCU) analysis revealed that the codon usage bias existed and effective number of codon (ENC) analysis showed that the bias was slight low. ENC-GC3s plot indicated that mutational pressure and other factors both play a role in PCV3 codon usage and neutrality plot analysis showed that natural selection was the main force influencing the codon usage pattern. In summary, the results provided the important basic data on codon usage pattern of Rep and Cap genes, and a better understanding of the evolution and potential origin of PCV3.

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