NDLI: Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses

Content Provider	PubMed Central
Author	Butt, Azeem Mehmood Izza, Nasrullah Tong, Yigang
Editor	Fausto, Baldanti
Copyright Year	2014
Abstract	Chikungunya virus (CHIKV) is an arthropod-borne virus of the family Togaviridae that is transmitted to humans by Aedes spp. mosquitoes. Its genome comprises a 12 kb single-strand positive-sense RNA. In the present study, we report the patterns of synonymous codon usage in 141 CHIKV genomes by calculating several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis showed that the preferred synonymous codons were G/C and A-ended. A comparative analysis of RSCU between CHIKV and its hosts showed that codon usage patterns of CHIKV are a mixture of coincidence and antagonism. Similarity index analysis showed that the overall codon usage patterns of CHIKV have been strongly influenced by Pan troglodytes and Aedes albopictus during evolution. The overall codon usage bias was low in CHIKV genomes, as inferred from the analysis of effective number of codons (ENC) and codon adaptation index (CAI). Our data suggested that although mutation pressure dominates codon usage in CHIKV, patterns of codon usage in CHIKV are also under the influence of natural selection from its hosts and geography. To the best of our knowledge, this is first report describing codon usage analysis in CHIKV genomes. The findings from this study are expected to increase our understanding of factors involved in viral evolution, and fitness towards hosts and the environment.
Related Links	http://dx.doi.org/10.1371/journal.pone.0090905
Starting Page	90905
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	3
Volume Number	9
Language	English
Publisher	Public Library of Science
Publisher Date	2014-03-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses

Causes and Implications of Codon Usage Bias in RNA Viruses

Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes

Genome-Wide Analysis of Host Factors in Nodavirus RNA Replication

Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1

Genome Wide Host Gene Expression Analysis in Chicken Lungs Infected with Avian Influenza Viruses

Comparative Analysis of Codon Usage Bias and Codon Context Patterns between Dipteran and Hymenopteran Sequenced Genomes

Genome-Wide Analysis of Human Metapneumovirus Evolution

Genome-Wide Comparison of Cowpox Viruses Reveals a New Clade Related to Variola Virus

Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses

Similar Documents

Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses

Causes and Implications of Codon Usage Bias in RNA Viruses

Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes

Genome-Wide Analysis of Host Factors in Nodavirus RNA Replication

Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1

Genome Wide Host Gene Expression Analysis in Chicken Lungs Infected with Avian Influenza Viruses

Comparative Analysis of Codon Usage Bias and Codon Context Patterns between Dipteran and Hymenopteran Sequenced Genomes

Genome-Wide Analysis of Human Metapneumovirus Evolution

Genome-Wide Comparison of Cowpox Viruses Reveals a New Clade Related to Variola Virus

Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses