About: Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution

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About: Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution
Creator	Tong, Yigang Nasrullah, Izza Idrees, Muhammad Tahir, Shifa Butt, Azeem
source	PMC
abstract	BACKGROUND: The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. To understand the evolution of MARV at the codon level, we report a comprehensive analysis of synonymous codon usage patterns in MARV genomes. Multiple codon analysis approaches and statistical methods were performed to determine overall codon usage patterns, biases in codon usage, and influence of various factors, including mutation pressure, natural selection, and its two hosts, Homo sapiens and Rousettus aegyptiacus. RESULTS: Nucleotide composition and relative synonymous codon usage (RSCU) analysis revealed that MARV shows mutation bias and prefers U- and A-ended codons to code amino acids. Effective number of codons analysis indicated that overall codon usage among MARV genomes is slightly biased. The Parity Rule 2 plot analysis showed that GC and AU nucleotides were not used proportionally which accounts for the presence of natural selection. Codon usage patterns of MARV were also found to be influenced by its hosts. This indicates that MARV have evolved codon usage patterns that are specific to both of its hosts. Moreover, selection pressure from R. aegyptiacus on the MARV RSCU patterns was found to be dominant compared with that from H. sapiens. Overall, mutation pressure was found to be the most important and dominant force that shapes codon usage patterns in MARV. CONCLUSIONS: To our knowledge, this is the first detailed codon usage analysis of MARV and extends our understanding of the mechanisms that contribute to codon usage and evolution of MARV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-015-0456-4) contains supplementary material, which is available to authorized users.
has issue date	2015-08-26(xsd:dateTime)
bibo:doi	10.1186/s12862-015-0456-4
bibo:pmid	26306510
has license	cc-by
sha1sum (hex)	f2e06c174008ed721d0a244309601c9923548901
schema:url	https://doi.org/10.1186/s12862-015-0456-4
resource representing a document's title	Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution
has PubMed Central identifier	PMC4550055
has PubMed identifier	26306510
schema:publication	BMC Evol Biol
resource representing a document's body	covid:f2e06c174008ed721d0a244309601c9923548901#body_text
is schema:about of	named entity 'APPROACHES' named entity 'CODON USAGE' named entity 'BACKGROUND' named entity 'EVOLUTION' named entity 'OUTBREAKS' named entity 'HOMO SAPIENS' named entity 'PRESSURE' named entity 'LEVEL' named entity 'GENOMES' named entity 'CHANGES' named entity 'HOSTS' named entity 'SURVIVAL RATES' named entity 'HEMORRHAGIC FEVER' named entity 'TO SHAPE' named entity 'RESPONSIBLE' named entity 'INCLUDING' named entity 'COMPREHENSIVE ANALYSIS' named entity 'ENVIRONMENT' named entity 'SERIES' named entity 'REPORT' named entity 'UNDERSTAND' named entity 'NATURAL SELECTION' named entity 'biases' named entity 'family' named entity 'environment' named entity 'MARV' named entity 'genomes' named entity 'RNA GENOME' named entity 'MUTATION' named entity 'INFLUENCE' named entity 'MARBURG VIRUS ' named entity 'EVOLUTION' named entity 'PRESSURE' named entity 'THEIR' named entity 'FATAL' named entity 'MULTIPLE' named entity 'BIASES' named entity 'MARBURG VIRUS ' named entity 'FEATURES' named entity 'ANALYSIS' named entity 'GENOMIC' named entity 'NATURAL SELECTION' named entity 'HOST' named entity 'PERFORMED' named entity 'ROUSETTUS AEGYPTIACUS' named entity 'MUTATION' named entity 'PATTERNS' named entity 'ITS' named entity 'INFLUENCE' named entity 'NEGATIVE' named entity 'STATISTICAL METHODS' named entity 'CODON USAGE' named entity 'SENSE' named entity 'VIRUSES' named entity 'REFLECT' named entity 'HIGHLY' named entity 'ENABLE' named entity 'OVERALL' named entity 'CODON' named entity 'FITNESS' named entity 'SINGLE-STRANDED RNA' named entity 'ANALYSIS' named entity 'DETERMINE' named entity 'SYNONYMOUS CODON' named entity 'VARIOUS' named entity 'FAMILY FILOVIRIDAE' named entity 'EXTERNAL' covid:arg/f2e06c174008ed721d0a244309601c9923548901 named entity 'determine' named entity 'coding sequences' named entity 'genomes' named entity 'codons' named entity 'coding sequences' named entity 'codons' named entity 'vaccine design' named entity 'codons' named entity 'codons'

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