About: A case for a negative-strand coding sequence in a group of positive-sense RNA viruses

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.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	A case for a negative-strand coding sequence in a group of positive-sense RNA viruses
Creator	Olendraite, Ingrida Firth, Andrew Dinan, Adam Lukhovitskaya, Nina
source	PMC
abstract	Positive-sense single-stranded RNA viruses form the largest and most diverse group of eukaryote-infecting viruses. Their genomes comprise one or more segments of coding-sense RNA that function directly as messenger RNAs upon release into the cytoplasm of infected cells. Positive-sense RNA viruses are generally accepted to encode proteins solely on the positive strand. However, we previously identified a surprisingly long (∼1,000-codon) open reading frame (ORF) on the negative strand of some members of the family Narnaviridae which, together with RNA bacteriophages of the family Leviviridae, form a sister group to all other positive-sense RNA viruses. Here, we completed the genomes of three mosquito-associated narnaviruses, all of which have the long reverse-frame ORF. We systematically identified narnaviral sequences in public data sets from a wide range of sources, including arthropod, fungal, and plant transcriptomic data sets. Long reverse-frame ORFs are widespread in one clade of narnaviruses, where they frequently occupy >95 per cent of the genome. The reverse-frame ORFs correspond to a specific avoidance of CUA, UUA, and UCA codons (i.e. stop codon reverse complements) in the forward-frame RNA-dependent RNA polymerase ORF. However, absence of these codons cannot be explained by other factors such as inability to decode these codons or GC3 bias. Together with other analyses, we provide the strongest evidence yet of coding capacity on the negative strand of a positive-sense RNA virus. As these ORFs comprise some of the longest known overlapping genes, their study may be of broad relevance to understanding overlapping gene evolution and de novo origin of genes.
has issue date	2020-02-10(xsd:dateTime)
bibo:doi	10.1093/ve/veaa007
bibo:pmid	32064120
has license	cc-by
sha1sum (hex)	46c464442591d7777212f7ee389bcbfa362ddc8e
schema:url	https://doi.org/10.1093/ve/veaa007
resource representing a document's title	A case for a negative-strand coding sequence in a group of positive-sense RNA viruses
has PubMed Central identifier	PMC7010960
has PubMed identifier	32064120
schema:publication	Virus Evol
resource representing a document's body	covid:46c464442591d7777212f7ee389bcbfa362ddc8e#body_text
is schema:about of	named entity 'STRAND' named entity 'RNA-dependent RNA polymerase' named entity 'RNA virus' named entity 'release' named entity 'CUA' named entity 'However' named entity 'viruses' named entity 'codons' named entity 'RNA' named entity 'Long' named entity 'positive' named entity 'fungal' named entity 'origin' named entity 'ORIGIN' named entity 'MEMBERS' named entity 'CODON' named entity 'COMPRISE' named entity 'DIVERSE' named entity 'CODING SEQUENCE' named entity 'NEGATIVE' named entity 'FREQUENTLY' named entity 'FAMILY NARNAVIRIDAE' named entity 'POSITIVE STRAND' named entity 'GENES' named entity 'MESSENGER' named entity 'PROTEINS' named entity 'FORM' named entity 'INFECTING' covid:arg/46c464442591d7777212f7ee389bcbfa362ddc8e named entity 'IDENTIFIED' named entity 'COMPLEMENTS' named entity 'OPEN READING FRAME' named entity 'GROUP' named entity 'OVERLAPPING GENE' named entity 'MAY BE' named entity 'FRAME' named entity 'EVIDENCE' named entity 'WIDESPREAD' named entity 'FUNCTION' named entity 'KNOWN' named entity 'CYTOPLASM' named entity 'AVOIDANCE' named entity 'CLADE' named entity 'PROVIDE' named entity 'UUA' named entity 'WHERE' named entity 'PREVIOUSLY' named entity 'FAMILY LEVIVIRIDAE' named entity 'BROAD' named entity 'HERE' named entity 'RNA VIRUSES' named entity 'POSITIVE-SENSE RNA VIRUSES' named entity 'CASE' named entity 'EUKARYOTE' named entity 'POSITIVE-SENSE RNA VIRUSES' named entity 'DATA SETS' named entity 'RANGE' named entity 'POSITIVE' named entity 'RELEVANCE' named entity 'SINGLE-STRANDED RNA' named entity 'UCA' named entity '28I' named entity 'BIAS' named entity 'RNA' named entity 'SEQUENCES' named entity 'MOSQUITO' named entity 'TRANSCRIPTOMIC DATA' named entity 'LONGEST' named entity 'THESE' named entity 'HAVE' named entity 'CAPACITY' named entity 'VIRUSES' named entity 'UNDERSTANDING' named entity 'SPECIFIC' named entity 'GC3' named entity 'SEGMENTS' named entity 'SOURCES' named entity 'INABILITY'

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