About: Phylogenetic and recombination analysis of Tobacco bushy top virus in China

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About: Phylogenetic and recombination analysis of Tobacco bushy top virus in China Goto Sponge NotDistinct Permalink

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Phylogenetic and recombination analysis of Tobacco bushy top virus in China
Creator	Li, Fan Shi, Kerong Wang, Deya Wang, Guolu Yu, Chengming Yuan, Xuefeng
Source	Medline; PMC
abstract	BACKGROUND: During the past decade, tobacco bushy top disease, which is mainly caused by a combination of Tobacco bushy top virus (TBTV) and Tobacco vein-distorting virus (TVDV), underwent a sudden appearance, extreme virulence and degeneration of the epidemic in the Yunnan province of China. In addition to integrative control of its aphid vector, it is of interest to examine diversity and evolution among different TBTV isolates. METHODS: 5’ and 3’ RACE, combined with one step full-length RT-PCR, were used to clone the full-length genome of three new isolates of TBTV that exhibited mild pathogenicity in Chinese fields. Nucleotide and amino acid sequences for the TBTV isolates were analyzed by DNAMAN. MEGA 5.0 was used to construct phylogenetic trees. RDP4 was used to detect recombination events during evolution of these isolates. RESULTS: The genomes of three isolates, termed TBTV-JC, TBTV-MD-I and TBTV-MD-II, were 4152 nt in length and included one distinctive difference from previously reported TBTV isolates: the first nucleotide of the genome was a guanylate instead of an adenylate. Diversity and phylogenetic analyses among these three new TBTV isolates and five other available isolates suggest that ORFs and 3’UTRs of TBTV may have evolved separately. Moreover, the RdRp-coding region was the most variable. Recombination analysis detected a total of 29 recombination events in the 8 TBTV isolates, in which 24 events are highly likely and 5 events have low-level likelihood based on their correlation with the phylogenetic trees. The three new TBTV isolates have individual recombination patterns with subtle divergences in parents and locations. CONCLUSIONS: The genome sizes of TBTV isolates were constant while different ORF-coding regions and 3’UTRs may have evolved separately. The RdRp-coding region was the most variable. Frequent recombination occurred among TBTV isolates. Three new TBTV isolates have individual recombination patterns and may have different progenitors. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-015-0340-2) contains supplementary material, which is available to authorized users.
has issue date	2015-07-25(xsd:dateTime)
bibo:doi	10.1186/s12985-015-0340-2
bibo:pmid	26209518
has license	cc-by
sha1sum (hex)	8da1231a64d73bc59f2af993bf1a2466265ffa4a
schema:url	https://doi.org/10.1186/s12985-015-0340-2
resource representing a document's title	Phylogenetic and recombination analysis of Tobacco bushy top virus in China
has PubMed Central identifier	PMC4514990
has PubMed identifier	26209518
schema:publication	Virol J
resource representing a document's body	covid:8da1231a64d73bc59f2af993bf1a2466265ffa4a#body_text
is schema:about of	named entity 'clone' named entity 'VIRULENCE' named entity 'USED' named entity 'CHINA' named entity 'ANALYZED' named entity 'LENGTH' named entity 'DECADE' named entity 'TOBACCO BUSHY TOP VIRUS' named entity 'OF INTEREST' named entity 'EVOLUTION' named entity 'CHINESE' named entity 'TOBACCO BUSHY TOP VIRUS' named entity 'RACE' named entity 'YUNNAN PROVINCE' named entity 'DIVERSITY' named entity 'NUCLEOTIDE' named entity 'ONE STEP' named entity 'EVENTS' named entity 'DIFFERENT' named entity 'RECOMBINATION' named entity 'ANALYSIS' named entity 'DEGENERATION' named entity 'TOBACCO VEIN-DISTORTING VIRUS' named entity 'AMINO ACID SEQUENCES' named entity 'GENOME' named entity 'COMBINED' named entity 'EXTREME' named entity 'TO EXAMINE' named entity 'BUSHY' named entity 'APPEARANCE' named entity 'EPIDEMIC' named entity 'TOBACCO' named entity 'ADDITION' named entity 'RECOMBINATION' named entity 'MILD' named entity 'APHID' named entity 'COMBINATION' named entity 'THESE' named entity 'VECTOR' named entity 'NEW' named entity 'CAUSED BY' named entity 'CHINA' named entity 'BACKGROUND' named entity 'ISOLATES' named entity 'ITS' named entity 'MEGA' named entity 'CONTROL' named entity 'TREES' named entity 'METHODS' named entity 'SUDDEN' named entity 'DISEASE' named entity 'CLONE' named entity 'CONSTRUCT' named entity 'TO DETECT' named entity 'PAST' named entity 'PATHOGENICITY' named entity 'RT-PCR' covid:arg/8da1231a64d73bc59f2af993bf1a2466265ffa4a named entity 'evolution' named entity 'top' named entity 'aphid' named entity 'China' named entity 'events' named entity 'Background' named entity 'amino acid' named entity 'recombination' named entity 'tobacco' named entity 'Phylogenetic' named entity 'recombination events' named entity 'epidemic' named entity '5.0' named entity 'aphid' named entity 'evolution' named entity 'clone' named entity 'virulence' named entity 'Yunnan'

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