The complete nucleotide sequence and genome organization of a novel virus of the order Tymovirales isolated from Prunus davidiana (Carr.) Franch. in Liaoning, China.
Identifieur interne : 000176 ( Main/Corpus ); précédent : 000175; suivant : 000177The complete nucleotide sequence and genome organization of a novel virus of the order Tymovirales isolated from Prunus davidiana (Carr.) Franch. in Liaoning, China.
Auteurs : Qiushi Hou ; Tong Han ; Liang Li ; Junzhu Wang ; Meichun Yu ; Song Zhang ; Mengji Cao ; Caixia YangSource :
- Archives of virology [ 1432-8798 ] ; 2019.
English descriptors
- KwdEn :
- Capsid Proteins (genetics), China (MeSH), Genome, Viral (genetics), High-Throughput Nucleotide Sequencing (MeSH), Plant Diseases (virology), Plant Leaves (virology), Prunus (virology), RNA Replicase (genetics), RNA, Viral (genetics), Tymoviridae (classification), Tymoviridae (genetics), Tymoviridae (isolation & purification).
- MESH :
- chemical , genetics : Capsid Proteins, RNA Replicase, RNA, Viral.
- geographic : China.
- classification : Tymoviridae.
- genetics : Genome, Viral, Tymoviridae.
- isolation & purification : Tymoviridae.
- virology : Plant Diseases, Plant Leaves, Prunus.
- High-Throughput Nucleotide Sequencing.
Abstract
In September 2017, a yellow spot leaf disease was noted on the leaves of Prunus davidiana (Carr.) Franch. plants in Liaoning, China, and spherical virions (approx. 30 nm in diameter) were later observed in preparations of symptomatic leaves. Subsequent deep sequencing of small RNA revealed the presence of a virus in these symptomatic leaves The complete genome of this viral isolate consists of 6,072 nucleotides, excluding the poly(A) tail. The virus showed the closest genetic relationship to grapevine-associated tymo-like virus, reported in Colmar, France (GaTLV, MH383239), which is the sole member of the newly proposed genus "Gratylivirus" within the order Tymovirales, which is currently unassigned to a particular family. The virus clustered closely with GaTLV in a phylogenetic tree constructed based on complete genomic sequences. On the basis of the nucleotide and amino acid sequences of the replicase and coat protein genes, this virus shares the highest (although still relatively low) sequence similarity with those of GaTLV (41.6%-60.8% identity), indicating that the virus is a distinct member of the order Tymovirales, for which the name "prunus yellow spot-associated virus" (PYSaV) is proposed. To our knowledge, this is the first report of a virus naturally infecting P. davidiana.
DOI: 10.1007/s00705-019-04220-1
PubMed: 30923968
Links to Exploration step
pubmed:30923968Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The complete nucleotide sequence and genome organization of a novel virus of the order Tymovirales isolated from Prunus davidiana (Carr.) Franch. in Liaoning, China.</title><author><name sortKey="Hou, Qiushi" sort="Hou, Qiushi" uniqKey="Hou Q" first="Qiushi" last="Hou">Qiushi Hou</name><affiliation><nlm:affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</nlm:affiliation></affiliation></author><author><name sortKey="Han, Tong" sort="Han, Tong" uniqKey="Han T" first="Tong" last="Han">Tong Han</name><affiliation><nlm:affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Liang" sort="Li, Liang" uniqKey="Li L" first="Liang" last="Li">Liang Li</name><affiliation><nlm:affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Junzhu" sort="Wang, Junzhu" uniqKey="Wang J" first="Junzhu" last="Wang">Junzhu Wang</name><affiliation><nlm:affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</nlm:affiliation></affiliation></author><author><name sortKey="Yu, Meichun" sort="Yu, Meichun" uniqKey="Yu M" first="Meichun" last="Yu">Meichun Yu</name><affiliation><nlm:affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Song" sort="Zhang, Song" uniqKey="Zhang S" first="Song" last="Zhang">Song Zhang</name><affiliation><nlm:affiliation>National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China.</nlm:affiliation></affiliation></author><author><name sortKey="Cao, Mengji" sort="Cao, Mengji" uniqKey="Cao M" first="Mengji" last="Cao">Mengji Cao</name><affiliation><nlm:affiliation>National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China. caomengji@cric.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Yang, Caixia" sort="Yang, Caixia" uniqKey="Yang C" first="Caixia" last="Yang">Caixia Yang</name><affiliation><nlm:affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China. xueyang27@126.com.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:30923968</idno><idno type="pmid">30923968</idno><idno type="doi">10.1007/s00705-019-04220-1</idno><idno type="wicri:Area/Main/Corpus">000176</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000176</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">The complete nucleotide sequence and genome organization of a novel virus of the order Tymovirales isolated from Prunus davidiana (Carr.) Franch. in Liaoning, China.</title><author><name sortKey="Hou, Qiushi" sort="Hou, Qiushi" uniqKey="Hou Q" first="Qiushi" last="Hou">Qiushi Hou</name><affiliation><nlm:affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</nlm:affiliation></affiliation></author><author><name sortKey="Han, Tong" sort="Han, Tong" uniqKey="Han T" first="Tong" last="Han">Tong Han</name><affiliation><nlm:affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Liang" sort="Li, Liang" uniqKey="Li L" first="Liang" last="Li">Liang Li</name><affiliation><nlm:affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Junzhu" sort="Wang, Junzhu" uniqKey="Wang J" first="Junzhu" last="Wang">Junzhu Wang</name><affiliation><nlm:affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</nlm:affiliation></affiliation></author><author><name sortKey="Yu, Meichun" sort="Yu, Meichun" uniqKey="Yu M" first="Meichun" last="Yu">Meichun Yu</name><affiliation><nlm:affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Song" sort="Zhang, Song" uniqKey="Zhang S" first="Song" last="Zhang">Song Zhang</name><affiliation><nlm:affiliation>National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China.</nlm:affiliation></affiliation></author><author><name sortKey="Cao, Mengji" sort="Cao, Mengji" uniqKey="Cao M" first="Mengji" last="Cao">Mengji Cao</name><affiliation><nlm:affiliation>National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China. caomengji@cric.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Yang, Caixia" sort="Yang, Caixia" uniqKey="Yang C" first="Caixia" last="Yang">Caixia Yang</name><affiliation><nlm:affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China. xueyang27@126.com.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Archives of virology</title><idno type="eISSN">1432-8798</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Capsid Proteins (genetics)</term><term>China (MeSH)</term><term>Genome, Viral (genetics)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Plant Diseases (virology)</term><term>Plant Leaves (virology)</term><term>Prunus (virology)</term><term>RNA Replicase (genetics)</term><term>RNA, Viral (genetics)</term><term>Tymoviridae (classification)</term><term>Tymoviridae (genetics)</term><term>Tymoviridae (isolation & purification)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Capsid Proteins</term><term>RNA Replicase</term><term>RNA, Viral</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>China</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Tymoviridae</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome, Viral</term><term>Tymoviridae</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Tymoviridae</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Plant Diseases</term><term>Plant Leaves</term><term>Prunus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In September 2017, a yellow spot leaf disease was noted on the leaves of Prunus davidiana (Carr.) Franch. plants in Liaoning, China, and spherical virions (approx. 30 nm in diameter) were later observed in preparations of symptomatic leaves. Subsequent deep sequencing of small RNA revealed the presence of a virus in these symptomatic leaves The complete genome of this viral isolate consists of 6,072 nucleotides, excluding the poly(A) tail. The virus showed the closest genetic relationship to grapevine-associated tymo-like virus, reported in Colmar, France (GaTLV, MH383239), which is the sole member of the newly proposed genus "Gratylivirus" within the order Tymovirales, which is currently unassigned to a particular family. The virus clustered closely with GaTLV in a phylogenetic tree constructed based on complete genomic sequences. On the basis of the nucleotide and amino acid sequences of the replicase and coat protein genes, this virus shares the highest (although still relatively low) sequence similarity with those of GaTLV (41.6%-60.8% identity), indicating that the virus is a distinct member of the order Tymovirales, for which the name "prunus yellow spot-associated virus" (PYSaV) is proposed. To our knowledge, this is the first report of a virus naturally infecting P. davidiana.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30923968</PMID><DateCompleted><Year>2019</Year><Month>05</Month><Day>03</Day></DateCompleted><DateRevised><Year>2019</Year><Month>05</Month><Day>03</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-8798</ISSN><JournalIssue CitedMedium="Internet"><Volume>164</Volume><Issue>5</Issue><PubDate><Year>2019</Year><Month>May</Month></PubDate></JournalIssue><Title>Archives of virology</Title><ISOAbbreviation>Arch Virol</ISOAbbreviation></Journal><ArticleTitle>The complete nucleotide sequence and genome organization of a novel virus of the order Tymovirales isolated from Prunus davidiana (Carr.) Franch. in Liaoning, China.</ArticleTitle><Pagination><MedlinePgn>1245-1248</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00705-019-04220-1</ELocationID><Abstract><AbstractText>In September 2017, a yellow spot leaf disease was noted on the leaves of Prunus davidiana (Carr.) Franch. plants in Liaoning, China, and spherical virions (approx. 30 nm in diameter) were later observed in preparations of symptomatic leaves. Subsequent deep sequencing of small RNA revealed the presence of a virus in these symptomatic leaves The complete genome of this viral isolate consists of 6,072 nucleotides, excluding the poly(A) tail. The virus showed the closest genetic relationship to grapevine-associated tymo-like virus, reported in Colmar, France (GaTLV, MH383239), which is the sole member of the newly proposed genus "Gratylivirus" within the order Tymovirales, which is currently unassigned to a particular family. The virus clustered closely with GaTLV in a phylogenetic tree constructed based on complete genomic sequences. On the basis of the nucleotide and amino acid sequences of the replicase and coat protein genes, this virus shares the highest (although still relatively low) sequence similarity with those of GaTLV (41.6%-60.8% identity), indicating that the virus is a distinct member of the order Tymovirales, for which the name "prunus yellow spot-associated virus" (PYSaV) is proposed. To our knowledge, this is the first report of a virus naturally infecting P. davidiana.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hou</LastName><ForeName>Qiushi</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Han</LastName><ForeName>Tong</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Liang</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Junzhu</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yu</LastName><ForeName>Meichun</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Song</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cao</LastName><ForeName>Mengji</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China. caomengji@cric.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Caixia</ForeName><Initials>C</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-0574-2404</Identifier><AffiliationInfo><Affiliation>Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China. xueyang27@126.com.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>2015020806</GrantID><Agency>Natural Science Foundation of Liaoning Province</Agency><Country></Country></Grant><Grant><GrantID>20180550863</GrantID><Agency>Natural Science Foundation of Liaoning Province</Agency><Country></Country></Grant><Grant><GrantID>XDJK2018AA002</GrantID><Agency>the Fundamental Research Funds for the Central Universities</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>03</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>Austria</Country><MedlineTA>Arch Virol</MedlineTA><NlmUniqueID>7506870</NlmUniqueID><ISSNLinking>0304-8608</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D036022">Capsid Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012367">RNA, Viral</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.7.7.48</RegistryNumber><NameOfSubstance UI="D012324">RNA Replicase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D036022" MajorTopicYN="N">Capsid Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002681" MajorTopicYN="N" Type="Geographic">China</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018515" MajorTopicYN="N">Plant Leaves</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D027861" MajorTopicYN="N">Prunus</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012324" MajorTopicYN="N">RNA Replicase</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012367" MajorTopicYN="N">RNA, Viral</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D046830" MajorTopicYN="N">Tymoviridae</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>01</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>02</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>3</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>5</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>3</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30923968</ArticleId><ArticleId IdType="doi">10.1007/s00705-019-04220-1</ArticleId><ArticleId IdType="pii">10.1007/s00705-019-04220-1</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/GrapevineDiseaseV1/Data/Main/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000176 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Corpus/biblio.hfd -nk 000176 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= GrapevineDiseaseV1
|flux= Main
|étape= Corpus
|type= RBID
|clé= pubmed:30923968
|texte= The complete nucleotide sequence and genome organization of a novel virus of the order Tymovirales isolated from Prunus davidiana (Carr.) Franch. in Liaoning, China.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Corpus/RBID.i -Sk "pubmed:30923968" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a GrapevineDiseaseV1
| This area was generated with Dilib version V0.6.37. |  |