The partial sequence of RNA 1 of the ophiovirus Ranunculus white mottle virus indicates its relationship to rhabdoviruses and provides candidate primers for an ophiovirus-specific RT-PCR test
A 4018 nucleotide sequence was obtained for RNA 1 of Ranunculus white mottle virus (RWMV), genus Ophiovirus, representing an incomplete ORF of 1339 aa. Amino acid sequence analysis revealed significant similarities with RNA polymerases of viruses in the family Rhabdoviridae and a conserved domain of...
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| Veröffentlicht in: | Archives of virology 2003-06, Vol.148 (6), p.1037-1050 |
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| creator | VAIRA, A. M ACCOTTO, G. P COSTANTINI, A MILNE, R. G |
| description | A 4018 nucleotide sequence was obtained for RNA 1 of Ranunculus white mottle virus (RWMV), genus Ophiovirus, representing an incomplete ORF of 1339 aa. Amino acid sequence analysis revealed significant similarities with RNA polymerases of viruses in the family Rhabdoviridae and a conserved domain of 685 aa, corresponding to the RdRp domain of those in the order Mononegavirales. Phylogenetic analysis indicated that the genus Ophiovirus is not related to the genus Tenuivirus or the family Bunyaviridae, with which it has been linked, and probably deserves a special taxonomic position, within a new family. A pair of degenerate primers was designed from a consensus sequence obtained from a relatively conserved region in the RNA 1 of two members of the genus, Citrus psorosis virus (CPsV) and RWMV. The primers, used in RT-PCR experiments, amplified a 136 bp DNA fragment from all the three recognized members of the genus, i.e. CPsV, RWMV and Tulip mild mottle mosaic virus (TMMMV) and from two tentative ophioviruses from lettuce and freesia. The amplified DNAs were sequenced and compared with the corresponding sequences of CPsV and RWMV and phylogenetic relationships were evaluated. Assays using extracts from plants infected by viruses belonging to the genera Tospovirus, Tenuivirus, Rhabdovirus and Varicosavirus indicated that the primers are genus-specific. |
| doi_str_mv | 10.1007/s00705-003-0016-x |
| format | Article |
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The primers, used in RT-PCR experiments, amplified a 136 bp DNA fragment from all the three recognized members of the genus, i.e. CPsV, RWMV and Tulip mild mottle mosaic virus (TMMMV) and from two tentative ophioviruses from lettuce and freesia. The amplified DNAs were sequenced and compared with the corresponding sequences of CPsV and RWMV and phylogenetic relationships were evaluated. Assays using extracts from plants infected by viruses belonging to the genera Tospovirus, Tenuivirus, Rhabdovirus and Varicosavirus indicated that the primers are genus-specific.</description><identifier>ISSN: 0304-8608</identifier><identifier>EISSN: 1432-8798</identifier><identifier>DOI: 10.1007/s00705-003-0016-x</identifier><identifier>PMID: 12756613</identifier><language>eng</language><publisher>Wien: Springer</publisher><subject>Amino Acid Sequence ; Biological and medical sciences ; Cloning ; DNA Primers - genetics ; Experiments ; Fundamental and applied biological sciences. Psychology ; Genes, Viral - genetics ; Genetics ; Lettuce ; Microbiology ; Molecular Sequence Data ; Phylogenetics ; Phylogeny ; Plant Diseases - virology ; Ranunculus - virology ; Reverse Transcriptase Polymerase Chain Reaction - methods ; Rhabdoviridae - genetics ; RNA polymerase ; RNA Viruses - chemistry ; RNA Viruses - classification ; RNA Viruses - genetics ; RNA, Viral - genetics ; Sensitivity and Specificity ; Sequence Alignment ; Taxonomy ; Virology ; Viruses</subject><ispartof>Archives of virology, 2003-06, Vol.148 (6), p.1037-1050</ispartof><rights>2003 INIST-CNRS</rights><rights>Copyright Springer-Verlag 2003</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c451t-22d378248e0bdd580d78797e7f18a02c4dee106366fe890f57523e0ae75a78b13</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=14852880$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/12756613$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>VAIRA, A. M</creatorcontrib><creatorcontrib>ACCOTTO, G. P</creatorcontrib><creatorcontrib>COSTANTINI, A</creatorcontrib><creatorcontrib>MILNE, R. G</creatorcontrib><title>The partial sequence of RNA 1 of the ophiovirus Ranunculus white mottle virus indicates its relationship to rhabdoviruses and provides candidate primers for an ophiovirus-specific RT-PCR test</title><title>Archives of virology</title><addtitle>Arch Virol</addtitle><description>A 4018 nucleotide sequence was obtained for RNA 1 of Ranunculus white mottle virus (RWMV), genus Ophiovirus, representing an incomplete ORF of 1339 aa. Amino acid sequence analysis revealed significant similarities with RNA polymerases of viruses in the family Rhabdoviridae and a conserved domain of 685 aa, corresponding to the RdRp domain of those in the order Mononegavirales. Phylogenetic analysis indicated that the genus Ophiovirus is not related to the genus Tenuivirus or the family Bunyaviridae, with which it has been linked, and probably deserves a special taxonomic position, within a new family. A pair of degenerate primers was designed from a consensus sequence obtained from a relatively conserved region in the RNA 1 of two members of the genus, Citrus psorosis virus (CPsV) and RWMV. The primers, used in RT-PCR experiments, amplified a 136 bp DNA fragment from all the three recognized members of the genus, i.e. CPsV, RWMV and Tulip mild mottle mosaic virus (TMMMV) and from two tentative ophioviruses from lettuce and freesia. The amplified DNAs were sequenced and compared with the corresponding sequences of CPsV and RWMV and phylogenetic relationships were evaluated. Assays using extracts from plants infected by viruses belonging to the genera Tospovirus, Tenuivirus, Rhabdovirus and Varicosavirus indicated that the primers are genus-specific.</description><subject>Amino Acid Sequence</subject><subject>Biological and medical sciences</subject><subject>Cloning</subject><subject>DNA Primers - genetics</subject><subject>Experiments</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes, Viral - genetics</subject><subject>Genetics</subject><subject>Lettuce</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant Diseases - virology</subject><subject>Ranunculus - virology</subject><subject>Reverse Transcriptase Polymerase Chain Reaction - methods</subject><subject>Rhabdoviridae - genetics</subject><subject>RNA polymerase</subject><subject>RNA Viruses - chemistry</subject><subject>RNA Viruses - classification</subject><subject>RNA Viruses - genetics</subject><subject>RNA, Viral - genetics</subject><subject>Sensitivity and Specificity</subject><subject>Sequence Alignment</subject><subject>Taxonomy</subject><subject>Virology</subject><subject>Viruses</subject><issn>0304-8608</issn><issn>1432-8798</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2003</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFks2O1DAMgCMEYmcXHoALipDgVshP26TH1Yg_aQVoNJyjTOKqWXWakqTs8nS8Gh51pEVcOMSxk892YpuQF5y95YypdxkFayrGJC7eVvePyIbXUlRadfox2TDJ6kq3TF-Qy5xvGYJMNk_JBReqaVsuN-T3fgA621SCHWmGHwtMDmjs6e7LNeUnpSAQ5yHEnyEtme7stExuGVG9G0IBeoyljEDX2zD54GwB1EqmCUZbQpzyEGZaIk2DPfg1DhJ28nROaHo0HFrBoycehSOkTPuYEPkrdZVncKEPju721bftjmKa8ow86e2Y4fl5vyLfP7zfbz9VN18_ft5e31SubniphPBSaVFrYAfvG828whopUD3XlglXewDOWtm2PeiO9Y1qhARmQTVW6QOXV-TNGhdfjEXKxRxDdjCOdoK4ZKOk0Ix3_wc55u1ULRB89Q94G5c04SeM4KLmqmslQnyFXIo5J-jNqTw2_TKcmdMMmHUGDLbWnGbA3KPPy3Pg5XAE_-BxbjoCr8-Azc6OfbKTC_mBq3UjtGbyD_9XvNg</recordid><startdate>20030601</startdate><enddate>20030601</enddate><creator>VAIRA, A. 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M</au><au>ACCOTTO, G. P</au><au>COSTANTINI, A</au><au>MILNE, R. G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The partial sequence of RNA 1 of the ophiovirus Ranunculus white mottle virus indicates its relationship to rhabdoviruses and provides candidate primers for an ophiovirus-specific RT-PCR test</atitle><jtitle>Archives of virology</jtitle><addtitle>Arch Virol</addtitle><date>2003-06-01</date><risdate>2003</risdate><volume>148</volume><issue>6</issue><spage>1037</spage><epage>1050</epage><pages>1037-1050</pages><issn>0304-8608</issn><eissn>1432-8798</eissn><abstract>A 4018 nucleotide sequence was obtained for RNA 1 of Ranunculus white mottle virus (RWMV), genus Ophiovirus, representing an incomplete ORF of 1339 aa. Amino acid sequence analysis revealed significant similarities with RNA polymerases of viruses in the family Rhabdoviridae and a conserved domain of 685 aa, corresponding to the RdRp domain of those in the order Mononegavirales. Phylogenetic analysis indicated that the genus Ophiovirus is not related to the genus Tenuivirus or the family Bunyaviridae, with which it has been linked, and probably deserves a special taxonomic position, within a new family. A pair of degenerate primers was designed from a consensus sequence obtained from a relatively conserved region in the RNA 1 of two members of the genus, Citrus psorosis virus (CPsV) and RWMV. The primers, used in RT-PCR experiments, amplified a 136 bp DNA fragment from all the three recognized members of the genus, i.e. CPsV, RWMV and Tulip mild mottle mosaic virus (TMMMV) and from two tentative ophioviruses from lettuce and freesia. The amplified DNAs were sequenced and compared with the corresponding sequences of CPsV and RWMV and phylogenetic relationships were evaluated. 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| ispartof | Archives of virology, 2003-06, Vol.148 (6), p.1037-1050 |
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| subjects | Amino Acid Sequence Biological and medical sciences Cloning DNA Primers - genetics Experiments Fundamental and applied biological sciences. Psychology Genes, Viral - genetics Genetics Lettuce Microbiology Molecular Sequence Data Phylogenetics Phylogeny Plant Diseases - virology Ranunculus - virology Reverse Transcriptase Polymerase Chain Reaction - methods Rhabdoviridae - genetics RNA polymerase RNA Viruses - chemistry RNA Viruses - classification RNA Viruses - genetics RNA, Viral - genetics Sensitivity and Specificity Sequence Alignment Taxonomy Virology Viruses |
| title | The partial sequence of RNA 1 of the ophiovirus Ranunculus white mottle virus indicates its relationship to rhabdoviruses and provides candidate primers for an ophiovirus-specific RT-PCR test |
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