Genome characterization of fig umbra-like virus
The complete genome of a new umbra-like virus from edible fig ( Ficus carica ) was identified by high-throughput sequencing. Based on its similarity to umbra-like virus genome sequences available in GenBank, the proposed name of this new virus is “fig umbra-like virus” (FULV). The genome of full-len...
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| Veröffentlicht in: | Virus genes 2021-12, Vol.57 (6), p.566-570 |
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| creator | Wang, Xupeng Olmedo-Velarde, Alejandro Larrea-Sarmiento, Adriana Simon, Anne E. Kong, Alexandra Borth, Wayne Suzuki, Jon Y. Wall, Marisa M. Hu, John Melzer, Michael |
| description | The complete genome of a new umbra-like virus from edible fig (
Ficus carica
) was identified by high-throughput sequencing. Based on its similarity to umbra-like virus genome sequences available in GenBank, the proposed name of this new virus is “fig umbra-like virus” (FULV). The genome of full-length FULV-1 consists of 3049 nucleotides organized into three open reading frames (ORFs). Pairwise comparisons showed that the complete nucleotide sequence of the virus had the highest identity (71.3%) to citrus yellow vein-associated virus (CYVaV). In addition, phylogenetic trees based on whole-genome nucleotide sequences and amino acid sequences of the RNA-dependent RNA polymerase showed that FULV forms a monophyletic lineage with CYVaV and other umbra-like viruses. Based on the demarcation criteria of the genus
Umbravirus
, and lack of two umbravirus ORFs, we propose that FULV is a putative new member of the umbra-like virus clade within the family
Tombusviridae
. |
| doi_str_mv | 10.1007/s11262-021-01867-4 |
| format | Article |
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Ficus carica
) was identified by high-throughput sequencing. Based on its similarity to umbra-like virus genome sequences available in GenBank, the proposed name of this new virus is “fig umbra-like virus” (FULV). The genome of full-length FULV-1 consists of 3049 nucleotides organized into three open reading frames (ORFs). Pairwise comparisons showed that the complete nucleotide sequence of the virus had the highest identity (71.3%) to citrus yellow vein-associated virus (CYVaV). In addition, phylogenetic trees based on whole-genome nucleotide sequences and amino acid sequences of the RNA-dependent RNA polymerase showed that FULV forms a monophyletic lineage with CYVaV and other umbra-like viruses. Based on the demarcation criteria of the genus
Umbravirus
, and lack of two umbravirus ORFs, we propose that FULV is a putative new member of the umbra-like virus clade within the family
Tombusviridae
.</description><identifier>ISSN: 0920-8569</identifier><identifier>EISSN: 1572-994X</identifier><identifier>DOI: 10.1007/s11262-021-01867-4</identifier><identifier>PMID: 34524603</identifier><language>eng</language><publisher>New York: Springer US</publisher><subject>Animals ; Biomedical and Life Sciences ; Biomedicine ; Citrus ; DNA Viruses ; DNA-directed RNA polymerase ; Ficus ; Ficus carica ; Genome, Viral ; Genomes ; High-Throughput Nucleotide Sequencing ; Medical Microbiology ; Next-generation sequencing ; Nucleotide sequence ; Open Reading Frames ; Phylogeny ; Plant Sciences ; RNA polymerase ; RNA, Viral - genetics ; RNA-directed RNA polymerase ; Short Report ; Tombusviridae - genetics ; Umbridae ; Virology ; Viruses ; Viruses, Unclassified</subject><ispartof>Virus genes, 2021-12, Vol.57 (6), p.566-570</ispartof><rights>The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021</rights><rights>2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.</rights><rights>The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c375t-3e087a14e7b21fb8399039e43a5cb3874568b92cdde6482cd3822cd41361d0163</citedby><cites>FETCH-LOGICAL-c375t-3e087a14e7b21fb8399039e43a5cb3874568b92cdde6482cd3822cd41361d0163</cites><orcidid>0000-0003-3003-4140</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11262-021-01867-4$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11262-021-01867-4$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34524603$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Xupeng</creatorcontrib><creatorcontrib>Olmedo-Velarde, Alejandro</creatorcontrib><creatorcontrib>Larrea-Sarmiento, Adriana</creatorcontrib><creatorcontrib>Simon, Anne E.</creatorcontrib><creatorcontrib>Kong, Alexandra</creatorcontrib><creatorcontrib>Borth, Wayne</creatorcontrib><creatorcontrib>Suzuki, Jon Y.</creatorcontrib><creatorcontrib>Wall, Marisa M.</creatorcontrib><creatorcontrib>Hu, John</creatorcontrib><creatorcontrib>Melzer, Michael</creatorcontrib><title>Genome characterization of fig umbra-like virus</title><title>Virus genes</title><addtitle>Virus Genes</addtitle><addtitle>Virus Genes</addtitle><description>The complete genome of a new umbra-like virus from edible fig (
Ficus carica
) was identified by high-throughput sequencing. Based on its similarity to umbra-like virus genome sequences available in GenBank, the proposed name of this new virus is “fig umbra-like virus” (FULV). The genome of full-length FULV-1 consists of 3049 nucleotides organized into three open reading frames (ORFs). Pairwise comparisons showed that the complete nucleotide sequence of the virus had the highest identity (71.3%) to citrus yellow vein-associated virus (CYVaV). In addition, phylogenetic trees based on whole-genome nucleotide sequences and amino acid sequences of the RNA-dependent RNA polymerase showed that FULV forms a monophyletic lineage with CYVaV and other umbra-like viruses. Based on the demarcation criteria of the genus
Umbravirus
, and lack of two umbravirus ORFs, we propose that FULV is a putative new member of the umbra-like virus clade within the family
Tombusviridae
.</description><subject>Animals</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Citrus</subject><subject>DNA Viruses</subject><subject>DNA-directed RNA polymerase</subject><subject>Ficus</subject><subject>Ficus carica</subject><subject>Genome, Viral</subject><subject>Genomes</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Medical Microbiology</subject><subject>Next-generation sequencing</subject><subject>Nucleotide sequence</subject><subject>Open Reading Frames</subject><subject>Phylogeny</subject><subject>Plant Sciences</subject><subject>RNA polymerase</subject><subject>RNA, Viral - genetics</subject><subject>RNA-directed RNA polymerase</subject><subject>Short Report</subject><subject>Tombusviridae - genetics</subject><subject>Umbridae</subject><subject>Virology</subject><subject>Viruses</subject><subject>Viruses, Unclassified</subject><issn>0920-8569</issn><issn>1572-994X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp9kD1PwzAQhi0EoqXwBxhQJBYW0_NH_DEiBAWpEgtIbJaTOCUlH8VOkODXY0gBiYHFN_i59-4ehI4JnBMAOQ-EUEExUIKBKCEx30FTkkqKteaPu2gKmgJWqdATdBDCGgCUonwfTRhPKRfApmi-cG3XuCR_st7mvfPVu-2rrk26MimrVTI0mbe4rp5d8lr5IRyivdLWwR1t6ww9XF_dX97g5d3i9vJiiXMm0x4zB0pawp3MKCkzxbQGph1nNs0zpiRPhco0zYvCCa5iZYrGlxMmSAFEsBk6G3M3vnsZXOhNU4Xc1bVtXTcEQ-OZmnGtaURP_6DrbvBt3C5SWmoOKSGRoiOV-y4E70qz8VVj_ZshYD51mlGniTrNl07DY9PJNnrIGlf8tHz7iwAbgRC_2pXzv7P_if0AHGx9Tw</recordid><startdate>20211201</startdate><enddate>20211201</enddate><creator>Wang, Xupeng</creator><creator>Olmedo-Velarde, Alejandro</creator><creator>Larrea-Sarmiento, Adriana</creator><creator>Simon, Anne E.</creator><creator>Kong, Alexandra</creator><creator>Borth, Wayne</creator><creator>Suzuki, Jon Y.</creator><creator>Wall, Marisa M.</creator><creator>Hu, John</creator><creator>Melzer, Michael</creator><general>Springer US</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-3003-4140</orcidid></search><sort><creationdate>20211201</creationdate><title>Genome characterization of fig umbra-like virus</title><author>Wang, Xupeng ; Olmedo-Velarde, Alejandro ; Larrea-Sarmiento, Adriana ; Simon, Anne E. ; Kong, Alexandra ; Borth, Wayne ; Suzuki, Jon Y. ; Wall, Marisa M. ; Hu, John ; Melzer, Michael</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c375t-3e087a14e7b21fb8399039e43a5cb3874568b92cdde6482cd3822cd41361d0163</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Animals</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedicine</topic><topic>Citrus</topic><topic>DNA Viruses</topic><topic>DNA-directed RNA polymerase</topic><topic>Ficus</topic><topic>Ficus carica</topic><topic>Genome, Viral</topic><topic>Genomes</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Medical Microbiology</topic><topic>Next-generation sequencing</topic><topic>Nucleotide sequence</topic><topic>Open Reading Frames</topic><topic>Phylogeny</topic><topic>Plant Sciences</topic><topic>RNA polymerase</topic><topic>RNA, Viral - genetics</topic><topic>RNA-directed RNA polymerase</topic><topic>Short Report</topic><topic>Tombusviridae - genetics</topic><topic>Umbridae</topic><topic>Virology</topic><topic>Viruses</topic><topic>Viruses, Unclassified</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Xupeng</creatorcontrib><creatorcontrib>Olmedo-Velarde, Alejandro</creatorcontrib><creatorcontrib>Larrea-Sarmiento, Adriana</creatorcontrib><creatorcontrib>Simon, Anne E.</creatorcontrib><creatorcontrib>Kong, Alexandra</creatorcontrib><creatorcontrib>Borth, Wayne</creatorcontrib><creatorcontrib>Suzuki, Jon Y.</creatorcontrib><creatorcontrib>Wall, Marisa M.</creatorcontrib><creatorcontrib>Hu, John</creatorcontrib><creatorcontrib>Melzer, Michael</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>ProQuest Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Virus genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Xupeng</au><au>Olmedo-Velarde, Alejandro</au><au>Larrea-Sarmiento, Adriana</au><au>Simon, Anne E.</au><au>Kong, Alexandra</au><au>Borth, Wayne</au><au>Suzuki, Jon Y.</au><au>Wall, Marisa M.</au><au>Hu, John</au><au>Melzer, Michael</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome characterization of fig umbra-like virus</atitle><jtitle>Virus genes</jtitle><stitle>Virus Genes</stitle><addtitle>Virus Genes</addtitle><date>2021-12-01</date><risdate>2021</risdate><volume>57</volume><issue>6</issue><spage>566</spage><epage>570</epage><pages>566-570</pages><issn>0920-8569</issn><eissn>1572-994X</eissn><abstract>The complete genome of a new umbra-like virus from edible fig (
Ficus carica
) was identified by high-throughput sequencing. Based on its similarity to umbra-like virus genome sequences available in GenBank, the proposed name of this new virus is “fig umbra-like virus” (FULV). The genome of full-length FULV-1 consists of 3049 nucleotides organized into three open reading frames (ORFs). Pairwise comparisons showed that the complete nucleotide sequence of the virus had the highest identity (71.3%) to citrus yellow vein-associated virus (CYVaV). In addition, phylogenetic trees based on whole-genome nucleotide sequences and amino acid sequences of the RNA-dependent RNA polymerase showed that FULV forms a monophyletic lineage with CYVaV and other umbra-like viruses. Based on the demarcation criteria of the genus
Umbravirus
, and lack of two umbravirus ORFs, we propose that FULV is a putative new member of the umbra-like virus clade within the family
Tombusviridae
.</abstract><cop>New York</cop><pub>Springer US</pub><pmid>34524603</pmid><doi>10.1007/s11262-021-01867-4</doi><tpages>5</tpages><orcidid>https://orcid.org/0000-0003-3003-4140</orcidid></addata></record> |
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| ispartof | Virus genes, 2021-12, Vol.57 (6), p.566-570 |
| issn | 0920-8569 1572-994X |
| language | eng |
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| source | MEDLINE; SpringerLink Journals - AutoHoldings |
| subjects | Animals Biomedical and Life Sciences Biomedicine Citrus DNA Viruses DNA-directed RNA polymerase Ficus Ficus carica Genome, Viral Genomes High-Throughput Nucleotide Sequencing Medical Microbiology Next-generation sequencing Nucleotide sequence Open Reading Frames Phylogeny Plant Sciences RNA polymerase RNA, Viral - genetics RNA-directed RNA polymerase Short Report Tombusviridae - genetics Umbridae Virology Viruses Viruses, Unclassified |
| title | Genome characterization of fig umbra-like virus |
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