Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae
Abstract In the attempt to identify the causal agent of Citrus chlorotic dwarf disease (CCDD), a virus-like disorder of citrus, the small RNA fraction and total DNA from symptomatic citrus plants were subjected to high-throughput sequencing. DNA fragments deriving from an apparently new geminivirus-...
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| Veröffentlicht in: | Virology (New York, N.Y.) N.Y.), 2012-10, Vol.432 (1), p.162-172 |
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| container_title | Virology (New York, N.Y.) |
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| creator | Loconsole, Giuliana Saldarelli, Pasquale Doddapaneni, Harshavardhan Savino, Vito Martelli, Giovanni P Saponari, Maria |
| description | Abstract In the attempt to identify the causal agent of Citrus chlorotic dwarf disease (CCDD), a virus-like disorder of citrus, the small RNA fraction and total DNA from symptomatic citrus plants were subjected to high-throughput sequencing. DNA fragments deriving from an apparently new geminivirus-like agent were found and assembled by NGS to re-construct the entire viral genome. The newly identified virus has a circular single-stranded DNA genome comprising five open reading frames (ORFs) with sequence homologies with those encoded by geminiviruses. PCR and qPCR assays were successfully used for determining its presence in the CCDD-affected plants obtained by graft propagation. The larger genome size (3.64 vs. 2.5–3.0 kb) and a number of differences in its structural organization, identified this virus as a highly divergent member of the family Geminiviridae , to which the provisional name of Citrus chlorotic dwarf-associated virus (CCDaV) is assigned. |
| doi_str_mv | 10.1016/j.virol.2012.06.005 |
| format | Article |
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DNA fragments deriving from an apparently new geminivirus-like agent were found and assembled by NGS to re-construct the entire viral genome. The newly identified virus has a circular single-stranded DNA genome comprising five open reading frames (ORFs) with sequence homologies with those encoded by geminiviruses. PCR and qPCR assays were successfully used for determining its presence in the CCDD-affected plants obtained by graft propagation. The larger genome size (3.64 vs. 2.5–3.0 kb) and a number of differences in its structural organization, identified this virus as a highly divergent member of the family Geminiviridae , to which the provisional name of Citrus chlorotic dwarf-associated virus (CCDaV) is assigned.</description><identifier>ISSN: 0042-6822</identifier><identifier>EISSN: 1096-0341</identifier><identifier>DOI: 10.1016/j.virol.2012.06.005</identifier><identifier>PMID: 22749878</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Citrus - virology ; Citrus chlorotic dwarf disease ; DNA, Single-Stranded - genetics ; DNA, Viral - chemistry ; DNA, Viral - genetics ; Geminiviridae - classification ; Geminiviridae - genetics ; Geminiviridae - isolation & purification ; Geminivirus ; Genome, Viral ; High-throughput sequencing ; Infectious Disease ; Molecular Sequence Data ; Open Reading Frames ; Plant Diseases - virology ; Sequence Analysis, DNA ; ssDNA</subject><ispartof>Virology (New York, N.Y.), 2012-10, Vol.432 (1), p.162-172</ispartof><rights>Elsevier Inc.</rights><rights>2012 Elsevier Inc.</rights><rights>Copyright © 2012 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c509t-ca4e09f5ec785f45df873580988e24038c1143b891669f20cf7be6c2c9fc6de43</citedby><cites>FETCH-LOGICAL-c509t-ca4e09f5ec785f45df873580988e24038c1143b891669f20cf7be6c2c9fc6de43</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.virol.2012.06.005$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22749878$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Loconsole, Giuliana</creatorcontrib><creatorcontrib>Saldarelli, Pasquale</creatorcontrib><creatorcontrib>Doddapaneni, Harshavardhan</creatorcontrib><creatorcontrib>Savino, Vito</creatorcontrib><creatorcontrib>Martelli, Giovanni P</creatorcontrib><creatorcontrib>Saponari, Maria</creatorcontrib><title>Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae</title><title>Virology (New York, N.Y.)</title><addtitle>Virology</addtitle><description>Abstract In the attempt to identify the causal agent of Citrus chlorotic dwarf disease (CCDD), a virus-like disorder of citrus, the small RNA fraction and total DNA from symptomatic citrus plants were subjected to high-throughput sequencing. DNA fragments deriving from an apparently new geminivirus-like agent were found and assembled by NGS to re-construct the entire viral genome. The newly identified virus has a circular single-stranded DNA genome comprising five open reading frames (ORFs) with sequence homologies with those encoded by geminiviruses. PCR and qPCR assays were successfully used for determining its presence in the CCDD-affected plants obtained by graft propagation. The larger genome size (3.64 vs. 2.5–3.0 kb) and a number of differences in its structural organization, identified this virus as a highly divergent member of the family Geminiviridae , to which the provisional name of Citrus chlorotic dwarf-associated virus (CCDaV) is assigned.</description><subject>Citrus - virology</subject><subject>Citrus chlorotic dwarf disease</subject><subject>DNA, Single-Stranded - genetics</subject><subject>DNA, Viral - chemistry</subject><subject>DNA, Viral - genetics</subject><subject>Geminiviridae - classification</subject><subject>Geminiviridae - genetics</subject><subject>Geminiviridae - isolation & purification</subject><subject>Geminivirus</subject><subject>Genome, Viral</subject><subject>High-throughput sequencing</subject><subject>Infectious Disease</subject><subject>Molecular Sequence Data</subject><subject>Open Reading Frames</subject><subject>Plant Diseases - virology</subject><subject>Sequence Analysis, DNA</subject><subject>ssDNA</subject><issn>0042-6822</issn><issn>1096-0341</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFUk1v1DAQjRCILoVfgIR85NAsYydxkgNIVQulUgUH4Gx57TE7SxIX2-lq_0B_Nw5bOHDhZHn0PjTvTVG85LDmwOWb3fqOgh_WArhYg1wDNI-KFYdellDV_HGxAqhFKTshTopnMe4g_9sWnhYnQrR137Xdqri_tjglcmR0Ij8x75hmkabvA5YxBT1ZtOzy0znLXnNkOkZvSKc83FPaMkNpGZvt4INPZJjd6-CYpYg64lnWmnDPRhw3GBhNLG2ROT3ScGBXONJEWZasxufFE6eHiC8e3tPi24f3Xy8-ljefr64vzm9K00CfSqNrhN41aNqucXVjXddWTQd916GooeoM53W16XouZe8EGNduUBphemekxbo6LV4fdW-D_zljTGqkaHAY9IR-joqDaHNgjRAZWh2hJvgYAzp1G2jU4ZBBailA7dTvAtRSgAKpcgGZ9erBYN6MaP9y_iSeAW-PAMxr3hEGFQ3hZNBSQJOU9fQfg3f_8M2QczR6-IEHjDs_hyknqLiKmaO-LDewnAAXABVIWf0CBeCuhg</recordid><startdate>20121010</startdate><enddate>20121010</enddate><creator>Loconsole, Giuliana</creator><creator>Saldarelli, Pasquale</creator><creator>Doddapaneni, Harshavardhan</creator><creator>Savino, Vito</creator><creator>Martelli, Giovanni P</creator><creator>Saponari, Maria</creator><general>Elsevier Inc</general><scope>6I.</scope><scope>AAFTH</scope><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>7X8</scope></search><sort><creationdate>20121010</creationdate><title>Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae</title><author>Loconsole, Giuliana ; Saldarelli, Pasquale ; Doddapaneni, Harshavardhan ; Savino, Vito ; Martelli, Giovanni P ; Saponari, Maria</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c509t-ca4e09f5ec785f45df873580988e24038c1143b891669f20cf7be6c2c9fc6de43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Citrus - virology</topic><topic>Citrus chlorotic dwarf disease</topic><topic>DNA, Single-Stranded - genetics</topic><topic>DNA, Viral - chemistry</topic><topic>DNA, Viral - genetics</topic><topic>Geminiviridae - classification</topic><topic>Geminiviridae - genetics</topic><topic>Geminiviridae - isolation & purification</topic><topic>Geminivirus</topic><topic>Genome, Viral</topic><topic>High-throughput sequencing</topic><topic>Infectious Disease</topic><topic>Molecular Sequence Data</topic><topic>Open Reading Frames</topic><topic>Plant Diseases - virology</topic><topic>Sequence Analysis, DNA</topic><topic>ssDNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Loconsole, Giuliana</creatorcontrib><creatorcontrib>Saldarelli, Pasquale</creatorcontrib><creatorcontrib>Doddapaneni, Harshavardhan</creatorcontrib><creatorcontrib>Savino, Vito</creatorcontrib><creatorcontrib>Martelli, Giovanni P</creatorcontrib><creatorcontrib>Saponari, Maria</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Virology (New York, N.Y.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Loconsole, Giuliana</au><au>Saldarelli, Pasquale</au><au>Doddapaneni, Harshavardhan</au><au>Savino, Vito</au><au>Martelli, Giovanni P</au><au>Saponari, Maria</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae</atitle><jtitle>Virology (New York, N.Y.)</jtitle><addtitle>Virology</addtitle><date>2012-10-10</date><risdate>2012</risdate><volume>432</volume><issue>1</issue><spage>162</spage><epage>172</epage><pages>162-172</pages><issn>0042-6822</issn><eissn>1096-0341</eissn><abstract>Abstract In the attempt to identify the causal agent of Citrus chlorotic dwarf disease (CCDD), a virus-like disorder of citrus, the small RNA fraction and total DNA from symptomatic citrus plants were subjected to high-throughput sequencing. 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| subjects | Citrus - virology Citrus chlorotic dwarf disease DNA, Single-Stranded - genetics DNA, Viral - chemistry DNA, Viral - genetics Geminiviridae - classification Geminiviridae - genetics Geminiviridae - isolation & purification Geminivirus Genome, Viral High-throughput sequencing Infectious Disease Molecular Sequence Data Open Reading Frames Plant Diseases - virology Sequence Analysis, DNA ssDNA |
| title | Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae |
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