First complete genomic characterization and phylogeny of a new recombinant of tomato yellow leaf curl virus (genus Begomovirus, family Geminiviridae) from Kuwait
While whitefly-transmitted begomoviruses are economically important constraints to tomato production in Kuwait, little is known about genomic features of these viruses from Kuwait. A begomovirus isolated from severely diseased tomatoes, collected over a two-year period in the main tomato-growing are...
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| Veröffentlicht in: | Archives of virology 2015-07, Vol.160 (7), p.1823-1826 |
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| creator | Al-Ali, Ebtisam H. M Al-Hashash, Hanadi K Ben-Hejji, Ahmed H Al-Shayjji, Nabella Al-Aqeel, Hamed A |
| description | While whitefly-transmitted begomoviruses are economically important constraints to tomato production in Kuwait, little is known about genomic features of these viruses from Kuwait. A begomovirus isolated from severely diseased tomatoes, collected over a two-year period in the main tomato-growing areas of Kuwait, was characterized at the molecular level. The complete genomic sequence of the begomovirus was determined, and phlylogeographic studies were conducted to better understand genetic diversity of the virus in the region. Based on genome properties and phylogenetic analysis, the begomovirus was found to be a strain of tomato yellow leaf curl virus (TYLCV). The virus genome was monopartite, as neither DNA B nor satellite DNA molecules were detected. Two isolates characterized in this study shared 97 % and 95 % nucleotide sequence identity with a previously characterized Kuwaiti isolate, TYLCV-KISR. Among TYLCV isolates with known genome sequences, the Kuwaiti isolates shared highest sequence identity (95 %) with TYLCV-Almeria (Spain). Genetic diversity and phylogenetic analysis showed that the three Kuwaiti isolates formed a distinct clade that was separate from those of known TYLCV sequences. One Kuwaiti isolate (KW 1-3) could be a novel variant of TYLCV. Two recombination events were detected in the genome sequence of KW 1-3, which appeared to be a recombinant derived from TYLCV parents from Oman and Kuwait. |
| doi_str_mv | 10.1007/s00705-015-2427-x |
| format | Article |
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M ; Al-Hashash, Hanadi K ; Ben-Hejji, Ahmed H ; Al-Shayjji, Nabella ; Al-Aqeel, Hamed A</creator><creatorcontrib>Al-Ali, Ebtisam H. M ; Al-Hashash, Hanadi K ; Ben-Hejji, Ahmed H ; Al-Shayjji, Nabella ; Al-Aqeel, Hamed A</creatorcontrib><description>While whitefly-transmitted begomoviruses are economically important constraints to tomato production in Kuwait, little is known about genomic features of these viruses from Kuwait. A begomovirus isolated from severely diseased tomatoes, collected over a two-year period in the main tomato-growing areas of Kuwait, was characterized at the molecular level. The complete genomic sequence of the begomovirus was determined, and phlylogeographic studies were conducted to better understand genetic diversity of the virus in the region. Based on genome properties and phylogenetic analysis, the begomovirus was found to be a strain of tomato yellow leaf curl virus (TYLCV). The virus genome was monopartite, as neither DNA B nor satellite DNA molecules were detected. Two isolates characterized in this study shared 97 % and 95 % nucleotide sequence identity with a previously characterized Kuwaiti isolate, TYLCV-KISR. Among TYLCV isolates with known genome sequences, the Kuwaiti isolates shared highest sequence identity (95 %) with TYLCV-Almeria (Spain). Genetic diversity and phylogenetic analysis showed that the three Kuwaiti isolates formed a distinct clade that was separate from those of known TYLCV sequences. One Kuwaiti isolate (KW 1-3) could be a novel variant of TYLCV. Two recombination events were detected in the genome sequence of KW 1-3, which appeared to be a recombinant derived from TYLCV parents from Oman and Kuwait.</description><identifier>ISSN: 0304-8608</identifier><identifier>EISSN: 1432-8798</identifier><identifier>DOI: 10.1007/s00705-015-2427-x</identifier><identifier>PMID: 25951968</identifier><language>eng</language><publisher>Vienna: Springer Vienna</publisher><subject>Animals ; Annotated Sequence Record ; Base Sequence ; Begomovirus ; Begomovirus - classification ; Begomovirus - genetics ; Begomovirus - isolation & purification ; Biomedical and Life Sciences ; Biomedicine ; crop production ; DNA ; Enzymes ; Geminiviridae ; Genetic diversity ; Genetic Variation ; genome ; Genome, Viral ; Genomes ; Genomics ; Hemiptera - virology ; Infectious Diseases ; Insect Vectors - parasitology ; Insect Vectors - virology ; Kuwait ; Lycopersicon esculentum ; Lycopersicon esculentum - virology ; Medical Microbiology ; Molecular Sequence Data ; parents ; Phylogenetics ; Phylogeny ; Plant Diseases - parasitology ; Plant Diseases - virology ; Proteins ; satellite DNA ; sequence analysis ; Tomato yellow leaf curl virus ; tomatoes ; Virology ; Viruses</subject><ispartof>Archives of virology, 2015-07, Vol.160 (7), p.1823-1826</ispartof><rights>Springer-Verlag Wien 2015</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c429t-49f1bc06c75b3ff716da1bfbf571391290f840ab67207b22b1a6d096fd48ed0e3</citedby><cites>FETCH-LOGICAL-c429t-49f1bc06c75b3ff716da1bfbf571391290f840ab67207b22b1a6d096fd48ed0e3</cites><orcidid>0000-0002-4365-8676</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/s00705-015-2427-x$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00705-015-2427-x$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27903,27904,41467,42536,51297</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25951968$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Al-Ali, Ebtisam H. M</creatorcontrib><creatorcontrib>Al-Hashash, Hanadi K</creatorcontrib><creatorcontrib>Ben-Hejji, Ahmed H</creatorcontrib><creatorcontrib>Al-Shayjji, Nabella</creatorcontrib><creatorcontrib>Al-Aqeel, Hamed A</creatorcontrib><title>First complete genomic characterization and phylogeny of a new recombinant of tomato yellow leaf curl virus (genus Begomovirus, family Geminiviridae) from Kuwait</title><title>Archives of virology</title><addtitle>Arch Virol</addtitle><addtitle>Arch Virol</addtitle><description>While whitefly-transmitted begomoviruses are economically important constraints to tomato production in Kuwait, little is known about genomic features of these viruses from Kuwait. A begomovirus isolated from severely diseased tomatoes, collected over a two-year period in the main tomato-growing areas of Kuwait, was characterized at the molecular level. The complete genomic sequence of the begomovirus was determined, and phlylogeographic studies were conducted to better understand genetic diversity of the virus in the region. Based on genome properties and phylogenetic analysis, the begomovirus was found to be a strain of tomato yellow leaf curl virus (TYLCV). The virus genome was monopartite, as neither DNA B nor satellite DNA molecules were detected. Two isolates characterized in this study shared 97 % and 95 % nucleotide sequence identity with a previously characterized Kuwaiti isolate, TYLCV-KISR. Among TYLCV isolates with known genome sequences, the Kuwaiti isolates shared highest sequence identity (95 %) with TYLCV-Almeria (Spain). Genetic diversity and phylogenetic analysis showed that the three Kuwaiti isolates formed a distinct clade that was separate from those of known TYLCV sequences. One Kuwaiti isolate (KW 1-3) could be a novel variant of TYLCV. Two recombination events were detected in the genome sequence of KW 1-3, which appeared to be a recombinant derived from TYLCV parents from Oman and Kuwait.</description><subject>Animals</subject><subject>Annotated Sequence Record</subject><subject>Base Sequence</subject><subject>Begomovirus</subject><subject>Begomovirus - classification</subject><subject>Begomovirus - genetics</subject><subject>Begomovirus - isolation & purification</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>crop production</subject><subject>DNA</subject><subject>Enzymes</subject><subject>Geminiviridae</subject><subject>Genetic diversity</subject><subject>Genetic Variation</subject><subject>genome</subject><subject>Genome, Viral</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Hemiptera - virology</subject><subject>Infectious Diseases</subject><subject>Insect Vectors - parasitology</subject><subject>Insect Vectors - virology</subject><subject>Kuwait</subject><subject>Lycopersicon esculentum</subject><subject>Lycopersicon esculentum - virology</subject><subject>Medical Microbiology</subject><subject>Molecular Sequence Data</subject><subject>parents</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant Diseases - parasitology</subject><subject>Plant Diseases - virology</subject><subject>Proteins</subject><subject>satellite DNA</subject><subject>sequence analysis</subject><subject>Tomato yellow leaf curl virus</subject><subject>tomatoes</subject><subject>Virology</subject><subject>Viruses</subject><issn>0304-8608</issn><issn>1432-8798</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</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>eNqFkc1u1DAUhSMEokPhAdiAJTZFInCv82N7CRUtiEosoGvLSeypq8QebIdpeBveFA8pCLGAja90_J1jXZ-ieIzwEgHYq5gPaErApqQ1ZeXNnWKDdUVLzgS_W2yggrrkLfCj4kGM1wBZqJr7xRFtRIOi5Zvi-5kNMZHeT7tRJ0222vnJ9qS_UkH1SQf7TSXrHVFuILurZfSZWIg3RBGn9yTobO2sUy4dxOQnlTxZ9Dj6PRm1MqSfw0i-2jBHcpK9ebzRWz_5n9ILYtRkx4Wc68k6mzU7KP2cmOAn8mHeK5seFveMGqN-dDuPi8uzt59P35UXH8_fn76-KPuailTWwmDXQ9uzpquMYdgOCjvTmYZhJZAKMLwG1bWMAuso7VC1A4jWDDXXA-jquDhZc3fBf5l1THKysc-LKKf9HCUywJo3HOH_aMt5_uwGm4w--wu99nNweZFMCUGxYpRmCleqDz7GoI3cBTupsEgEeaharlXLXLU8VC1vsufJbfLcTXr47fjVbQboCsR85bY6_PH0P1KfriajvFTbYKO8_EQBWwCkrGa0-gEw8r_p</recordid><startdate>20150701</startdate><enddate>20150701</enddate><creator>Al-Ali, Ebtisam H. 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M</au><au>Al-Hashash, Hanadi K</au><au>Ben-Hejji, Ahmed H</au><au>Al-Shayjji, Nabella</au><au>Al-Aqeel, Hamed A</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>First complete genomic characterization and phylogeny of a new recombinant of tomato yellow leaf curl virus (genus Begomovirus, family Geminiviridae) from Kuwait</atitle><jtitle>Archives of virology</jtitle><stitle>Arch Virol</stitle><addtitle>Arch Virol</addtitle><date>2015-07-01</date><risdate>2015</risdate><volume>160</volume><issue>7</issue><spage>1823</spage><epage>1826</epage><pages>1823-1826</pages><issn>0304-8608</issn><eissn>1432-8798</eissn><abstract>While whitefly-transmitted begomoviruses are economically important constraints to tomato production in Kuwait, little is known about genomic features of these viruses from Kuwait. A begomovirus isolated from severely diseased tomatoes, collected over a two-year period in the main tomato-growing areas of Kuwait, was characterized at the molecular level. The complete genomic sequence of the begomovirus was determined, and phlylogeographic studies were conducted to better understand genetic diversity of the virus in the region. Based on genome properties and phylogenetic analysis, the begomovirus was found to be a strain of tomato yellow leaf curl virus (TYLCV). The virus genome was monopartite, as neither DNA B nor satellite DNA molecules were detected. Two isolates characterized in this study shared 97 % and 95 % nucleotide sequence identity with a previously characterized Kuwaiti isolate, TYLCV-KISR. Among TYLCV isolates with known genome sequences, the Kuwaiti isolates shared highest sequence identity (95 %) with TYLCV-Almeria (Spain). Genetic diversity and phylogenetic analysis showed that the three Kuwaiti isolates formed a distinct clade that was separate from those of known TYLCV sequences. One Kuwaiti isolate (KW 1-3) could be a novel variant of TYLCV. Two recombination events were detected in the genome sequence of KW 1-3, which appeared to be a recombinant derived from TYLCV parents from Oman and Kuwait.</abstract><cop>Vienna</cop><pub>Springer Vienna</pub><pmid>25951968</pmid><doi>10.1007/s00705-015-2427-x</doi><tpages>4</tpages><orcidid>https://orcid.org/0000-0002-4365-8676</orcidid></addata></record> |
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| subjects | Animals Annotated Sequence Record Base Sequence Begomovirus Begomovirus - classification Begomovirus - genetics Begomovirus - isolation & purification Biomedical and Life Sciences Biomedicine crop production DNA Enzymes Geminiviridae Genetic diversity Genetic Variation genome Genome, Viral Genomes Genomics Hemiptera - virology Infectious Diseases Insect Vectors - parasitology Insect Vectors - virology Kuwait Lycopersicon esculentum Lycopersicon esculentum - virology Medical Microbiology Molecular Sequence Data parents Phylogenetics Phylogeny Plant Diseases - parasitology Plant Diseases - virology Proteins satellite DNA sequence analysis Tomato yellow leaf curl virus tomatoes Virology Viruses |
| title | First complete genomic characterization and phylogeny of a new recombinant of tomato yellow leaf curl virus (genus Begomovirus, family Geminiviridae) from Kuwait |
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