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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Sequence diversity among badnavirus isolate<italic>s</italic>
infecting black pepper and related species in India</title>
<author><name sortKey="Bhat, A I" sort="Bhat, A I" uniqKey="Bhat A" first="A. I." last="Bhat">A. I. Bhat</name>
<affiliation><nlm:aff id="Aff1">Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Sasi, Shina" sort="Sasi, Shina" uniqKey="Sasi S" first="Shina" last="Sasi">Shina Sasi</name>
<affiliation><nlm:aff id="Aff1">Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Revathy, K A" sort="Revathy, K A" uniqKey="Revathy K" first="K. A." last="Revathy">K. A. Revathy</name>
<affiliation><nlm:aff id="Aff1">Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Deeshma, K P" sort="Deeshma, K P" uniqKey="Deeshma K" first="K. P." last="Deeshma">K. P. Deeshma</name>
<affiliation><nlm:aff id="Aff1">Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Saji, K V" sort="Saji, K V" uniqKey="Saji K" first="K. V." last="Saji">K. V. Saji</name>
<affiliation><nlm:aff id="Aff1">Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India</nlm:aff>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">25674613</idno>
<idno type="pmc">4188196</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4188196</idno>
<idno type="RBID">PMC:4188196</idno>
<idno type="doi">10.1007/s13337-014-0221-0</idno>
<date when="2014">2014</date>
<idno type="wicri:Area/Pmc/Corpus">000488</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Sequence diversity among badnavirus isolate<italic>s</italic>
infecting black pepper and related species in India</title>
<author><name sortKey="Bhat, A I" sort="Bhat, A I" uniqKey="Bhat A" first="A. I." last="Bhat">A. I. Bhat</name>
<affiliation><nlm:aff id="Aff1">Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Sasi, Shina" sort="Sasi, Shina" uniqKey="Sasi S" first="Shina" last="Sasi">Shina Sasi</name>
<affiliation><nlm:aff id="Aff1">Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Revathy, K A" sort="Revathy, K A" uniqKey="Revathy K" first="K. A." last="Revathy">K. A. Revathy</name>
<affiliation><nlm:aff id="Aff1">Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Deeshma, K P" sort="Deeshma, K P" uniqKey="Deeshma K" first="K. P." last="Deeshma">K. P. Deeshma</name>
<affiliation><nlm:aff id="Aff1">Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Saji, K V" sort="Saji, K V" uniqKey="Saji K" first="K. V." last="Saji">K. V. Saji</name>
<affiliation><nlm:aff id="Aff1">Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India</nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">VirusDisease</title>
<idno type="ISSN">2347-3584</idno>
<idno type="eISSN">2347-3517</idno>
<imprint><date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>The badnavirus, piper yellow mottle virus (PYMoV) is known to infect black pepper (<italic>Piper nigrum</italic>
), betelvine (<italic>P. betle</italic>
) and Indian long pepper (<italic>P. longum</italic>
) in India and other parts of the world. Occurrence of PYMoV or other badnaviruses in other species of <italic>Piper</italic>
and its variability is not reported so far. We have analysed sequence variability in the conserved putative reverse transcriptase (RT)/ribonuclease H (RNase H) coding region of the virus using specific badnavirus primers from 13 virus isolates of black pepper collected from different cultivars and regions and one isolate each from 23 other species of <italic>Piper.</italic>
Of these, four species failed to produce expected amplicon while amplicon from four other species showed more similarities to plant sequences than to badnaviruses. Of the remaining, isolates from black pepper, <italic>P. argyrophyllum, P. attenuatum</italic>
, <italic>P. barberi</italic>
, <italic>P. betle</italic>
, <italic>P. colubrinum</italic>
, <italic>P. galeatum</italic>
, <italic>P. longum</italic>
, <italic>P. ornatum</italic>
, <italic>P. sarmentosum</italic>
and <italic>P. trichostachyon</italic>
showed an identity of >85 % at the nucleotide and >90 % at the amino acid level with PYMoV indicating that they are isolates of PYMoV. On the other hand high sequence variability of 21–43 % at nucleotide and 17–46 % at amino acid level compared to PYMoV was found among isolates infecting <italic>P. bababudani</italic>
, <italic>P. chaba</italic>
, <italic>P. peepuloides, P. mullesua</italic>
and <italic>P. thomsonii</italic>
suggesting the presence of new badnaviruses. Phylogenetic analyses showed close clustering of all PYMoV isolates that were well separated from other known badnaviruses. This is the first report of occurrence of PYMoV in eight <italic>Piper</italic>
spp and likely occurrence of four new species in five <italic>Piper</italic>
spp.</p>
</div>
</front>
</TEI>
<pmc article-type="brief-report"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Virusdisease</journal-id>
<journal-id journal-id-type="iso-abbrev">Virusdisease</journal-id>
<journal-title-group><journal-title>VirusDisease</journal-title>
</journal-title-group>
<issn pub-type="ppub">2347-3584</issn>
<issn pub-type="epub">2347-3517</issn>
<publisher><publisher-name>Springer India</publisher-name>
<publisher-loc>India</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25674613</article-id>
<article-id pub-id-type="pmc">4188196</article-id>
<article-id pub-id-type="publisher-id">221</article-id>
<article-id pub-id-type="doi">10.1007/s13337-014-0221-0</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Short Communication</subject>
</subj-group>
</article-categories>
<title-group><article-title>Sequence diversity among badnavirus isolate<italic>s</italic>
infecting black pepper and related species in India</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes"><name><surname>Bhat</surname>
<given-names>A. I.</given-names>
</name>
<address><email>aib65@yahoo.co.in</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sasi</surname>
<given-names>Shina</given-names>
</name>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Revathy</surname>
<given-names>K. A.</given-names>
</name>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Deeshma</surname>
<given-names>K. P.</given-names>
</name>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Saji</surname>
<given-names>K. V.</given-names>
</name>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<aff id="Aff1">Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India</aff>
</contrib-group>
<pub-date pub-type="epub"><day>10</day>
<month>7</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="ppub"><month>9</month>
<year>2014</year>
</pub-date>
<volume>25</volume>
<issue>3</issue>
<fpage>402</fpage>
<lpage>407</lpage>
<history><date date-type="received"><day>11</day>
<month>2</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>7</day>
<month>5</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>© Indian Virological Society 2014</copyright-statement>
</permissions>
<abstract id="Abs1"><p>The badnavirus, piper yellow mottle virus (PYMoV) is known to infect black pepper (<italic>Piper nigrum</italic>
), betelvine (<italic>P. betle</italic>
) and Indian long pepper (<italic>P. longum</italic>
) in India and other parts of the world. Occurrence of PYMoV or other badnaviruses in other species of <italic>Piper</italic>
and its variability is not reported so far. We have analysed sequence variability in the conserved putative reverse transcriptase (RT)/ribonuclease H (RNase H) coding region of the virus using specific badnavirus primers from 13 virus isolates of black pepper collected from different cultivars and regions and one isolate each from 23 other species of <italic>Piper.</italic>
Of these, four species failed to produce expected amplicon while amplicon from four other species showed more similarities to plant sequences than to badnaviruses. Of the remaining, isolates from black pepper, <italic>P. argyrophyllum, P. attenuatum</italic>
, <italic>P. barberi</italic>
, <italic>P. betle</italic>
, <italic>P. colubrinum</italic>
, <italic>P. galeatum</italic>
, <italic>P. longum</italic>
, <italic>P. ornatum</italic>
, <italic>P. sarmentosum</italic>
and <italic>P. trichostachyon</italic>
showed an identity of >85 % at the nucleotide and >90 % at the amino acid level with PYMoV indicating that they are isolates of PYMoV. On the other hand high sequence variability of 21–43 % at nucleotide and 17–46 % at amino acid level compared to PYMoV was found among isolates infecting <italic>P. bababudani</italic>
, <italic>P. chaba</italic>
, <italic>P. peepuloides, P. mullesua</italic>
and <italic>P. thomsonii</italic>
suggesting the presence of new badnaviruses. Phylogenetic analyses showed close clustering of all PYMoV isolates that were well separated from other known badnaviruses. This is the first report of occurrence of PYMoV in eight <italic>Piper</italic>
spp and likely occurrence of four new species in five <italic>Piper</italic>
spp.</p>
</abstract>
<kwd-group xml:lang="en"><title>Keywords</title>
<kwd><italic>Piper yellow mottle virus</italic>
</kwd>
<kwd>Sequence variability</kwd>
<kwd><italic>Piper</italic>
spp. RT/RNase region</kwd>
</kwd-group>
<custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name>
<meta-value>© Indian Virological Society 2014</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
</record>
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