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Identification and characterization of jute LTR retrotransposons:

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Identification and characterization of jute LTR retrotransposons:

Auteurs : Salim Ahmed [Bangladesh] ; Md Shafiuddin [Bangladesh] ; Muhammad Shafiul Azam [Bangladesh] ; Md. Shahidul Islam [Bangladesh] ; Ajit Ghosh [Inde] ; Haseena Khan [Bangladesh]

Source :

Mobile Genetic Elements [ 2159-2543 ] ; 2011.

RBID : PMC:3190282

Abstract

Long Terminal Repeat (LTR) retrotransposons constitute a significant part of eukaryotic genomes and play an important role in genome evolution especially in plants. Jute is an important fiber crop with a large genome of 1,250 Mbps. This genome is still mostly unexplored. In this study we aimed at identifying and characterizing the LTR retrotransposons of jute with a view to understanding the jute genome better. In this study, the Reverse Transcriptase domain of Ty1-copia and Ty3-gypsy LTR retrotransposons of jute were amplified by degenerate primers and their expressions were examined by reverse transcription PCR. Copy numbers of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy elements were determined by dot blot analysis. Sequence analysis revealed higher heterogeneity among Ty1-copia retrotransposons than Ty3-gypsy and clustered each of them in three groups. Copy number of RT genes in Ty1-copia was found to be higher than that of Ty3-gypsy elements from dot blot hybridization. Cumulatively Ty1-copia and Ty3-gypsy may constitute around 19% of the jute genome where two groups of Ty1-copia were found to be transcriptionally active. Since the LTR retrotransposons constitute a large portion of jute genome, these findings imply the importance of these elements in the evolution of jute genome.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3190282

DOI: 10.4161/mge.1.1.16433
PubMed: 22016842
PubMed Central: 3190282

Affiliations:

Bangladesh, Inde

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PMC:3190282

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<author><name sortKey="Ahmed, Salim" sort="Ahmed, Salim" uniqKey="Ahmed S" first="Salim" last="Ahmed">Salim Ahmed</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Department of Genetic Engineering and Biotechnology; University of Dhaka; Dhaka, Bangladesh</nlm:aff>
<country xml:lang="fr">Bangladesh</country>
<wicri:regionArea>Department of Genetic Engineering and Biotechnology; University of Dhaka; Dhaka</wicri:regionArea>
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<author><name sortKey="Azam, Muhammad Shafiul" sort="Azam, Muhammad Shafiul" uniqKey="Azam M" first="Muhammad Shafiul" last="Azam">Muhammad Shafiul Azam</name>
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<author><name sortKey="Islam, Md Shahidul" sort="Islam, Md Shahidul" uniqKey="Islam M" first="Md. Shahidul" last="Islam">Md. Shahidul Islam</name>
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<country xml:lang="fr">Bangladesh</country>
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<author><name sortKey="Ghosh, Ajit" sort="Ghosh, Ajit" uniqKey="Ghosh A" first="Ajit" last="Ghosh">Ajit Ghosh</name>
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<author><name sortKey="Khan, Haseena" sort="Khan, Haseena" uniqKey="Khan H" first="Haseena" last="Khan">Haseena Khan</name>
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<author><name sortKey="Shafiuddin, Md" sort="Shafiuddin, Md" uniqKey="Shafiuddin M" first="Md" last="Shafiuddin">Md Shafiuddin</name>
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<country xml:lang="fr">Bangladesh</country>
<wicri:regionArea>Department of Biochemistry and Molecular Biology; University of Dhaka; Dhaka</wicri:regionArea>
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<author><name sortKey="Azam, Muhammad Shafiul" sort="Azam, Muhammad Shafiul" uniqKey="Azam M" first="Muhammad Shafiul" last="Azam">Muhammad Shafiul Azam</name>
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<author><name sortKey="Islam, Md Shahidul" sort="Islam, Md Shahidul" uniqKey="Islam M" first="Md. Shahidul" last="Islam">Md. Shahidul Islam</name>
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<author><name sortKey="Ghosh, Ajit" sort="Ghosh, Ajit" uniqKey="Ghosh A" first="Ajit" last="Ghosh">Ajit Ghosh</name>
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<series><title level="j">Mobile Genetic Elements</title>
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<front><div type="abstract" xml:lang="en"><p>Long Terminal Repeat (LTR) retrotransposons constitute a significant part of eukaryotic genomes and play an important role in genome evolution especially in plants. Jute is an important fiber crop with a large genome of 1,250 Mbps. This genome is still mostly unexplored. In this study we aimed at identifying and characterizing the LTR retrotransposons of jute with a view to understanding the jute genome better. In this study, the Reverse Transcriptase domain of Ty1-<italic>copia</italic>
 and Ty3-<italic>gypsy</italic>
 LTR retrotransposons of jute were amplified by degenerate primers and their expressions were examined by reverse transcription PCR. Copy numbers of reverse transcriptase (RT) genes of Ty1-<italic>copia</italic>
 and Ty3-<italic>gypsy</italic>
 elements were determined by dot blot analysis. Sequence analysis revealed higher heterogeneity among Ty1-<italic>copia</italic>
 retrotransposons than Ty3-<italic>gypsy</italic>
 and clustered each of them in three groups. Copy number of RT genes in Ty1-<italic>copia</italic>
 was found to be higher than that of Ty3-<italic>gypsy</italic>
 elements from dot blot hybridization. Cumulatively Ty1-<italic>copia</italic>
 and Ty3-<italic>gypsy</italic>
 may constitute around 19% of the jute genome where two groups of Ty1-<italic>copia</italic>
 were found to be transcriptionally active. Since the LTR retrotransposons constitute a large portion of jute genome, these findings imply the importance of these elements in the evolution of jute genome.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article"><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">Mob Genet Elements</journal-id>
<journal-id journal-id-type="publisher-id">10.4161/mge</journal-id>
<journal-title-group><journal-title>Mobile Genetic Elements</journal-title>
</journal-title-group>
<issn pub-type="ppub">2159-2543</issn>
<issn pub-type="epub">2159-256X</issn>
<publisher><publisher-name>Landes Bioscience</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22016842</article-id>
<article-id pub-id-type="pmc">3190282</article-id>
<article-id pub-id-type="publisher-id">2159-2543-1-1-4</article-id>
<article-id pub-id-type="doi">10.4161/mge.1.1.16433</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Paper</subject>
</subj-group>
</article-categories>
<title-group><article-title>Identification and characterization of jute LTR retrotransposons:</article-title>
<subtitle>Their abundance, heterogeneity and transcriptional activity</subtitle>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Ahmed</surname>
<given-names>Salim</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Shafiuddin</surname>
<given-names>MD</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Azam</surname>
<given-names>Muhammad Shafiul</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Islam</surname>
<given-names>Md. Shahidul</given-names>
</name>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ghosh</surname>
<given-names>Ajit</given-names>
</name>
<xref ref-type="aff" rid="A4">4</xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Khan</surname>
<given-names>Haseena</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
</contrib-group>
<aff id="A1"><label>1</label>
Department of Genetic Engineering and Biotechnology; University of Dhaka; Dhaka, Bangladesh</aff>
<aff id="A2"><label>2</label>
Department of Biochemistry and Molecular Biology; University of Dhaka; Dhaka, Bangladesh</aff>
<aff id="A3"><label>3</label>
Bangladesh Jute Research Institute; Dhaka, Bangladesh</aff>
<aff id="A4"><label>4</label>
International Center for Genetic Engineering and Biotechnology; New Delhi, India</aff>
<author-notes><corresp>Correspondence to: Haseena Khan; Email: <email>haseena@univdhaka.edu</email>
</corresp>
</author-notes>
<pub-date pub-type="ppub"><season>May-Jun</season>
<year>2011</year>
</pub-date>
<pub-date pub-type="epub"><season>May-Jun</season>
<year>2011</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>1</day>
<month>5</month>
<year>2011</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the 
 					. </pmc-comment>
      <volume>1</volume>
<issue>1</issue>
<fpage>18</fpage>
<lpage>28</lpage>
<history><date date-type="received"><day>19</day>
<month>3</month>
<year>2011</year>
</date>
<date date-type="rev-recd"><day>6</day>
<month>5</month>
<year>2011</year>
</date>
<date date-type="accepted"><day>7</day>
<month>5</month>
<year>2011</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2011 Landes Bioscience</copyright-statement>
<copyright-year>2011</copyright-year>
</permissions>
<abstract><p>Long Terminal Repeat (LTR) retrotransposons constitute a significant part of eukaryotic genomes and play an important role in genome evolution especially in plants. Jute is an important fiber crop with a large genome of 1,250 Mbps. This genome is still mostly unexplored. In this study we aimed at identifying and characterizing the LTR retrotransposons of jute with a view to understanding the jute genome better. In this study, the Reverse Transcriptase domain of Ty1-<italic>copia</italic>
 and Ty3-<italic>gypsy</italic>
 LTR retrotransposons of jute were amplified by degenerate primers and their expressions were examined by reverse transcription PCR. Copy numbers of reverse transcriptase (RT) genes of Ty1-<italic>copia</italic>
 and Ty3-<italic>gypsy</italic>
 elements were determined by dot blot analysis. Sequence analysis revealed higher heterogeneity among Ty1-<italic>copia</italic>
 retrotransposons than Ty3-<italic>gypsy</italic>
 and clustered each of them in three groups. Copy number of RT genes in Ty1-<italic>copia</italic>
 was found to be higher than that of Ty3-<italic>gypsy</italic>
 elements from dot blot hybridization. Cumulatively Ty1-<italic>copia</italic>
 and Ty3-<italic>gypsy</italic>
 may constitute around 19% of the jute genome where two groups of Ty1-<italic>copia</italic>
 were found to be transcriptionally active. Since the LTR retrotransposons constitute a large portion of jute genome, these findings imply the importance of these elements in the evolution of jute genome.</p>
</abstract>
<kwd-group><title>Key words</title>
<kwd>jute</kwd>
<kwd>LTR retrotransposons</kwd>
<kwd>transcriptional activity</kwd>
<kwd>copy number</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Bangladesh</li>
<li>Inde</li>
</country>
</list>
<tree><country name="Bangladesh"><noRegion><name sortKey="Ahmed, Salim" sort="Ahmed, Salim" uniqKey="Ahmed S" first="Salim" last="Ahmed">Salim Ahmed</name>
</noRegion>
<name sortKey="Azam, Muhammad Shafiul" sort="Azam, Muhammad Shafiul" uniqKey="Azam M" first="Muhammad Shafiul" last="Azam">Muhammad Shafiul Azam</name>
<name sortKey="Islam, Md Shahidul" sort="Islam, Md Shahidul" uniqKey="Islam M" first="Md. Shahidul" last="Islam">Md. Shahidul Islam</name>
<name sortKey="Khan, Haseena" sort="Khan, Haseena" uniqKey="Khan H" first="Haseena" last="Khan">Haseena Khan</name>
<name sortKey="Shafiuddin, Md" sort="Shafiuddin, Md" uniqKey="Shafiuddin M" first="Md" last="Shafiuddin">Md Shafiuddin</name>
</country>
<country name="Inde"><noRegion><name sortKey="Ghosh, Ajit" sort="Ghosh, Ajit" uniqKey="Ghosh A" first="Ajit" last="Ghosh">Ajit Ghosh</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

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Identification and characterization of jute LTR retrotransposons:

Identification and characterization of jute LTR retrotransposons:

Source :

Abstract

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