TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads
Identifieur interne : 000F58 ( Pmc/Curation ); précédent : 000F57; suivant : 000F59TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads
Auteurs : Petr Novák [République tchèque] ; Laura Ávila Robledillo [République tchèque] ; Andrea Koblížková [République tchèque] ; Iva Vrbová [République tchèque] ; Pavel Neumann [République tchèque] ; Ji Macas [République tchèque]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2017.
Abstract
Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent
Url:
DOI: 10.1093/nar/gkx257
PubMed: 28402514
PubMed Central: 5499541
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Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">28402514</idno><idno type="pmc">5499541</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499541</idno><idno type="RBID">PMC:5499541</idno><idno type="doi">10.1093/nar/gkx257</idno><date when="2017">2017</date><idno type="wicri:Area/Pmc/Corpus">000F58</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000F58</idno><idno type="wicri:Area/Pmc/Curation">000F58</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000F58</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads</title><author><name sortKey="Novak, Petr" sort="Novak, Petr" uniqKey="Novak P" first="Petr" last="Novák">Petr Novák</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005</wicri:regionArea></affiliation></author><author><name sortKey="Avila Robledillo, Laura" sort="Avila Robledillo, Laura" uniqKey="Avila Robledillo L" first="Laura" last="Ávila Robledillo">Laura Ávila Robledillo</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005</wicri:regionArea></affiliation></author><author><name sortKey="Koblizkova, Andrea" sort="Koblizkova, Andrea" uniqKey="Koblizkova A" first="Andrea" last="Koblížková">Andrea Koblížková</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005</wicri:regionArea></affiliation></author><author><name sortKey="Vrbova, Iva" sort="Vrbova, Iva" uniqKey="Vrbova I" first="Iva" last="Vrbová">Iva Vrbová</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005</wicri:regionArea></affiliation></author><author><name sortKey="Neumann, Pavel" sort="Neumann, Pavel" uniqKey="Neumann P" first="Pavel" last="Neumann">Pavel Neumann</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005</wicri:regionArea></affiliation></author><author><name sortKey="Macas, Ji" sort="Macas, Ji" uniqKey="Macas J" first="Ji" last="Macas">Ji Macas</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005</wicri:regionArea></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent <italic>k</italic>-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of <italic>Vicia faba</italic> and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence <italic>in situ</italic> hybridization.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Macas, J" uniqKey="Macas J">J. Macas</name></author><author><name sortKey="Meszaros, T" uniqKey="Meszaros T">T. Mészáros</name></author><author><name sortKey="Nouzova, M" uniqKey="Nouzova M">M. Nouzová</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Garrido Ramos, M A" uniqKey="Garrido Ramos M">M.A. Garrido-Ramos</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Plohl, M" uniqKey="Plohl M">M. Plohl</name></author><author><name sortKey="Luchetti, A" uniqKey="Luchetti A">A. Luchetti</name></author><author><name sortKey="Mestrovi, N" uniqKey="Mestrovi N">N. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-title-group><journal-title>Nucleic Acids Research</journal-title></journal-title-group><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">28402514</article-id><article-id pub-id-type="pmc">5499541</article-id><article-id pub-id-type="doi">10.1093/nar/gkx257</article-id><article-id pub-id-type="publisher-id">gkx257</article-id><article-categories><subj-group subj-group-type="heading"><subject>Methods Online</subject></subj-group></article-categories><title-group><article-title>TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Novák</surname><given-names>Petr</given-names></name><xref ref-type="aff" rid="AFF1"></xref></contrib><contrib contrib-type="author"><name><surname>Ávila Robledillo</surname><given-names>Laura</given-names></name><xref ref-type="aff" rid="AFF1"></xref></contrib><contrib contrib-type="author"><name><surname>Koblížková</surname><given-names>Andrea</given-names></name><xref ref-type="aff" rid="AFF1"></xref></contrib><contrib contrib-type="author"><name><surname>Vrbová</surname><given-names>Iva</given-names></name><xref ref-type="aff" rid="AFF1"></xref></contrib><contrib contrib-type="author"><name><surname>Neumann</surname><given-names>Pavel</given-names></name><xref ref-type="aff" rid="AFF1"></xref></contrib><contrib contrib-type="author"><name><surname>Macas</surname><given-names>Jiří</given-names></name><pmc-comment>macas@umbr.cas.cz </pmc-comment>
<xref ref-type="aff" rid="AFF1"></xref><xref ref-type="corresp" rid="COR1"></xref></contrib></contrib-group><aff id="AFF1">Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice CZ-37005, Czech Republic</aff><author-notes><corresp id="COR1"><label>*</label>To whom correspondence should be addressed. Tel: +420 387 775 516; Fax: +420 385 310 356; Email: <email>macas@umbr.cas.cz</email></corresp></author-notes><pub-date pub-type="ppub"><day>07</day><month>7</month><year>2017</year></pub-date><pub-date pub-type="epub" iso-8601-date="2017-04-10"><day>10</day><month>4</month><year>2017</year></pub-date><pub-date pub-type="pmc-release"><day>10</day><month>4</month><year>2017</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>45</volume><issue>12</issue><fpage>e111</fpage><lpage>e111</lpage><history><date date-type="accepted"><day>04</day><month>4</month><year>2017</year></date><date date-type="rev-recd"><day>23</day><month>3</month><year>2017</year></date><date date-type="received"><day>25</day><month>1</month><year>2017</year></date></history><permissions><copyright-statement>© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.</copyright-statement><copyright-year>2017</copyright-year><license license-type="cc-by-nc" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<uri xlink:href="http://creativecommons.org/licenses/by-nc/4.0/">http://creativecommons.org/licenses/by-nc/4.0/</uri>), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact <email>journals.permissions@oup.com</email></license-p></license></permissions><self-uri xlink:href="gkx257.pdf"></self-uri><abstract><title>Abstract</title><p>Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent <italic>k</italic>-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of <italic>Vicia faba</italic> and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence <italic>in situ</italic> hybridization.</p></abstract><counts><page-count count="10"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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