TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.
Identifieur interne : 000D21 ( PubMed/Curation ); précédent : 000D20; suivant : 000D22TAREAN: 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] ; Jirí Macas [République tchèque]Source :
- Nucleic acids research [ 1362-4962 ] ; 2017.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), ADN satellite (), ADN satellite (génétique), Analyse de regroupements, Analyse de séquence d'ADN, Cartographie chromosomique (), Cyperaceae (génétique), Génome végétal, Infographie, Logiciel, Métaphase, Pois (génétique), Séquence consensus, Séquence nucléotidique, Technique FISH, Vicia faba (génétique), Zea mays (génétique).
- MESH :
English descriptors
- KwdEn :
- Base Sequence, Chromosome Mapping (methods), Cluster Analysis, Computer Graphics, Consensus Sequence, Cyperaceae (genetics), DNA, Plant (genetics), DNA, Satellite (classification), DNA, Satellite (genetics), Genome, Plant, In Situ Hybridization, Fluorescence, Magnoliopsida (genetics), Metaphase, Peas (genetics), Sequence Analysis, DNA, Software, Vicia faba (genetics), Zea mays (genetics).
- MESH :
- chemical , classification : DNA, Satellite.
- chemical , genetics : DNA, Plant, DNA, Satellite.
- genetics : Cyperaceae, Magnoliopsida, Peas, Vicia faba, Zea mays.
- methods : Chromosome Mapping.
- Base Sequence, Cluster Analysis, Computer Graphics, Consensus Sequence, Genome, Plant, In Situ Hybridization, Fluorescence, Metaphase, Sequence Analysis, DNA, Software.
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 k-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 Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization.
DOI: 10.1093/nar/gkx257
PubMed: 28402514
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Novák</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice 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:affiliation>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice 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:affiliation>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice 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:affiliation>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice 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:affiliation>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005</wicri:regionArea></affiliation></author><author><name sortKey="Macas, Jiri" sort="Macas, Jiri" uniqKey="Macas J" first="Jirí" last="Macas">Jirí Macas</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005</wicri:regionArea></affiliation></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Chromosome Mapping (methods)</term><term>Cluster Analysis</term><term>Computer Graphics</term><term>Consensus Sequence</term><term>Cyperaceae (genetics)</term><term>DNA, Plant (genetics)</term><term>DNA, Satellite (classification)</term><term>DNA, Satellite (genetics)</term><term>Genome, Plant</term><term>In Situ Hybridization, Fluorescence</term><term>Magnoliopsida (genetics)</term><term>Metaphase</term><term>Peas (genetics)</term><term>Sequence Analysis, DNA</term><term>Software</term><term>Vicia faba (genetics)</term><term>Zea mays (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (génétique)</term><term>ADN satellite ()</term><term>ADN satellite (génétique)</term><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN</term><term>Cartographie chromosomique ()</term><term>Cyperaceae (génétique)</term><term>Génome végétal</term><term>Infographie</term><term>Logiciel</term><term>Métaphase</term><term>Pois (génétique)</term><term>Séquence consensus</term><term>Séquence nucléotidique</term><term>Technique FISH</term><term>Vicia faba (génétique)</term><term>Zea mays (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>DNA, Satellite</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term><term>DNA, Satellite</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cyperaceae</term><term>Magnoliopsida</term><term>Peas</term><term>Vicia faba</term><term>Zea mays</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des plantes</term><term>ADN satellite</term><term>Cyperaceae</term><term>Pois</term><term>Vicia faba</term><term>Zea mays</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Chromosome Mapping</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Cluster Analysis</term><term>Computer Graphics</term><term>Consensus Sequence</term><term>Genome, Plant</term><term>In Situ Hybridization, Fluorescence</term><term>Metaphase</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN satellite</term><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN</term><term>Cartographie chromosomique</term><term>Génome végétal</term><term>Infographie</term><term>Logiciel</term><term>Métaphase</term><term>Séquence consensus</term><term>Séquence nucléotidique</term><term>Technique FISH</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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 k-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 Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28402514</PMID><DateCompleted><Year>2017</Year><Month>10</Month><Day>11</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN><JournalIssue CitedMedium="Internet"><Volume>45</Volume><Issue>12</Issue><PubDate><Year>2017</Year><Month>Jul</Month><Day>07</Day></PubDate></JournalIssue><Title>Nucleic acids research</Title><ISOAbbreviation>Nucleic Acids Res.</ISOAbbreviation></Journal><ArticleTitle>TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.</ArticleTitle><Pagination><MedlinePgn>e111</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/nar/gkx257</ELocationID><Abstract><AbstractText>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 k-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 Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization.</AbstractText><CopyrightInformation>© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Novák</LastName><ForeName>Petr</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ávila Robledillo</LastName><ForeName>Laura</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Koblížková</LastName><ForeName>Andrea</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vrbová</LastName><ForeName>Iva</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Neumann</LastName><ForeName>Pavel</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Macas</LastName><ForeName>Jirí</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Nucleic Acids Res</MedlineTA><NlmUniqueID>0411011</NlmUniqueID><ISSNLinking>0305-1048</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004276">DNA, Satellite</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003196" MajorTopicYN="N">Computer Graphics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016384" MajorTopicYN="N">Consensus Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D029785" MajorTopicYN="N">Cyperaceae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004276" MajorTopicYN="N">DNA, Satellite</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017404" MajorTopicYN="N">In Situ Hybridization, Fluorescence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019684" MajorTopicYN="N">Magnoliopsida</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008677" MajorTopicYN="N">Metaphase</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018532" MajorTopicYN="N">Peas</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D031307" MajorTopicYN="N">Vicia faba</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003313" MajorTopicYN="N">Zea mays</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>01</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>04</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>4</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>10</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>4</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28402514</ArticleId><ArticleId IdType="pii">3574061</ArticleId><ArticleId IdType="doi">10.1093/nar/gkx257</ArticleId><ArticleId 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