TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads
Identifieur interne : 001A11 ( Ncbi/Checkpoint ); précédent : 001A10; suivant : 001A12TAREAN: 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.
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
Url:
DOI: 10.1093/nar/gkx257
PubMed: 28402514
PubMed Central: 5499541
Affiliations:
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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><wicri:noRegion>České Budějovice CZ-37005</wicri:noRegion></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><wicri:noRegion>České Budějovice CZ-37005</wicri:noRegion></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><wicri:noRegion>České Budějovice CZ-37005</wicri:noRegion></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><wicri:noRegion>České Budějovice CZ-37005</wicri:noRegion></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><wicri:noRegion>České Budějovice CZ-37005</wicri:noRegion></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><wicri:noRegion>České Budějovice CZ-37005</wicri:noRegion></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><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"><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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Mészáros</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République tchèque</li></country></list><tree><country name="République tchèque"><noRegion><name sortKey="Novak, Petr" sort="Novak, Petr" uniqKey="Novak P" first="Petr" last="Novák">Petr Novák</name></noRegion><name sortKey="Avila Robledillo, Laura" sort="Avila Robledillo, Laura" uniqKey="Avila Robledillo L" first="Laura" last="Ávila Robledillo">Laura Ávila Robledillo</name><name sortKey="Koblizkova, Andrea" sort="Koblizkova, Andrea" uniqKey="Koblizkova A" first="Andrea" last="Koblížková">Andrea Koblížková</name><name sortKey="Macas, Ji" sort="Macas, Ji" uniqKey="Macas J" first="Ji" last="Macas">Ji Macas</name><name sortKey="Neumann, Pavel" sort="Neumann, Pavel" uniqKey="Neumann P" first="Pavel" last="Neumann">Pavel Neumann</name><name sortKey="Vrbova, Iva" sort="Vrbova, Iva" uniqKey="Vrbova I" first="Iva" last="Vrbová">Iva Vrbová</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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