Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants
Identifieur interne : 002263 ( Main/Exploration ); précédent : 002262; suivant : 002264Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants
Auteurs : Nicole Gruenheit [Nouvelle-Zélande] ; Oliver Deusch [Nouvelle-Zélande] ; Christian Esser [Allemagne] ; Matthias Becker [Nouvelle-Zélande] ; Claudia Voelckel [Nouvelle-Zélande] ; Peter Lockhart [Nouvelle-Zélande]Source :
- BMC Genomics [ 1471-2164 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Messenger.
- cytology : Brassicaceae.
- genetics : Brassicaceae, Genes, Plant.
- methods : Gene Expression Profiling.
- Contig Mapping, Polyploidy, Quality Control, Sequence Homology, Nucleic Acid.
Abstract
Transcriptome analysis is increasingly being used to study the evolutionary origins and ecology of non-model plants. One issue for both transcriptome assembly and differential gene expression analyses is the common occurrence in plants of hybridisation and whole genome duplication (WGD) and hybridization resulting in allopolyploidy. The divergence of duplicated genes following WGD creates near identical homeologues that can be problematic for
Here we report a successful strategy for the assembly of two transcriptomes made using 75 bp Illumina reads from
To obtain optimal transcriptome assemblies for allopolyploid plants, k-mer size and k-mer coverage need to be considered simultaneously across a broad parameter space. This is important for assembling a maximum number of full length ESTs and for avoiding chimeric assemblies of homeologous and paralogous gene copies.
Url:
DOI: 10.1186/1471-2164-13-92
PubMed: 22417298
PubMed Central: 3378427
Affiliations:
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type="wicri:Area/Main/Exploration">002263</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants</title><author><name sortKey="Gruenheit, Nicole" sort="Gruenheit, Nicole" uniqKey="Gruenheit N" first="Nicole" last="Gruenheit">Nicole Gruenheit</name><affiliation wicri:level="1"><nlm:aff id="I1">Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand</nlm:aff><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea>Institute of Molecular Biosciences, Massey University, Palmerston North</wicri:regionArea><wicri:noRegion>Palmerston North</wicri:noRegion></affiliation></author><author><name sortKey="Deusch, Oliver" sort="Deusch, Oliver" uniqKey="Deusch O" first="Oliver" last="Deusch">Oliver Deusch</name><affiliation wicri:level="1"><nlm:aff id="I1">Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand</nlm:aff><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea>Institute of Molecular Biosciences, Massey University, Palmerston North</wicri:regionArea><wicri:noRegion>Palmerston North</wicri:noRegion></affiliation></author><author><name sortKey="Esser, Christian" sort="Esser, Christian" uniqKey="Esser C" first="Christian" last="Esser">Christian Esser</name><affiliation wicri:level="3"><nlm:aff id="I2">Institute for Computer Science, Heinrich-Heine-University, 40225 Düsseldorf, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute for Computer Science, Heinrich-Heine-University, 40225 Düsseldorf</wicri:regionArea><placeName><region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region><region type="district" nuts="2">District de Düsseldorf</region><settlement type="city">Düsseldorf</settlement></placeName></affiliation></author><author><name sortKey="Becker, Matthias" sort="Becker, Matthias" uniqKey="Becker M" first="Matthias" last="Becker">Matthias Becker</name><affiliation wicri:level="1"><nlm:aff id="I1">Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand</nlm:aff><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea>Institute of Molecular Biosciences, Massey University, Palmerston North</wicri:regionArea><wicri:noRegion>Palmerston North</wicri:noRegion></affiliation></author><author><name sortKey="Voelckel, Claudia" sort="Voelckel, Claudia" uniqKey="Voelckel C" first="Claudia" last="Voelckel">Claudia Voelckel</name><affiliation wicri:level="1"><nlm:aff id="I1">Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand</nlm:aff><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea>Institute of Molecular Biosciences, Massey University, Palmerston North</wicri:regionArea><wicri:noRegion>Palmerston North</wicri:noRegion></affiliation></author><author><name sortKey="Lockhart, Peter" sort="Lockhart, Peter" uniqKey="Lockhart P" first="Peter" last="Lockhart">Peter Lockhart</name><affiliation wicri:level="1"><nlm:aff id="I1">Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand</nlm:aff><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea>Institute of Molecular Biosciences, Massey University, Palmerston North</wicri:regionArea><wicri:noRegion>Palmerston North</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Brassicaceae (cytology)</term><term>Brassicaceae (genetics)</term><term>Contig Mapping</term><term>Gene Expression Profiling (methods)</term><term>Genes, Plant (genetics)</term><term>Polyploidy</term><term>Quality Control</term><term>RNA, Messenger (genetics)</term><term>Sequence Homology, Nucleic Acid</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN messager (génétique)</term><term>Analyse de profil d'expression de gènes ()</term><term>Brassicaceae (cytologie)</term><term>Brassicaceae (génétique)</term><term>Cartographie de contigs</term><term>Contrôle de qualité</term><term>Gènes de plante (génétique)</term><term>Polyploïdie</term><term>Similitude de séquences d'acides nucléiques</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Messenger</term></keywords><keywords scheme="MESH" qualifier="cytologie" xml:lang="fr"><term>Brassicaceae</term></keywords><keywords scheme="MESH" qualifier="cytology" xml:lang="en"><term>Brassicaceae</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Brassicaceae</term><term>Genes, Plant</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN messager</term><term>Brassicaceae</term><term>Gènes de plante</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Gene Expression Profiling</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Contig Mapping</term><term>Polyploidy</term><term>Quality Control</term><term>Sequence Homology, Nucleic Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Cartographie de contigs</term><term>Contrôle de qualité</term><term>Polyploïdie</term><term>Similitude de séquences d'acides nucléiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Transcriptome analysis is increasingly being used to study the evolutionary origins and ecology of non-model plants. One issue for both transcriptome assembly and differential gene expression analyses is the common occurrence in plants of hybridisation and whole genome duplication (WGD) and hybridization resulting in allopolyploidy. The divergence of duplicated genes following WGD creates near identical homeologues that can be problematic for <italic>de novo </italic>assembly and also reference based assembly protocols that use short reads (35 - 100 bp).</p></sec><sec><title>Results</title><p>Here we report a successful strategy for the assembly of two transcriptomes made using 75 bp Illumina reads from <italic>Pachycladon fastigiatum </italic>and <italic>Pachycladon cheesemanii</italic>. Both are allopolyploid plant species (2n = 20) that originated in the New Zealand Alps about 0.8 million years ago. In a systematic analysis of 19 different coverage cutoffs and 20 different k-mer sizes we showed that i) none of the genes could be assembled across all of the parameter space ii) assembly of each gene required an optimal set of parameter values and iii) these parameter values could be explained in part by different gene expression levels and different degrees of similarity between genes.</p></sec><sec><title>Conclusions</title><p>To obtain optimal transcriptome assemblies for allopolyploid plants, k-mer size and k-mer coverage need to be considered simultaneously across a broad parameter space. This is important for assembling a maximum number of full length ESTs and for avoiding chimeric assemblies of homeologous and paralogous gene copies.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Cui, L" uniqKey="Cui L">L Cui</name></author><author><name sortKey="Wall, Pk" uniqKey="Wall P">PK Wall</name></author><author><name sortKey="Leebens Mack, Jh" uniqKey="Leebens Mack J">JH Leebens-Mack</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jiao, Y" uniqKey="Jiao Y">Y Jiao</name></author><author><name sortKey="Wickett, Nj" uniqKey="Wickett N">NJ Wickett</name></author><author><name sortKey="Ayyampalayam, S" uniqKey="Ayyampalayam S">S Ayyampalayam</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van De Peer, Y" uniqKey="Van De Peer Y">Y Van de Peer</name></author><author><name sortKey="Fawcett, Ja" uniqKey="Fawcett J">JA 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sortKey="Peterson, Da" uniqKey="Peterson D">DA Peterson</name></author><author><name sortKey="Biggs, Pj" uniqKey="Biggs P">PJ Biggs</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Swarbreck, D" uniqKey="Swarbreck D">D Swarbreck</name></author><author><name sortKey="Wilks, C" uniqKey="Wilks C">C Wilks</name></author><author><name sortKey="Lamesch, P" uniqKey="Lamesch P">P Lamesch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hu, Tt" uniqKey="Hu T">TT Hu</name></author><author><name sortKey="Pattyn, P" uniqKey="Pattyn P">P Pattyn</name></author><author><name sortKey="Bakker, Eg" uniqKey="Bakker E">EG Bakker</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li><li>Nouvelle-Zélande</li></country><region><li>District de Düsseldorf</li><li>Rhénanie-du-Nord-Westphalie</li></region><settlement><li>Düsseldorf</li></settlement></list><tree><country name="Nouvelle-Zélande"><noRegion><name sortKey="Gruenheit, Nicole" sort="Gruenheit, Nicole" uniqKey="Gruenheit N" first="Nicole" last="Gruenheit">Nicole Gruenheit</name></noRegion><name sortKey="Becker, Matthias" sort="Becker, Matthias" uniqKey="Becker M" first="Matthias" last="Becker">Matthias Becker</name><name sortKey="Deusch, Oliver" sort="Deusch, Oliver" uniqKey="Deusch O" first="Oliver" last="Deusch">Oliver Deusch</name><name sortKey="Lockhart, Peter" sort="Lockhart, Peter" uniqKey="Lockhart P" first="Peter" last="Lockhart">Peter Lockhart</name><name sortKey="Voelckel, Claudia" sort="Voelckel, Claudia" uniqKey="Voelckel C" first="Claudia" last="Voelckel">Claudia Voelckel</name></country><country name="Allemagne"><region name="Rhénanie-du-Nord-Westphalie"><name sortKey="Esser, Christian" sort="Esser, Christian" uniqKey="Esser C" first="Christian" 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