Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms
Identifieur interne : 001293 ( Pmc/Checkpoint ); précédent : 001292; suivant : 001294Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms
Auteurs : Berat Z. Haznedaroglu [États-Unis] ; Darryl Reeves [États-Unis] ; Hamid Rismani-Yazdi [États-Unis] ; Jordan Peccia [États-Unis]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2012.
Abstract
The
Analyses of single
This study demonstrated that different
Url:
DOI: 10.1186/1471-2105-13-170
PubMed: 22808927
PubMed Central: 3489510
Affiliations:
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PMC:3489510Le document en format XML
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transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms</title>
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<author><name sortKey="Rismani Yazdi, Hamid" sort="Rismani Yazdi, Hamid" uniqKey="Rismani Yazdi H" first="Hamid" last="Rismani-Yazdi">Hamid Rismani-Yazdi</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Optimization of <italic>de novo</italic>
transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms</title>
<author><name sortKey="Haznedaroglu, Berat Z" sort="Haznedaroglu, Berat Z" uniqKey="Haznedaroglu B" first="Berat Z" last="Haznedaroglu">Berat Z. Haznedaroglu</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06511, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06511</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Reeves, Darryl" sort="Reeves, Darryl" uniqKey="Reeves D" first="Darryl" last="Reeves">Darryl Reeves</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
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</affiliation>
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<author><name sortKey="Rismani Yazdi, Hamid" sort="Rismani Yazdi, Hamid" uniqKey="Rismani Yazdi H" first="Hamid" last="Rismani-Yazdi">Hamid Rismani-Yazdi</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06511, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06511</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
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<affiliation wicri:level="2"><nlm:aff id="I3">Now at the Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Now at the Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA</wicri:regionArea>
<placeName><region type="state">Massachusetts</region>
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</affiliation>
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<author><name sortKey="Peccia, Jordan" sort="Peccia, Jordan" uniqKey="Peccia J" first="Jordan" last="Peccia">Jordan Peccia</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06511, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06511</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
</affiliation>
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<series><title level="j">BMC Bioinformatics</title>
<idno type="eISSN">1471-2105</idno>
<imprint><date when="2012">2012</date>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>The <italic>k</italic>
-mer hash length is a key factor affecting the output of <italic>de novo</italic>
transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single <italic>k</italic>
-mer choices might result in the loss of unique contiguous sequences (contigs) and relevant biological information. A common solution to this problem is the clustering of single <italic>k</italic>
-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of <italic>k</italic>
-mer selection on the annotation output. This study provides an in-depth <italic>k</italic>
-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual <italic>k</italic>
-mers and clustered assemblies (CA) were considered using three representative software packages. Pair-wise comparison analyses (between individual <italic>k</italic>
-mers and CAs) were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog identifiers (KOIs), and to determine a strategy that maximizes the recovery of biological information in a <italic>de novo</italic>
transcriptome assembly.</p>
</sec>
<sec><title>Results</title>
<p>Analyses of single <italic>k</italic>
-mer assemblies resulted in the generation of various quantities of contigs and functional annotations within the selection window of <italic>k</italic>
-mers (<italic>k-</italic>
19 to <italic>k-</italic>
63). For each <italic>k</italic>
-mer in this window, generated assemblies contained certain unique contigs and KOIs that were not present in the other <italic>k</italic>
-mer assemblies. Producing a non-redundant CA of <italic>k</italic>
-mers 19 to 63 resulted in a more complete functional annotation than any single <italic>k</italic>
-mer assembly. However, a fraction of unique annotations remained (~0.19 to 0.27% of total KOIs) in the assemblies of individual <italic>k</italic>
-mers (<italic>k-</italic>
19 to <italic>k-</italic>
63) that were not present in the non-redundant CA. A workflow to recover these unique annotations is presented.</p>
</sec>
<sec><title>Conclusions</title>
<p>This study demonstrated that different <italic>k</italic>
-mer choices result in various quantities of unique contigs per single <italic>k</italic>
-mer assembly which affects biological information that is retrievable from the transcriptome. This undesirable effect can be minimized, but not eliminated, with clustering of multi-<italic>k</italic>
assemblies with redundancy removal. The complete extraction of biological information in <italic>de novo</italic>
transcriptomics studies requires both the production of a CA and efforts to identify unique contigs that are present in individual <italic>k</italic>
-mer assemblies but not in the CA.</p>
</sec>
</div>
</front>
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<pmc article-type="research-article" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Bioinformatics</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Bioinformatics</journal-id>
<journal-title-group><journal-title>BMC Bioinformatics</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2105</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22808927</article-id>
<article-id pub-id-type="pmc">3489510</article-id>
<article-id pub-id-type="publisher-id">1471-2105-13-170</article-id>
<article-id pub-id-type="doi">10.1186/1471-2105-13-170</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Optimization of <italic>de novo</italic>
transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" id="A1"><name><surname>Haznedaroglu</surname>
<given-names>Berat Z</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>berat.haznedaroglu@yale.edu</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Reeves</surname>
<given-names>Darryl</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>darryl.reeves@yale.edu</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Rismani-Yazdi</surname>
<given-names>Hamid</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I3">3</xref>
<email>hrismani@mit.edu</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A4"><name><surname>Peccia</surname>
<given-names>Jordan</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>jordan.peccia@yale.edu</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06511, USA</aff>
<aff id="I2"><label>2</label>
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA</aff>
<aff id="I3"><label>3</label>
Now at the Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA</aff>
<pub-date pub-type="collection"><year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>18</day>
<month>7</month>
<year>2012</year>
</pub-date>
<volume>13</volume>
<fpage>170</fpage>
<lpage>170</lpage>
<history><date date-type="received"><day>25</day>
<month>2</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>26</day>
<month>6</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>Copyright ©2012 Haznedaroglu et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2012</copyright-year>
<copyright-holder>Haznedaroglu et al.; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2105/13/170"></self-uri>
<abstract><sec><title>Background</title>
<p>The <italic>k</italic>
-mer hash length is a key factor affecting the output of <italic>de novo</italic>
transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single <italic>k</italic>
-mer choices might result in the loss of unique contiguous sequences (contigs) and relevant biological information. A common solution to this problem is the clustering of single <italic>k</italic>
-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of <italic>k</italic>
-mer selection on the annotation output. This study provides an in-depth <italic>k</italic>
-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual <italic>k</italic>
-mers and clustered assemblies (CA) were considered using three representative software packages. Pair-wise comparison analyses (between individual <italic>k</italic>
-mers and CAs) were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog identifiers (KOIs), and to determine a strategy that maximizes the recovery of biological information in a <italic>de novo</italic>
transcriptome assembly.</p>
</sec>
<sec><title>Results</title>
<p>Analyses of single <italic>k</italic>
-mer assemblies resulted in the generation of various quantities of contigs and functional annotations within the selection window of <italic>k</italic>
-mers (<italic>k-</italic>
19 to <italic>k-</italic>
63). For each <italic>k</italic>
-mer in this window, generated assemblies contained certain unique contigs and KOIs that were not present in the other <italic>k</italic>
-mer assemblies. Producing a non-redundant CA of <italic>k</italic>
-mers 19 to 63 resulted in a more complete functional annotation than any single <italic>k</italic>
-mer assembly. However, a fraction of unique annotations remained (~0.19 to 0.27% of total KOIs) in the assemblies of individual <italic>k</italic>
-mers (<italic>k-</italic>
19 to <italic>k-</italic>
63) that were not present in the non-redundant CA. A workflow to recover these unique annotations is presented.</p>
</sec>
<sec><title>Conclusions</title>
<p>This study demonstrated that different <italic>k</italic>
-mer choices result in various quantities of unique contigs per single <italic>k</italic>
-mer assembly which affects biological information that is retrievable from the transcriptome. This undesirable effect can be minimized, but not eliminated, with clustering of multi-<italic>k</italic>
assemblies with redundancy removal. The complete extraction of biological information in <italic>de novo</italic>
transcriptomics studies requires both the production of a CA and efforts to identify unique contigs that are present in individual <italic>k</italic>
-mer assemblies but not in the CA.</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Connecticut</li>
<li>Massachusetts</li>
</region>
</list>
<tree><country name="États-Unis"><region name="Connecticut"><name sortKey="Haznedaroglu, Berat Z" sort="Haznedaroglu, Berat Z" uniqKey="Haznedaroglu B" first="Berat Z" last="Haznedaroglu">Berat Z. Haznedaroglu</name>
</region>
<name sortKey="Peccia, Jordan" sort="Peccia, Jordan" uniqKey="Peccia J" first="Jordan" last="Peccia">Jordan Peccia</name>
<name sortKey="Reeves, Darryl" sort="Reeves, Darryl" uniqKey="Reeves D" first="Darryl" last="Reeves">Darryl Reeves</name>
<name sortKey="Rismani Yazdi, Hamid" sort="Rismani Yazdi, Hamid" uniqKey="Rismani Yazdi H" first="Hamid" last="Rismani-Yazdi">Hamid Rismani-Yazdi</name>
<name sortKey="Rismani Yazdi, Hamid" sort="Rismani Yazdi, Hamid" uniqKey="Rismani Yazdi H" first="Hamid" last="Rismani-Yazdi">Hamid Rismani-Yazdi</name>
</country>
</tree>
</affiliations>
</record>
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