Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods
Identifieur interne : 001C94 ( Main/Curation ); précédent : 001C93; suivant : 001C95Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods
Auteurs : Guillaume Martin ; Franc-Christophe Baurens ; Gaëtan Droc ; Mathieu Rouard ; Alberto Cenci ; Andrzej Kilian ; Alex Hastie [États-Unis] ; Jaroslav Doležel [République tchèque] ; Jean-Marc Aury [France] ; Adriana Alberti [France] ; Françoise Carreel ; Angélique D OntSource :
- BMC Genomics [ 1471-2164 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical : Genetic Markers.
- genetics : Musa.
- methods : Computational Biology.
- Contig Mapping, Genome, Plant, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Sequence Analysis, DNA.
Abstract
Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana (
We have developed a modular bioinformatics pipeline to improve genome sequence assemblies, which can handle various types of data. The pipeline comprises several semi-automated tools. However, unlike classical automated tools that are based on global parameters, the semi-automated tools proposed an expert mode for a user who can decide on suggested improvements through local compromises. The pipeline was used to improve the draft genome sequence of
The release of the
The online version of this article (doi:10.1186/s12864-016-2579-4) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-016-2579-4
PubMed: 26984673
PubMed Central: 4793746
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Guillaume Martin<affiliation><nlm:aff id="Aff1">CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5 France</nlm:aff><wicri:noCountry code="subfield">cedex 5 France</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff1">CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5 France</nlm:aff><wicri:noCountry code="subfield">cedex 5 France</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff1">CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5 France</nlm:aff><wicri:noCountry code="subfield">cedex 5 France</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5 France</nlm:aff><wicri:noCountry code="subfield">Cedex 5 France</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5 France</nlm:aff><wicri:noCountry code="subfield">Cedex 5 France</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff3">Diversity Arrays Technology, Yarralumla, Australian Capital Territory 2600 Australia</nlm:aff><wicri:noCountry code="subfield">Australian Capital Territory 2600 Australia</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff1">CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5 France</nlm:aff><wicri:noCountry code="subfield">cedex 5 France</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff1">CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5 France</nlm:aff><wicri:noCountry code="subfield">cedex 5 France</wicri:noCountry></affiliation>Le document en format XML
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type="state">Californie</region></placeName><wicri:cityArea>BioNano Genomics, 9640 Towne Centre Drive, San Diego</wicri:cityArea></affiliation></author><author><name sortKey="Dolezel, Jaroslav" sort="Dolezel, Jaroslav" uniqKey="Dolezel J" first="Jaroslav" last="Doležel">Jaroslav Doležel</name><affiliation wicri:level="1"><nlm:aff id="Aff5">Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc</wicri:regionArea><wicri:noRegion>CZ-78371 Olomouc</wicri:noRegion></affiliation></author><author><name sortKey="Aury, Jean Marc" sort="Aury, Jean Marc" uniqKey="Aury J" first="Jean-Marc" last="Aury">Jean-Marc Aury</name><affiliation wicri:level="1"><nlm:aff id="Aff6">Commissariat à l’Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Commissariat à l’Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057 Evry</wicri:regionArea><wicri:noRegion>91057 Evry</wicri:noRegion><wicri:noRegion>91057 Evry</wicri:noRegion></affiliation></author><author><name sortKey="Alberti, Adriana" sort="Alberti, Adriana" uniqKey="Alberti A" first="Adriana" last="Alberti">Adriana Alberti</name><affiliation wicri:level="1"><nlm:aff id="Aff6">Commissariat à l’Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Commissariat à l’Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057 Evry</wicri:regionArea><wicri:noRegion>91057 Evry</wicri:noRegion><wicri:noRegion>91057 Evry</wicri:noRegion></affiliation></author><author><name sortKey="Carreel, Francoise" sort="Carreel, Francoise" uniqKey="Carreel F" first="Françoise" last="Carreel">Françoise Carreel</name><affiliation><nlm:aff id="Aff1">CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5 France</nlm:aff><wicri:noCountry code="subfield">cedex 5 France</wicri:noCountry></affiliation></author><author><name sortKey="D Ont, Angelique" sort="D Ont, Angelique" uniqKey="D Ont A" first="Angélique" last="D Ont">Angélique D Ont</name><affiliation><nlm:aff id="Aff1">CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5 France</nlm:aff><wicri:noCountry code="subfield">cedex 5 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Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5 France</nlm:aff><wicri:noCountry code="subfield">cedex 5 France</wicri:noCountry></affiliation></author><author><name sortKey="Baurens, Franc Christophe" sort="Baurens, Franc Christophe" uniqKey="Baurens F" first="Franc-Christophe" last="Baurens">Franc-Christophe Baurens</name><affiliation><nlm:aff id="Aff1">CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5 France</nlm:aff><wicri:noCountry code="subfield">cedex 5 France</wicri:noCountry></affiliation></author><author><name sortKey="Droc, Gaetan" sort="Droc, Gaetan" uniqKey="Droc G" first="Gaëtan" last="Droc">Gaëtan Droc</name><affiliation><nlm:aff id="Aff1">CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5 France</nlm:aff><wicri:noCountry code="subfield">cedex 5 France</wicri:noCountry></affiliation></author><author><name sortKey="Rouard, Mathieu" sort="Rouard, Mathieu" uniqKey="Rouard M" first="Mathieu" last="Rouard">Mathieu Rouard</name><affiliation><nlm:aff id="Aff2">Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5 France</nlm:aff><wicri:noCountry code="subfield">Cedex 5 France</wicri:noCountry></affiliation></author><author><name sortKey="Cenci, Alberto" sort="Cenci, Alberto" uniqKey="Cenci A" first="Alberto" last="Cenci">Alberto Cenci</name><affiliation><nlm:aff id="Aff2">Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5 France</nlm:aff><wicri:noCountry code="subfield">Cedex 5 France</wicri:noCountry></affiliation></author><author><name sortKey="Kilian, Andrzej" sort="Kilian, Andrzej" uniqKey="Kilian A" first="Andrzej" last="Kilian">Andrzej Kilian</name><affiliation><nlm:aff id="Aff3">Diversity Arrays Technology, Yarralumla, Australian Capital Territory 2600 Australia</nlm:aff><wicri:noCountry code="subfield">Australian Capital Territory 2600 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Hastie, Alex" sort="Hastie, Alex" uniqKey="Hastie A" first="Alex" last="Hastie">Alex Hastie</name><affiliation wicri:level="2"><nlm:aff id="Aff4">BioNano Genomics, 9640 Towne Centre Drive, San Diego, CA 92121 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>BioNano Genomics, 9640 Towne Centre Drive, San Diego</wicri:cityArea></affiliation></author><author><name sortKey="Dolezel, Jaroslav" sort="Dolezel, Jaroslav" uniqKey="Dolezel J" first="Jaroslav" last="Doležel">Jaroslav Doležel</name><affiliation wicri:level="1"><nlm:aff id="Aff5">Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc</wicri:regionArea><wicri:noRegion>CZ-78371 Olomouc</wicri:noRegion></affiliation></author><author><name sortKey="Aury, Jean Marc" sort="Aury, Jean Marc" uniqKey="Aury J" first="Jean-Marc" last="Aury">Jean-Marc Aury</name><affiliation wicri:level="1"><nlm:aff id="Aff6">Commissariat à l’Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Commissariat à l’Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057 Evry</wicri:regionArea><wicri:noRegion>91057 Evry</wicri:noRegion><wicri:noRegion>91057 Evry</wicri:noRegion></affiliation></author><author><name sortKey="Alberti, Adriana" sort="Alberti, Adriana" uniqKey="Alberti A" first="Adriana" last="Alberti">Adriana Alberti</name><affiliation wicri:level="1"><nlm:aff id="Aff6">Commissariat à l’Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Commissariat à l’Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057 Evry</wicri:regionArea><wicri:noRegion>91057 Evry</wicri:noRegion><wicri:noRegion>91057 Evry</wicri:noRegion></affiliation></author><author><name sortKey="Carreel, Francoise" sort="Carreel, Francoise" uniqKey="Carreel F" first="Françoise" last="Carreel">Françoise Carreel</name><affiliation><nlm:aff id="Aff1">CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5 France</nlm:aff><wicri:noCountry code="subfield">cedex 5 France</wicri:noCountry></affiliation></author><author><name sortKey="D Ont, Angelique" sort="D Ont, Angelique" uniqKey="D Ont A" first="Angélique" last="D Ont">Angélique D Ont</name><affiliation><nlm:aff id="Aff1">CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5 France</nlm:aff><wicri:noCountry code="subfield">cedex 5 France</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term><term>Contig Mapping</term><term>Genetic Markers</term><term>Genome, Plant</term><term>High-Throughput Nucleotide Sequencing</term><term>Molecular Sequence Annotation</term><term>Musa (genetics)</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Annotation de séquence moléculaire</term><term>Biologie informatique ()</term><term>Cartographie de contigs</term><term>Génome végétal</term><term>Marqueurs génétiques</term><term>Musa (génétique)</term><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Musa</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Musa</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Contig Mapping</term><term>Genome, Plant</term><term>High-Throughput Nucleotide Sequencing</term><term>Molecular Sequence Annotation</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Annotation de séquence moléculaire</term><term>Biologie informatique</term><term>Cartographie de contigs</term><term>Génome végétal</term><term>Marqueurs génétiques</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana (<italic>Musa acuminata</italic>).</p></sec><sec><title>Results</title><p>We have developed a modular bioinformatics pipeline to improve genome sequence assemblies, which can handle various types of data. The pipeline comprises several semi-automated tools. However, unlike classical automated tools that are based on global parameters, the semi-automated tools proposed an expert mode for a user who can decide on suggested improvements through local compromises. The pipeline was used to improve the draft genome sequence of <italic>Musa acuminata.</italic> Genotyping by sequencing (GBS) of a segregating population and paired-end sequencing were used to detect and correct scaffold misassemblies. Long insert size paired-end reads identified scaffold junctions and fusions missed by automated assembly methods. GBS markers were used to anchor scaffolds to pseudo-molecules with a new bioinformatics approach that avoids the tedious step of marker ordering during genetic map construction. Furthermore, a genome map was constructed and used to assemble scaffolds into super scaffolds. Finally, a consensus gene annotation was projected on the new assembly from two pre-existing annotations. This approach reduced the total <italic>Musa</italic> scaffold number from 7513 to 1532 (i.e. by 80 %), with an N50 that increased from 1.3 Mb (65 scaffolds) to 3.0 Mb (26 scaffolds). 89.5 % of the assembly was anchored to the 11 <italic>Musa</italic> chromosomes compared to the previous 70 %. Unknown sites (N) were reduced from 17.3 to 10.0 %.</p></sec><sec><title>Conclusion</title><p>The release of the <italic>Musa acuminata</italic> reference genome version 2 provides a platform for detailed analysis of banana genome variation, function and evolution. Bioinformatics tools developed in this work can be used to improve genome sequence assemblies in other species.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-016-2579-4) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bolger, Me" uniqKey="Bolger M">ME Bolger</name></author><author><name sortKey="Weisshaar, B" uniqKey="Weisshaar B">B Weisshaar</name></author><author><name sortKey="Scholz, U" uniqKey="Scholz U">U Scholz</name></author><author><name sortKey="Stein, N" uniqKey="Stein N">N Stein</name></author><author><name sortKey="Usadel, B" uniqKey="Usadel B">B Usadel</name></author><author><name sortKey="Mayer, Kf" uniqKey="Mayer K">KF Mayer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Feuillet, C" uniqKey="Feuillet C">C 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Cenci</name></author><author><name sortKey="Pitollat, B" uniqKey="Pitollat B">B Pitollat</name></author><author><name sortKey="D Ont, A" uniqKey="D Ont A">A D’Hont</name></author><author><name sortKey="Ruiz, M" uniqKey="Ruiz M">M Ruiz</name></author><author><name sortKey="Rouard, M" uniqKey="Rouard M">M Rouard</name></author><author><name sortKey="Bocs, S" uniqKey="Bocs S">S Bocs</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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