Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.
Identifieur interne : 002152 ( PubMed/Curation ); précédent : 002151; suivant : 002153Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.
Auteurs : Guillaume Martin [France] ; Franc-Christophe Baurens [France] ; Gaëtan Droc [France] ; Mathieu Rouard [France] ; Alberto Cenci [France] ; Andrzej Kilian [Australie] ; Alex Hastie [États-Unis] ; Jaroslav Doležel [République tchèque] ; Jean-Marc Aury [France] ; Adriana Alberti [France] ; Françoise Carreel [France] ; Angélique D'Hont [France]Source :
- 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 (Musa acuminata).
DOI: 10.1186/s12864-016-2579-4
PubMed: 26984673
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sort="Dolezel, Jaroslav" uniqKey="Dolezel J" first="Jaroslav" last="Doležel">Jaroslav Doležel</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.</nlm:affiliation><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></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:affiliation>Commissariat à l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057, Evry, France.</nlm:affiliation><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></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:affiliation>Commissariat à l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057, Evry, France.</nlm:affiliation><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></affiliation></author><author><name sortKey="Carreel, Francoise" sort="Carreel, Francoise" uniqKey="Carreel F" first="Françoise" last="Carreel">Françoise Carreel</name><affiliation wicri:level="1"><nlm:affiliation>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:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5</wicri:regionArea></affiliation></author><author><name sortKey="D Hont, Angelique" sort="D Hont, Angelique" uniqKey="D Hont A" first="Angélique" last="D'Hont">Angélique D'Hont</name><affiliation wicri:level="1"><nlm:affiliation>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. dhont@cirad.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 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Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5</wicri:regionArea></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 wicri:level="1"><nlm:affiliation>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:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5</wicri:regionArea></affiliation></author><author><name sortKey="Droc, Gaetan" sort="Droc, Gaetan" uniqKey="Droc G" first="Gaëtan" last="Droc">Gaëtan Droc</name><affiliation wicri:level="1"><nlm:affiliation>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:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5</wicri:regionArea></affiliation></author><author><name sortKey="Rouard, Mathieu" sort="Rouard, Mathieu" uniqKey="Rouard M" first="Mathieu" last="Rouard">Mathieu Rouard</name><affiliation wicri:level="1"><nlm:affiliation>Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5</wicri:regionArea></affiliation></author><author><name sortKey="Cenci, Alberto" sort="Cenci, Alberto" uniqKey="Cenci A" first="Alberto" last="Cenci">Alberto Cenci</name><affiliation wicri:level="1"><nlm:affiliation>Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5</wicri:regionArea></affiliation></author><author><name sortKey="Kilian, Andrzej" sort="Kilian, Andrzej" uniqKey="Kilian A" first="Andrzej" last="Kilian">Andrzej Kilian</name><affiliation wicri:level="1"><nlm:affiliation>Diversity Arrays Technology, Yarralumla, Australian Capital Territory, 2600, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Diversity Arrays Technology, Yarralumla, Australian Capital Territory, 2600</wicri:regionArea></affiliation></author><author><name sortKey="Hastie, Alex" sort="Hastie, Alex" uniqKey="Hastie A" first="Alex" last="Hastie">Alex Hastie</name><affiliation wicri:level="1"><nlm:affiliation>BioNano Genomics, 9640 Towne Centre Drive, San Diego, CA, 92121, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>BioNano Genomics, 9640 Towne Centre Drive, San Diego, CA, 92121</wicri:regionArea></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:affiliation>Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.</nlm:affiliation><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></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:affiliation>Commissariat à l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057, Evry, France.</nlm:affiliation><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></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:affiliation>Commissariat à l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057, Evry, France.</nlm:affiliation><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></affiliation></author><author><name sortKey="Carreel, Francoise" sort="Carreel, Francoise" uniqKey="Carreel F" first="Françoise" last="Carreel">Françoise Carreel</name><affiliation wicri:level="1"><nlm:affiliation>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:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5</wicri:regionArea></affiliation></author><author><name sortKey="D Hont, Angelique" sort="D Hont, Angelique" uniqKey="D Hont A" first="Angélique" last="D'Hont">Angélique D'Hont</name><affiliation wicri:level="1"><nlm:affiliation>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. dhont@cirad.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5</wicri:regionArea></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016" type="published">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">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 (Musa acuminata).</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26984673</PMID><DateCreated><Year>2016</Year><Month>03</Month><Day>17</Day></DateCreated><DateCompleted><Year>2016</Year><Month>11</Month><Day>03</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>17</Volume><PubDate><Year>2016</Year><Month>Mar</Month><Day>16</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.</ArticleTitle><Pagination><MedlinePgn>243</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-016-2579-4</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">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 (Musa acuminata).</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">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 Musa acuminata. 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 Musa 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 Musa chromosomes compared to the previous 70%. Unknown sites (N) were reduced from 17.3 to 10.0%.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">The release of the Musa acuminata 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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Martin</LastName><ForeName>Guillaume</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>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.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Baurens</LastName><ForeName>Franc-Christophe</ForeName><Initials>FC</Initials><AffiliationInfo><Affiliation>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.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Droc</LastName><ForeName>Gaëtan</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>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.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rouard</LastName><ForeName>Mathieu</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cenci</LastName><ForeName>Alberto</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kilian</LastName><ForeName>Andrzej</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Diversity Arrays Technology, Yarralumla, Australian Capital Territory, 2600, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hastie</LastName><ForeName>Alex</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>BioNano Genomics, 9640 Towne Centre Drive, San Diego, CA, 92121, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Doležel</LastName><ForeName>Jaroslav</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Aury</LastName><ForeName>Jean-Marc</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>Commissariat à l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057, Evry, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Alberti</LastName><ForeName>Adriana</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Commissariat à l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057, Evry, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Carreel</LastName><ForeName>Françoise</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>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.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>D'Hont</LastName><ForeName>Angélique</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>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. dhont@cirad.fr.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType 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Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020451" MajorTopicYN="N">Contig Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D028521" MajorTopicYN="N">Musa</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading></MeshHeadingList><OtherID 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