Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco.
Identifieur interne : 000135 ( Main/Exploration ); précédent : 000134; suivant : 000136Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco.
Auteurs : Thomas Brockmöller [Allemagne] ; Zhihao Ling [Allemagne] ; Dapeng Li [Allemagne] ; Emmanuel Gaquerel [Allemagne] ; Ian T. Baldwin [Allemagne] ; Shuqing Xu [Allemagne]Source :
- BMC genomics [ 1471-2164 ] ; 2017.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Bases de données génétiques (MeSH), Biologie informatique (méthodes), Génomique (méthodes), Métabolome (MeSH), Métabolomique (méthodes), Phylogenèse (MeSH), Régulation de l'expression des gènes (MeSH), Tabac (classification), Tabac (génétique), Tabac (métabolisme), Transcriptome (MeSH).
- MESH :
- génétique : Tabac.
- métabolisme : Tabac.
- méthodes : Biologie informatique, Génomique, Métabolomique.
- classification : Analyse de profil d'expression de gènes, Bases de données génétiques, Métabolome, Phylogenèse, Régulation de l'expression des gènes, Tabac, Transcriptome.
English descriptors
- KwdEn :
- MESH :
- classification : Tobacco.
- genetics : Tobacco.
- metabolism : Tobacco.
- methods : Computational Biology, Genomics, Metabolomics.
- Databases, Genetic, Gene Expression Profiling, Gene Expression Regulation, Metabolome, Phylogeny, Transcriptome.
Abstract
BACKGROUND
Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now.
DESCRIPTION
We present the Nicotiana attenuata Data Hub (NaDH) as a centralized platform for integrating and visualizing genomic, phylogenomic, transcriptomic and metabolomic data in N. attenuata. The NaDH currently hosts collections of predicted protein coding sequences of 11 plant species, including two recently sequenced Nicotiana species, and their functional annotations, 222 microarray datasets from 10 different experiments, a transcriptomic atlas based on 20 RNA-seq expression profiles and a metabolomic atlas based on 895 metabolite spectra analyzed by mass spectrometry. We implemented several visualization tools, including a modified version of the Electronic Fluorescent Pictograph (eFP) browser, co-expression networks and the Interactive Tree Of Life (iTOL) for studying gene expression divergence among duplicated homologous. In addition, the NaDH allows researchers to query phylogenetic trees of 16,305 gene families and provides tools for analyzing their evolutionary history. Furthermore, we also implemented tools to identify co-expressed genes and metabolites, which can be used for predicting the functions of genes. Using the transcription factor NaMYB8 as an example, we illustrate that the tools and data in NaDH can facilitate identification of candidate genes involved in the biosynthesis of specialized metabolites.
CONCLUSION
The NaDH provides interactive visualization and data analysis tools that integrate the expression and evolutionary history of genes in Nicotiana, which can facilitate rapid gene discovery and comparative genomic analysis. Because N. attenuata shares many genome-wide features with other Nicotiana species including cultivated tobacco, and hence NaDH can be a resource for exploring the function and evolution of genes in Nicotiana species in general. The NaDH can be accessed at: http://nadh.ice.mpg.de/ .
DOI: 10.1186/s12864-016-3465-9
PubMed: 28086860
PubMed Central: PMC5237228
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Baldwin</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena</wicri:regionArea><wicri:noRegion>07745, Jena</wicri:noRegion><wicri:noRegion>07745, Jena</wicri:noRegion><wicri:noRegion>Jena</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Shuqing" sort="Xu, Shuqing" uniqKey="Xu S" first="Shuqing" last="Xu">Shuqing Xu</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany. sxu@ice.mpg.de.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena</wicri:regionArea><wicri:noRegion>07745, Jena</wicri:noRegion><wicri:noRegion>07745, Jena</wicri:noRegion><wicri:noRegion>Jena</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term><term>Databases, Genetic (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation (MeSH)</term><term>Genomics (methods)</term><term>Metabolome (MeSH)</term><term>Metabolomics (methods)</term><term>Phylogeny (MeSH)</term><term>Tobacco (classification)</term><term>Tobacco (genetics)</term><term>Tobacco (metabolism)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Bases de données génétiques (MeSH)</term><term>Biologie informatique (méthodes)</term><term>Génomique (méthodes)</term><term>Métabolome (MeSH)</term><term>Métabolomique (méthodes)</term><term>Phylogenèse (MeSH)</term><term>Régulation de l'expression des gènes (MeSH)</term><term>Tabac (classification)</term><term>Tabac (génétique)</term><term>Tabac (métabolisme)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Tobacco</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Tobacco</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Tabac</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Tobacco</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Genomics</term><term>Metabolomics</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Tabac</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie informatique</term><term>Génomique</term><term>Métabolomique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation</term><term>Metabolome</term><term>Phylogeny</term><term>Transcriptome</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Bases de données génétiques</term><term>Métabolome</term><term>Phylogenèse</term><term>Régulation de l'expression des gènes</term><term>Tabac</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now.</p></div><div type="abstract" xml:lang="en"><p><b>DESCRIPTION</b></p><p>We present the Nicotiana attenuata Data Hub (NaDH) as a centralized platform for integrating and visualizing genomic, phylogenomic, transcriptomic and metabolomic data in N. attenuata. The NaDH currently hosts collections of predicted protein coding sequences of 11 plant species, including two recently sequenced Nicotiana species, and their functional annotations, 222 microarray datasets from 10 different experiments, a transcriptomic atlas based on 20 RNA-seq expression profiles and a metabolomic atlas based on 895 metabolite spectra analyzed by mass spectrometry. We implemented several visualization tools, including a modified version of the Electronic Fluorescent Pictograph (eFP) browser, co-expression networks and the Interactive Tree Of Life (iTOL) for studying gene expression divergence among duplicated homologous. In addition, the NaDH allows researchers to query phylogenetic trees of 16,305 gene families and provides tools for analyzing their evolutionary history. Furthermore, we also implemented tools to identify co-expressed genes and metabolites, which can be used for predicting the functions of genes. Using the transcription factor NaMYB8 as an example, we illustrate that the tools and data in NaDH can facilitate identification of candidate genes involved in the biosynthesis of specialized metabolites.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>The NaDH provides interactive visualization and data analysis tools that integrate the expression and evolutionary history of genes in Nicotiana, which can facilitate rapid gene discovery and comparative genomic analysis. Because N. attenuata shares many genome-wide features with other Nicotiana species including cultivated tobacco, and hence NaDH can be a resource for exploring the function and evolution of genes in Nicotiana species in general. The NaDH can be accessed at: http://nadh.ice.mpg.de/ .</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28086860</PMID><DateCompleted><Year>2017</Year><Month>09</Month><Day>11</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>18</Volume><Issue>1</Issue><PubDate><Year>2017</Year><Month>01</Month><Day>13</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco.</ArticleTitle><Pagination><MedlinePgn>79</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-016-3465-9</ELocationID><Abstract><AbstractText Label="BACKGROUND">Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now.</AbstractText><AbstractText Label="DESCRIPTION">We present the Nicotiana attenuata Data Hub (NaDH) as a centralized platform for integrating and visualizing genomic, phylogenomic, transcriptomic and metabolomic data in N. attenuata. The NaDH currently hosts collections of predicted protein coding sequences of 11 plant species, including two recently sequenced Nicotiana species, and their functional annotations, 222 microarray datasets from 10 different experiments, a transcriptomic atlas based on 20 RNA-seq expression profiles and a metabolomic atlas based on 895 metabolite spectra analyzed by mass spectrometry. We implemented several visualization tools, including a modified version of the Electronic Fluorescent Pictograph (eFP) browser, co-expression networks and the Interactive Tree Of Life (iTOL) for studying gene expression divergence among duplicated homologous. In addition, the NaDH allows researchers to query phylogenetic trees of 16,305 gene families and provides tools for analyzing their evolutionary history. Furthermore, we also implemented tools to identify co-expressed genes and metabolites, which can be used for predicting the functions of genes. Using the transcription factor NaMYB8 as an example, we illustrate that the tools and data in NaDH can facilitate identification of candidate genes involved in the biosynthesis of specialized metabolites.</AbstractText><AbstractText Label="CONCLUSION">The NaDH provides interactive visualization and data analysis tools that integrate the expression and evolutionary history of genes in Nicotiana, which can facilitate rapid gene discovery and comparative genomic analysis. Because N. attenuata shares many genome-wide features with other Nicotiana species including cultivated tobacco, and hence NaDH can be a resource for exploring the function and evolution of genes in Nicotiana species in general. The NaDH can be accessed at: http://nadh.ice.mpg.de/ .</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Brockmöller</LastName><ForeName>Thomas</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ling</LastName><ForeName>Zhihao</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Dapeng</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gaquerel</LastName><ForeName>Emmanuel</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, Heidelberg, D-69120, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Baldwin</LastName><ForeName>Ian T</ForeName><Initials>IT</Initials><AffiliationInfo><Affiliation>Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Shuqing</ForeName><Initials>S</Initials><Identifier Source="ORCID">0000-0001-7010-4604</Identifier><AffiliationInfo><Affiliation>Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany. sxu@ice.mpg.de.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>01</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="Y">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005786" MajorTopicYN="N">Gene Expression Regulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055442" MajorTopicYN="Y">Metabolome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055432" MajorTopicYN="N">Metabolomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014026" MajorTopicYN="N">Tobacco</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="Y">Transcriptome</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Co-expression analysis</Keyword><Keyword MajorTopicYN="Y">Metabolomics</Keyword><Keyword MajorTopicYN="Y">Nicotiana attenuata</Keyword><Keyword MajorTopicYN="Y">Phylogenomics</Keyword><Keyword MajorTopicYN="Y">Transcriptomics</Keyword><Keyword MajorTopicYN="Y">genomics</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>06</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>12</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>1</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>1</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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