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µgreen-db: a reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria

hal.structure.identifierAgroécologie [Dijon]
dc.contributor.authorDJEMIEL, Christophe
hal.structure.identifierInstitut de Génétique et de Biologie Moléculaire et Cellulaire [IGBMC]
dc.contributor.authorPLASSARD, Damien
hal.structure.identifierAgroécologie [Dijon]
dc.contributor.authorTERRAT, Sébastien
hal.structure.identifierEcologie fonctionnelle et écotoxicologie des agroécosystèmes [ECOSYS]
dc.contributor.authorCROUZET, Olivier
hal.structure.identifierInteractions Sol Plante Atmosphère [UMR ISPA]
dc.contributor.authorSAUZE, Joana
hal.structure.identifierAgroécologie [Dijon]
dc.contributor.authorMONDY, Samuel
hal.structure.identifierAgroécologie [Dijon]
dc.contributor.authorNOWAK, Virginie
hal.structure.identifierInteractions Sol Plante Atmosphère [UMR ISPA]
dc.contributor.authorWINGATE, Lisa
hal.structure.identifierInteractions Sol Plante Atmosphère [UMR ISPA]
dc.contributor.authorOGÉE, Jérôme
hal.structure.identifierAgroécologie [Dijon]
dc.contributor.authorMARON, Pierre-Alain
dc.date.accessioned2024-04-08T11:53:21Z
dc.date.available2024-04-08T11:53:21Z
dc.date.issued2020-12
dc.identifier.issn2045-2322
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/195530
dc.description.abstractEnStudying the ecology of photosynthetic microeukaryotes and prokaryotic cyanobacterial communities requires molecular tools to complement morphological observations. These tools rely on specific genetic markers and require the development of specialised databases to achieve taxonomic assignment. We set up a reference database, called µgreen-db, for the 23S rRNA gene. The sequences were retrieved from generalist (NCBI, SILVA) or Comparative RNA Web (CRW) databases, in addition to a more original approach involving recursive BLAST searches to obtain the best possible sequence recovery. At present, µgreen-db includes 2,326 23S rRNA sequences belonging to both eukaryotes and prokaryotes encompassing 442 unique genera and 736 species of photosynthetic microeukaryotes, cyanobacteria and non-vascular land plants based on the NCBI and AlgaeBase taxonomy. When PR2/SILVA taxonomy is used instead, µgreen-db contains 2,217 sequences (399 unique genera and 696 unique species). Using µgreen-db, we were able to assign 96% of the sequences of the V domain of the 23S rRNA gene obtained by metabarcoding after amplification from soil DNA at the genus level, highlighting good coverage of the database. µgreen-db is accessible at http://microgreen-23sdatabase.ea.inra.fr.
dc.description.sponsorshipEtude des mécanismes de régulation de l'anhydrase carbonique et des flux de COS et CO18O dans les écosystèmes terrestres - ANR-13-BS06-0005
dc.language.isoen
dc.publisherNature Publishing Group
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subjectMicroeucaryote
dc.subjectMarqueur génétique
dc.title.enµgreen-db: a reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria
dc.typeArticle de revue
dc.identifier.doi10.1038/s41598-020-62555-1
dc.subject.halSciences de l'environnement
bordeaux.journalScientific Reports
bordeaux.page1-11
bordeaux.volume10
bordeaux.hal.laboratoriesInteractions Soil Plant Atmosphere (ISPA) - UMR 1391*
bordeaux.issue1
bordeaux.institutionBordeaux Sciences Agro
bordeaux.institutionINRAE
bordeaux.peerReviewedoui
hal.identifierhal-02937987
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02937987v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Scientific%20Reports&rft.date=2020-12&rft.volume=10&rft.issue=1&rft.spage=1-11&rft.epage=1-11&rft.eissn=2045-2322&rft.issn=2045-2322&rft.au=DJEMIEL,%20Christophe&PLASSARD,%20Damien&TERRAT,%20S%C3%A9bastien&CROUZET,%20Olivier&SAUZE,%20Joana&rft.genre=article


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