Skip to Main content Skip to Navigation
Journal articles

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

Abstract : Studying 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.
Document type :
Journal articles
Complete list of metadatas

Cited literature [80 references]  Display  Hide  Download

https://hal.inrae.fr/hal-02937987
Contributor : Marion Desailly <>
Submitted on : Monday, September 14, 2020 - 3:53:43 PM
Last modification on : Wednesday, October 14, 2020 - 4:21:39 AM

File

2020_Djemiel_Nature.pdf
Publisher files allowed on an open archive

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

Citation

Christophe Djemiel, Damien Plassard, Sébastien Terrat, Olivier Crouzet, Joana Sauze, et al.. µgreen-db: a reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria. Scientific Reports, 2020, 10 (1), pp.1-11. ⟨10.1038/s41598-020-62555-1⟩. ⟨hal-02937987⟩

Share

Metrics

Record views

56

Files downloads

85