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

摘要: Studying the ecology of photosynthetic microeukaryotes and prokaryotic cyanobacterial communities requires molecular tools to complement morphological observations. These rely on specific genetic markers require development specialised databases achieve taxonomic assignment. We set up a reference database, called µgreen-db, for 23S rRNA gene. The sequences were retrieved from generalist (NCBI, SILVA) or Comparative RNA Web (CRW) databases, in addition more original approach involving recursive BLAST searches obtain best possible sequence recovery. At present, µgreen-db includes 2,326 belonging both eukaryotes prokaryotes encompassing 442 unique genera 736 species microeukaryotes, cyanobacteria non-vascular land plants based NCBI AlgaeBase taxonomy. When PR2/SILVA taxonomy is used instead, contains 2,217 (399 696 species). Using we able assign 96% V domain gene obtained by metabarcoding after amplification soil DNA at genus level, highlighting good coverage database. accessible http://microgreen-23sdatabase.ea.inra.fr.