ArticleScientific reports2020
µgreen-db: a reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 50 citations in OpenAlex.
- Bioinformatics Strategy for 16s and 23s rRNA Metabarcoding Data.Biotech (Basel (Switzerland)) · 2026Article
- Rotating algal biofilm reactors retain core microbial communities during scale-up.Journal of biological engineering · 2026Article
- Different phytoplankton distributions and assembly processes in marine water masses with contrasting nutrient conditions.BMC microbiology · 2025Article
- Microbial and bryospheric photosynthesis of boreal peatlands have peatland-type-specific responses to long-term drying.The New phytologist · 2025Article
- A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.Molecular ecology resources · 2024Review
- Article
- Phytoplankton ecology in the early years of a boreal oil sands end pit lake.Environmental microbiome · 2024Article
- Phototrophic and fungal communities inhabiting the Roman cryptoporticus of the national museum Machado de Castro (UNESCO site, Coimbra, Portugal).World journal of microbiology & biotechnology · 2022Article
- Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production.Frontiers in microbiology · 2022Review
- Molecular diet analysis enables detection of diatom and cyanobacteria DNA in the gut of Macoma balthica.PloS one · 2022Article
- BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons.BMC bioinformatics · 2020Article
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Authors and funding
10 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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 PR
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