ena-STUDY-INRA-CMSE-07-12-2018-14:29:14:909-212
µgreen-db: a reference database of the plastidial 23S rRNA gene of photosynthetic eukaryotic algae and cyanobacteria
Photosynthetic eukaryotic microalgae and prokaryotic cyanobacteria play tremendous ecological roles in biogeochemical cycles and can be found both in aquatic and terrestrial habitats. Given their importance molecular tools need to be developed to decipher the evolution and the ecology of these organisms in situ. They would represent promising tools complementary to the historically used morphological observations. The increase in High-Throughput Sequencing coupled metabarcoding was associated to the development of large generalist databases of prokaryotes or eukaryotes with historical molecular markers. However, it is now becoming more common to use new markers to target specific groups more closely, hence requiring the development of specialized databases to achieve taxonomic assignment of detected organisms. Here, we set up a reference database for the plastidial 23S rRNA gene used to characterize the group of photosynthetic eukaryotic algae and prokaryotic cyanobacteria. The sequences were retrieved from generalist NCBI, SILVA or CRW databases but also in a more original way by making recursive BLASTS to get the best sequences recovery. At present, this database, called ?green-db, includes 2 326 plastidial 23S rRNA sequences across four Kingdoms (Eubacteria, Chromista, Protozoa and Plantae) encompassing 442 unique genera and 736 species of eukaryotic algae, cyanobacteria and non-vascular land plants. In order to test the effectiveness of this database, we sequenced the domain V of the 23S rRNA plastid gene (commonly known as the Universal Plastid Amplicon) from two contrasting soil samples, and then performed a taxonomic assignment of the OTUs.
Photosynthetic eukaryotic microalgae and prokaryotic cyanobacteria play tremendous ecological roles in biogeochemical cycles and can be found both in aquatic and terrestrial habitats. Given their importance molecular tools need to be developed to decipher the evolution and the ecology of these organisms in situ. They would represent promising tools complementary to the historically used morphological observations. The increase in High-Throughput Sequencing coupled metabarcoding was associated to the development of large generalist databases of prokaryotes or eukaryotes with historical molecular markers. However, it is now becoming more common to use new markers to target specific groups more closely, hence requiring the development of specialized databases to achieve taxonomic assignment of detected organisms. Here, we set up a reference database for the plastidial 23S rRNA gene used to characterize the group of photosynthetic eukaryotic algae and prokaryotic cyanobacteria. The sequences were retrieved from generalist NCBI, SILVA or CRW databases but also in a more original way by making recursive BLASTS to get the best sequences recovery. At present, this database, called ?green-db, includes 2 326 plastidial 23S rRNA sequences across four Kingdoms (Eubacteria, Chromista, Protozoa and Plantae) encompassing 442 unique genera and 736 species of eukaryotic algae, cyanobacteria and non-vascular land plants. In order to test the effectiveness of this database, we sequenced the domain V of the 23S rRNA plastid gene (commonly known as the Universal Plastid Amplicon) from two contrasting soil samples, and then performed a taxonomic assignment of the OTUs.