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R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring
- Source :
- Database-The journal of Biological Databases and Curation, Database-The journal of Biological Databases and Curation, Oxford University Press, 2016, 2016, ⟨10.1093/database/baw016⟩, Database-The journal of Biological Databases and Curation, 2016, 2016, pp.baw016. ⟨10.1093/database/baw016⟩, Database-The journal of Biological Databases and Curation, Oxford University Press, 2016, 2016, pp.baw016. ⟨10.1093/database/baw016⟩, Database (2016), baw016. (2016), Database: The Journal of Biological Databases and Curation
- Publication Year :
- 2016
- Publisher :
- HAL CCSD, 2016.
-
Abstract
- Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the number of barcodes and diatom taxa. In addition to these information, morphological features (e.g. biovolumes, chloroplasts…), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom.[br/] Database URL: http://www.rsyst.inra.fr/
- Subjects :
- 0106 biological sciences
code barre adn
taxonomie
Sequencing data
Statistics as Topic
pollution de l'eau
Fresh Water
Biology
Barcode
computer.software_genre
010603 evolutionary biology
01 natural sciences
DNA barcoding
General Biochemistry, Genetics and Molecular Biology
18S ribosomal RNA
law.invention
Access to Information
diatomées
law
Databases, Genetic
séquençage
DNA Barcoding, Taxonomic
Data Curation
Phylogeny
2. Zero hunger
Diatoms
Database
Data curation
Base Sequence
010604 marine biology & hydrobiology
biology.organism_classification
Freshwater algae
Diatom
Phenotype
Identification (biology)
Original Article
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
General Agricultural and Biological Sciences
computer
algorithme
Information Systems
Environmental Monitoring
Subjects
Details
- Language :
- English
- ISSN :
- 17580463
- Database :
- OpenAIRE
- Journal :
- Database-The journal of Biological Databases and Curation, Database-The journal of Biological Databases and Curation, Oxford University Press, 2016, 2016, ⟨10.1093/database/baw016⟩, Database-The journal of Biological Databases and Curation, 2016, 2016, pp.baw016. ⟨10.1093/database/baw016⟩, Database-The journal of Biological Databases and Curation, Oxford University Press, 2016, 2016, pp.baw016. ⟨10.1093/database/baw016⟩, Database (2016), baw016. (2016), Database: The Journal of Biological Databases and Curation
- Accession number :
- edsair.doi.dedup.....46b8ff7cf674b77f65396842cb71e815