ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences

Abstract A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may...

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Bibliographic Details
Published in:Nucleic acids research 2018-01, Vol.46 (D1), p.D127-D132
Main Authors: Santamaria, Monica, Fosso, Bruno, Licciulli, Flavio, Balech, Bachir, Larini, Ilaria, Grillo, Giorgio, De Caro, Giorgio, Liuni, Sabino, Pesole, Graziano
Format: Article
Language:English
Subjects:
Animals
Database Issue
Databases, Nucleic Acid
DNA Barcoding, Taxonomic
DNA, Ribosomal Spacer - genetics
Eukaryota - genetics
Humans
Internet
Metagenomics - methods
Metagenomics - trends
Molecular Sequence Annotation
Multigene Family
RNA, Ribosomal - genetics
User-Computer Interface
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Summary:Abstract A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels. As metabarcoding data analysis rely on the availability of a well-curated barcode reference resource, a comprehensive collection of ITS1 sequences supplied with robust taxonomies, is highly needed. To address this issue, we created ITSoneDB (available at http://itsonedb.cloud.ba.infn.it/) which in its current version hosts 985 240 ITS1 sequences spanning over 134 000 eukaryotic species. Each ITS1 is mapped on the NCBI reference taxonomy with its start and end positions precisely annotated. ITSoneDB has been developed in agreement to the FAIR guidelines by enabling the users to query and download its content through a simple web-interface and access relevant metadata by cross-linking to European Nucleotide Archive.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkx855