The amplicon-based Metagenomics approach here referred as DNA Metabarcoding, is the method of choice to quickly infer the global composition of both bacterial and eukaryotic communities in a variety of environments, including the human body. In this respect, whereas 16S rRNA is the de facto standard locus for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster is gaining popularity for its high potential in discriminating eukaryotes at the deepest taxonomic levels. In this context the availability of well-curated reference databases, interfaced with established analysis tools, is mandatory to obtain reliable taxonomic profiles. This is not a trivial issue given the paucity of ITS1 targeted databases to date, structured to feed a number of popular tools and services for their use in taxonomic assignment workflows. In order to provide the first curated resource of ITS1 sequences covering all the Eukaryotic domains and well suited for eukaryotic DNA metabarcoding surveys and enhance its connectivity with established analysis pipelines we deployed ITSoneWB (ITS1 workbench). Its virtual instance has been deployed on the INFN-Bari ReCaS cloud facility running OpenStack and includes three taxonomic analysis pipelines pointing to ITSoneDB release 1.138. The current ITSoneDB version (available at itsonedb.cloud.ba.infn.it) hosts 1,174,761 ITS1 sequences spanning 157,531 species, a tool for the barcoding gap computation and for the design of taxon targeted amplification primers and, recently, a system enabling to identify ITS1 regions in shotgun environmental data. ITSoneWB has been designed and developed in the mainframe of the ELIXIR 2017 Implementation Studies for integration of Italian node and the EXCELERATE marine Metagenomics activities. ITSoneWB is available at itsonewb.cloud.ba.infn.it/galaxy and its design allows to scale the underlying resources in order to support large project and/or to include new tools.
ITSoneDB & ITSoneWB: supporting the metabarcoding investigation of eukaryotic communities
Monica Santamaria
;Graziano Pesole
;Bruno Fosso;Marco Antonio Tangaro;Giuseppe Defazio
2019-01-01
Abstract
The amplicon-based Metagenomics approach here referred as DNA Metabarcoding, is the method of choice to quickly infer the global composition of both bacterial and eukaryotic communities in a variety of environments, including the human body. In this respect, whereas 16S rRNA is the de facto standard locus for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster is gaining popularity for its high potential in discriminating eukaryotes at the deepest taxonomic levels. In this context the availability of well-curated reference databases, interfaced with established analysis tools, is mandatory to obtain reliable taxonomic profiles. This is not a trivial issue given the paucity of ITS1 targeted databases to date, structured to feed a number of popular tools and services for their use in taxonomic assignment workflows. In order to provide the first curated resource of ITS1 sequences covering all the Eukaryotic domains and well suited for eukaryotic DNA metabarcoding surveys and enhance its connectivity with established analysis pipelines we deployed ITSoneWB (ITS1 workbench). Its virtual instance has been deployed on the INFN-Bari ReCaS cloud facility running OpenStack and includes three taxonomic analysis pipelines pointing to ITSoneDB release 1.138. The current ITSoneDB version (available at itsonedb.cloud.ba.infn.it) hosts 1,174,761 ITS1 sequences spanning 157,531 species, a tool for the barcoding gap computation and for the design of taxon targeted amplification primers and, recently, a system enabling to identify ITS1 regions in shotgun environmental data. ITSoneWB has been designed and developed in the mainframe of the ELIXIR 2017 Implementation Studies for integration of Italian node and the EXCELERATE marine Metagenomics activities. ITSoneWB is available at itsonewb.cloud.ba.infn.it/galaxy and its design allows to scale the underlying resources in order to support large project and/or to include new tools.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
