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 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.

Phylogeny and character evolution in the Dacrymycetes, and systematics of Unilacrymaceae and Dacryonaemataceae fam. nov.

“…The ITS1 region was considered to start immediately after the highly conserved motif ‘AGGACATTA’ at the end of the 18S. The 5’ limit of the 5.8S region was defined by comparing the aligned sequences to annotated sequences from ITSoneBD ( Santamaria et al 2017 ). The 3’-end of the 5.8S and the 5’ start of the 28S were defined using the annotate option of the ITS2 database ( Keller et al 2009 ).…”

“…The ITS1 region was considered to start immediately after the highly conserved motif 'AGGACATTA' at the end of the 18S. The 5' limit of the 5.8S region was defined by comparing the aligned sequences to annotated sequences from ITSoneBD (Santamaria et al 2017). The 3'-end of the 5.8S and the 5' start of the 28S were defined using the annotate option of the ITS2 database (Keller et al 2009 Additionally, we excluded a highly variable and gappy region in the 12S appearing between two easily alignable regions (the one in the 5' ending with the motif 'AGGGTTYGTAG', and the one in 3' starting with the motif 'TAGAATCW').…”

A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa

“…Tomophagus cattienensis and T. colossus, G. subresinosum, G. tsunodae, G. ramosissimum and G. shandongense, Humphreya coffeata and G. sandunense. Hence, multiple alignments of seven different matrices (Table 2) were performed with the aid of the online version of MAFFT v. 7 (Katoh and Standley 2013; https:// mafft.cbrc.jp/alignment/software/) by using the progressive method G-INS-1 and were finally inspected and manually optimised in MEGA X (Kumar et al 2018). The 5' end and the 3' end of ITS1 and ITS2 were determined, based on hidden Markov models (HMMs), localisation deriving from the ITSoneDB (Santamaria et al 2018) and ITS2 Database (Ankenbrand et al 2015). Oligonucleotides marking the start and end of ITS regions are: TATCGA to ATATAC for ITS1, AACTTT to TCATGA for 5.8S and AATCTT to TTATGA for ITS2.…”

Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties

“…While several reference databases are available for 16S rRNA bacterial sequences, just a few databases are available for fungal metabarcoding: UNITE (User-friendly Nordic ITS Ectomycorrhiza Database) (Abarenkov et al, 2010 ), ITS2 Database (Ankenbrand et al, 2015 ), and ITSoneDB (Santamaria et al, 2017 ). The lack of a wider range of available databases and tools specific for fungal metabarcoding can be ascribed to the relatively recent interest in fungal metagenomics and to the lack of a consensus in the selection of the target used for metabarcoding.…”

“…The lack of a wider range of available databases and tools specific for fungal metabarcoding can be ascribed to the relatively recent interest in fungal metagenomics and to the lack of a consensus in the selection of the target used for metabarcoding. While UNITE encompasses entire ITS1-5.8S rRNA-ITS2 sequences (Abarenkov et al, 2010 ), the ITS2 database includes sequences of the ITS2 region (Ankenbrand et al, 2015 ), and the ITSoneDB includes sequences of the ITS1 region (Santamaria et al, 2017 ).…”