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ITS (Internal Transcript Spacer) project

The ITS RefSeq Targeted Loci project started with an international collaboration including fungal taxonomic specialists to verify and provide a curated set of records with public collection data and correct taxonomic names. Collaborators at MycoBank, Index Fungorum, ISHAM, UNITE and curators from various culture and herbarium collections around the world contributed to this effort. ITS RefSeq accessions (NR_ ) include sequences mostly obtained from type specimens and a few from verified specimens (ultimately to be replaced with sequences from type specimens). The collection source of material is indicated in each record and collection acronyms follow the collection codes maintained at the NCBI BioCollections database. An interactive distance tree is routinely used to review for nodes with high taxonomic disagreement counts to find issues such as subjective synonyms, classification revision needs, incorrect sequence-name associations and incorrect sequence-lineage associations. The curated set consist of complete and near full length sequences. Too short partial sequences are excluded by using thresholds derived from (genus, order, class) descriptive statistics using the lowest rank possible. The ITS region has been re-annotated using the predicted annotation produced by the ITSx script (DOI: 10.1111/2041-210X.12073).

A publication about the international collaboration and the curation of the first ~2,600 RefSeq ITS records published in the Journal Database (PMC4075928) has more detail about the process. An additional collaboration included curation of Trichoderma records and the outcome published in the Journal Database (PMC5641268).

Data Access:

Last updated: 2019-10-22T16:11:05Z