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Research article - Peer-reviewed, 2014

Improving ITS sequence data for identification of plant pathogenic fungi

Nilsson, R. Henrik; Berlin, Anna; Friberg, Hanna; Lindahl, Björn; Abarenkov, Kessy

Abstract

Plant pathogenic fungi are a large and diverseassemblage of eukaryotes with substantial impactson natural ecosystems and human endeavours. Thesetaxa often have complex and poorly understood lifecycles, lack observable, discriminatory morphologicalcharacters, and may not be amenable to in vitro culturing.As a result, species identification is frequentlydifficult. Molecular (DNA sequence) data have emergedas crucial information for the taxonomic identificationof plant pathogenic fungi, with the nuclear ribosomalinternal transcribed spacer (ITS) region being the mostpopular marker. However, international nucleotide sequencedatabases are accumulating numerous sequencesof compromised or low-resolution taxonomic annotationsand substandard technical quality, making theiruse in the molecular identification of plant pathogenicfungi problematic. Here we report on a concerted effortto identify high-quality reference sequences for variousplant pathogenic fungi and to re-annotate incorrectly orinsufficiently annotated public ITS sequences from thesefungal lineages. A third objective was to enrich thesequences with geographical and ecological metadata.The results – a total of 31,954 changes – are incorporatedin and made available through the UNITE databasefor molecular identification of fungi (http://unite.ut.ee),including standalone FASTA files of sequence data forlocal BLAST searches, use in the next-generation sequencinganalysis platforms QIIME and mothur, andrelated applications. The present initiative is just a beginningto cover the wide spectrum of plant pathogenicfungi, and we invite all researchers with pertinent expertiseto join the annotation effort.

Published in

Fungal Diversity
2014, Volume: 67, number: 1, pages: 11-19