uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
Improving ITS sequence data for identification of plant pathogenic fungi
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
Show others and affiliations
2014 (English)In: Fungal diversity, ISSN 1560-2745, Vol. 67, no 1, 11-19 p.Article in journal (Refereed) Published
Abstract [en]

Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results - a total of 31,954 changes - are incorporated in and made available through the UNITE database for molecular identification of fungi (including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.

Place, publisher, year, edition, pages
2014. Vol. 67, no 1, 11-19 p.
Keyword [en]
Phytopathogenic fungi, Molecular identification, ITS, Taxonomy, Annotation
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-235519DOI: 10.1007/s13225-014-0291-8ISI: 000342427300002OAI: oai:DiVA.org:uu-235519DiVA: diva2:761149
Available from: 2014-11-05 Created: 2014-11-05 Last updated: 2015-08-30Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text

Search in DiVA

By author/editor
Ryberg, MartinBahram, Mohammad
By organisation
Systematic Biology
In the same journal
Fungal diversity
Biological Sciences

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 255 hits
ReferencesLink to record
Permanent link

Direct link