An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity.
The environmental and distributional data associated with fungal internal transcribed spacer (ITS) sequences in GenBank are investigated and a new web-based tool with which these sequences can be explored is introduced. All fungal ITS sequences in GenBank were classified as either identified to species level or insufficiently identified and compared using BLAST. The results are made available as a biweekly updated web service that can be queried to retrieve all insufficiently identified sequences (IIS) associated with any fungal genus. The most commonly available annotation items in GenBank are isolation source (55%); country of origin (50%); and specific host (38%). The molecular sampling of fungi shows a bias towards North America, Europe, China, and Japan whereas vast geographical areas remain effectively unexplored. Mycorrhizal and parasitic genera are on average associated with more IIS than are saprophytic taxa. Glomus, Alternaria, and Tomentella are the genera represented by the highest number of insufficiently identified ITS sequences in GenBank. The web service presented (http://andromeda.botany.gu.se/emerencia.html#genus_search) offers new means, particularly for mycorrhizal and plant pathogenic fungi, to examine the IIS in GenBank in a taxon-oriented framework and to explore their metadata in an easily accessible and time-efficient manner.
Ryberg
Martin
M
Department of Plant and Environmental Sciences, University of Gothenburg, PO Box 461, 405 30 Göteborg, Sweden;Department of Zoology, University of Gothenburg, PO Box 463, 405 30 Göteborg, Sweden.
Kristiansson
Erik
E
Department of Plant and Environmental Sciences, University of Gothenburg, PO Box 461, 405 30 Göteborg, Sweden;Department of Zoology, University of Gothenburg, PO Box 463, 405 30 Göteborg, Sweden.
Sjökvist
Elisabet
E
Department of Plant and Environmental Sciences, University of Gothenburg, PO Box 461, 405 30 Göteborg, Sweden;Department of Zoology, University of Gothenburg, PO Box 463, 405 30 Göteborg, Sweden.
Nilsson
R Henrik
RH
Department of Plant and Environmental Sciences, University of Gothenburg, PO Box 461, 405 30 Göteborg, Sweden;Department of Zoology, University of Gothenburg, PO Box 463, 405 30 Göteborg, Sweden.
D001483:Base Sequence; D021901:DNA, Intergenic; D030561:Databases, Nucleic Acid; D005658:Fungi / Q000145:classification / Q000235:genetics*; D016247:Information Storage and Retrieval; D020407:Internet
D021901:DNA, Intergenic