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 New Phytologist
Martin RybergR Henrik Nilsson

Abstract

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 ...Continue Reading

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Citations

Apr 21, 2010·Applied Microbiology and Biotechnology·Dominik BegerowWolfgang Maier
Dec 16, 2011·Proceedings. Biological Sciences·Martin Ryberg, P Brandon Matheny
Jan 17, 2009·Source Code for Biology and Medicine·R Henrik NilssonNils Hallenberg
Apr 30, 2014·PloS One·Elisabet SjökvistKarl-Henrik Larsson
Sep 10, 2013·Applied and Environmental Microbiology·C Ryan PentonJames M Tiedje
May 9, 2009·Mycological Research·Matthew E Smith, Rosanne A Healy
May 14, 2011·Molecular Ecology Resources·R H NilssonErik Kristiansson
Nov 6, 2010·Molecular Ecology·Anthony S AmendThomas D Bruns
Apr 23, 2010·The New Phytologist·Kessy AbarenkovUrmas Kõljalg
May 23, 2009·FEMS Microbiology Letters·Rolf Henrik NilssonErik Kristiansson
Feb 12, 2013·Mycologia·Joshua M BirkebakP Brandon Matheny
Jan 3, 2018·Molecular Ecology·Teresita M Porter, Mehrdad Hajibabaei
Sep 8, 2018·PloS One·Teresita M Porter, Mehrdad Hajibabaei
Oct 1, 2010·Fungal Diversity·Sylvia KlaubaufMarkus Gorfer

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