An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology

被引：182

作者：

Nilsson, R. Henrik ^{[1
,2
]}

Veldre, Vilmar ^{[2
]}

Hartmann, Martin ^{[3
]}

Unterseher, Martin ^{[4
]}

Amend, Anthony ^{[5
]}

Bergsten, Johannes ^{[6
]}

Kristiansson, Erik ^{[7
,8
]}

Ryberg, Martin ^{[9
]}

Jumpponen, Ari ^{[10
]}

Abarenkov, Kessy ^{[2
]}

机构：

[1] Univ Gothenburg, Dept Plant & Environm Sci, S-40530 Gothenburg, Sweden

[2] Univ Tartu, Dept Bot, Inst Ecol & Earth Sci, EE-51005 Tartu, Estonia

[3] Univ British Columbia, Dept Microbiol & Immunol, Life Sci Ctr, Vancouver, BC V6T 1Z3, Canada

[4] Univ Greifswald, Inst Bot & Landscape Ecol, D-17487 Greifswald, Germany

[5] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA

[6] Swedish Museum Nat Hist, Dept Entomol, S-10405 Stockholm, Sweden

[7] Univ Gothenburg, Dept Zool, S-40530 Gothenburg, Sweden

[8] Univ Gothenburg, Sahlgrenska Acad, Dept Neurosci & Physiol, S-40530 Gothenburg, Sweden

[9] Univ Tennessee, Dept Ecol & Evolutionary Biol, Knoxville, TN 37996 USA

[10] Kansas State Univ, Div Biol, Manhattan, KS 66506 USA

来源：

FUNGAL ECOLOGY | 2010年 / 3卷 / 04期

关键词：

Environmental sampling; ITS; Molecular ecology; Nuclear ribosomal genes; Sequence identification; INTERNAL TRANSCRIBED SPACER; RIBOSOMAL DNA; KINGDOM FUNGI; DIVERSITY; GENERATION; BIOSPHERE; DATABASE; GENES;

D O I：

10.1016/j.funeco.2010.05.002

中图分类号：

Q14 [生态学（生物生态学）];

学科分类号：

071012 ; 0713 ;

摘要：

We introduce an open source software utility to extract the highly variable ITS1 and ITS2 subregions from fungal nuclear ITS sequences, the region of choice for environmental sampling and molecular identification of fungi. Inclusion of parts of the neighbouring, very conserved, ribosomal genes in the sequence identification process regularly leads to distorted results. The utility is available for UNIX-type operating systems, including MacOS X, and processes about 1000 sequences per minute. (C) 2010 Elsevier Ltd and The British Mycological Society. All rights reserved.

引用

页码：284 / 287

页数：4

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