High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples.
High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples.
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DOI：
10.1371/journal.pone.0040863
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Sato H
中科院分区：
文献类型：
--
作者：
Toju H;Tanabe AS;Yamamoto S;Sato H
真菌界估计包括150万或更多的物种，在地球上的每个生物群落中扮演着分解者，互利主义者和寄生虫的关键角色。为了全面了解这个巨大王国的多样性和生态学，靶向核核糖体重复序列的内转录间隔区（ITS）区域的DNA条形码被认为是一个先决条件。通过在公共数据库中广泛调查ITS序列，我们设计了新的ITS引物，与现有引物相比，其在不同分类群的真菌中的覆盖率有所提高。基于公共序列数据库的计算机分析表明，新设计的引物匹配99%的子囊菌和担子菌ITS分类群（种，亚种或变种），导致对任何真菌组的分类偏见很小。两个新设计的引物可以抑制植物序列的扩增，并将使菌根协会，土壤和其他类型的环境样品中的真菌群落的选择性调查。在体外研究中探索了引物的最佳PCR条件。本研究开发的新引物将为大规模DNA测序时代真菌多样性和群落结构的生态学研究提供基础。
The kingdom Fungi is estimated to include 1.5 million or more species, playing key roles as decomposers, mutualists, and parasites in every biome on the earth. To comprehensively understand the diversity and ecology of this huge kingdom, DNA barcoding targeting the internal transcribed spacer (ITS) region of the nuclear ribosomal repeat has been regarded as a prerequisite procedure. By extensively surveying ITS sequences in public databases, we designed new ITS primers with improved coverage across diverse taxonomic groups of fungi compared to existing primers. An in silico analysis based on public sequence databases indicated that the newly designed primers matched 99% of ascomycete and basidiomycete ITS taxa (species, subspecies or varieties), causing little taxonomic bias toward either fungal group. Two of the newly designed primers could inhibit the amplification of plant sequences and would enable the selective investigation of fungal communities in mycorrhizal associations, soil, and other types of environmental samples. Optimal PCR conditions for the primers were explored in an in vitro investigation. The new primers developed in this study will provide a basis for ecological studies on the diversity and community structures of fungi in the era of massive DNA sequencing.
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DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
影响因子：
4.2
作者：
Arfi, Yonathan;Buee, Marc;Record, Eric
通讯作者：
Record, Eric
影响因子：
4.9
作者：
GARDES, M;BRUNS, TD
通讯作者：
BRUNS, TD
影响因子：
4.8
作者：
CLAY, K
通讯作者：
CLAY, K
影响因子：
7.7
作者：
Corse, Emmanuel;Costedoat, Caroline;Gilles, Andre
通讯作者：
Gilles, Andre