Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences
Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences
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DOI：
10.1016/j.fbr.2011.01.001
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发表时间：
2011-03-01
影响因子：
6
通讯作者：
Nilsson, R. Henrik
中科院分区：
文献类型：
--
作者：
Hibbett, David S.;Ohman, Anders;Nilsson, R. Henrik
真菌分类学旨在发现，描述和分类所有真菌物种，并为它们的鉴定提供工具。到目前为止，已经描述了大约100，000种真菌物种，但估计可能有150万至510万种现存真菌物种。在过去的十年中，每年大约有1200种真菌被描述。按照这个速度，可能需要4000年来描述所有种类的真菌使用目前的基于真菌的方法。与此同时，在生态调查中发现的分子操作分类单位（MOTU）的数量也在急剧增加。我们分析了GenBank核苷酸数据库中的核糖体RNA内转录间隔区（ITS）序列，并将其归类为“环境”或“基于DNA的”。我们获得了91，225个序列，其中30，217个（33%）是环境来源的。在提取的ITS1和ITS2序列中以平均93%的同一性进行聚类，得到16，969个聚类，包括6230个（37%）仅具有环境序列的聚类，以及2223个（13%）具有环境和基于环境的序列的聚类。在2008年和2009年，基因库中保存的纯环境集群的数量超过了基于标本描述的物种数量，这还不包括焦磷酸测序研究中发现的大量未命名的MOTU。为了实现真菌多样性的交流，迫切需要开发基于环境序列的分类系统。MOTU的拉丁文双名法将促进MOTU与以科隆为基础的分类数据库的整合，而MOTU使用数字编码将使MOTU与分类学文献的脱节永久化。如果命名类型的概念扩大到包括环境样品或序列色谱图（或比对）的插图，MOTU可以根据现有的国际植物命名法规正式命名。或者，可以根据微生物学家采用的候选分类单元状态，为真菌创建一个“候选种”类别。(C)2011年英国真菌学会。由爱思唯尔有限公司出版。保留所有权利。
Fungal taxonomy seeks to discover, describe, and classify all species of Fungi and provide tools for their identification. About 100,000 fungal species have been described so far, but it has been estimated that there may be from 1.5 to 5.1 million extant fungal species. Over the last decade, about 1200 new species of Fungi have been described in each year. At that rate, it may take up to 4000 y to describe all species of Fungi using current specimen-based approaches. At the same time, the number of molecular operational taxonomic units (MOTUs) discovered in ecological surveys has been increasing dramatically. We analyzed ribosomal RNA internal transcribed spacer (ITS) sequences in the GenBank nucleotide database and classified them as "environmental" or "specimen-based". We obtained 91,225 sequences, of which 30,217 (33 %) were of environmental origin. Clustering at an average 93 % identity in extracted ITS1 and ITS2 sequences yielded 16,969 clusters, including 6230 (37 %) clusters with only environmental sequences, and 2223 (13 %) clusters with both environmental and specimen-based sequences. In 2008 and 2009, the number of purely environmental clusters deposited in GenBank exceeded the number of species described based on specimens, and this does not include the huge number of unnamed MOTUs discovered in pyrosequencing studies. To enable communication about fungal diversity, there is a pressing need to develop classification systems based on environmental sequences. Assigning Latin binomials to MOTUs would promote their integration with specimen-based taxonomic data-bases, whereas the use of numerical codes for MOTUs would perpetuate a disconnect with the taxonomic literature. MOTUs could be formally named under the existing International Code of Botanical Nomenclature if the concept of a nomenclatural type was expanded to include environmental samples or illustrations of sequence chromatograms (or alignments). Alternatively, a "candidate species" category could be created for Fungi, based on the candidatus taxon status employed by microbiologists. (C) 2011 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.