DNA barcoding of fungi: a case study using ITS sequences for identifying aquatic hyphomycete species
DNA barcoding of fungi: a case study using ITS sequences for identifying aquatic hyphomycete species
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DOI：
10.1007/s13225-010-0056-y
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发表时间：
2010-08
期刊：
影响因子：
20.3
通讯作者：
S. Seena;C. Pascoal;L. Marvanová;F. Cássio
中科院分区：
文献类型：
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作者：
S. Seena;C. Pascoal;L. Marvanová;F. Cássio
水生丝孢菌是一个多系真菌类群，在河流有机物周转中起着至关重要的作用。传统上，它们是根据从溪流中收集的分生孢子的形态或在实验室通风时从自然界定殖的叶子中获得的分生孢子来鉴定的。因此，物种鉴定受到我们诱导分生孢子产生和建立纯培养物的能力的限制。分生孢子的形状被认为是趋同进化的结果，因此相似的分生孢子可能由不同的分生孢子发生过程产生，这可能妨碍明确的鉴定。目前，真菌分类学正在努力引入一套基于选择的核苷酸序列的比较的标准，而不是或除了表型性状。通过对8年来从葡萄牙不同环境条件下采集的19个种的94个真菌分离株进行序列测定和比较，研究了ITS 1 -5. 8 S-ITS 2 rRNA基因区或其亚区（ITS 1和ITS 2）对水生丝孢菌鉴定的适用性。水生丝孢菌葡萄牙分离株与基因库中的分离株的ITS 1、ITS 2和ITS 1 -5. 8 S-ITS 2 rRNA基因序列具有分类学上的一致性，分离株与各自的种聚在一起，但Tricallladiumspecies没有聚在Tricladiumgenus内。分离株之间的凝聚力没有观察到的位置，条件的流或收集日期。同源分离物之间的进化分歧（ITS 1 -5. 8 S-ITS 2序列; Kimura 2参数距离）较浅，种间普遍存在较深的分歧。基于ITS 1或ITS 2 rRNA基因序列构建的NJ树对某些内部节点的支持度较低，因此建议将ITS 1 -5. 8 S-ITS 2 rRNA基因作为水生丝孢菌种的条形码。
Aquatic hyphomycetes are a polyphyletic group of fungi that play a crucial role in organic matter turnover in streams. They have been traditionally identified based on the morphology of conidia collected in stream water or obtained from leaves colonized in nature upon aeration in the laboratory. Therefore, species identification is limited by our ability to induce conidium production and to establish pure cultures. Conidial shapes are believed to be the result of convergent evolution, so similar conidia may be produced by different conidiogenesis processes, which may prevent unambiguous identification. Currently, a great effort in fungal taxonomy is being made at introducing a set of criteria based on comparisons of selected nucleotide sequences instead of or in addition to phenotypic characters. We examined the suitability of ITS1-5.8S-ITS2 rRNA gene region or its subregions (ITS1 and ITS2) to identify aquatic hyphomycetes, by sequencing and comparing these regions in 94 fungal isolates belonging to 19 species collected in Portuguese streams with different environmental conditions during 8 years. Sequences of ITS1, ITS2 and ITS1-5.8S-ITS2 rRNA genes of the Portuguese isolates of aquatic hyphomycetes and those from the GenBank exhibited taxonomic cohesiveness, the isolates grouped with their respective species but allTricladiumspecies did not group within theTricladiumgenus. Cohesiveness was not observed between isolates with respect to location, condition of stream or date of collection. Evolutionary divergences (ITS1-5.8S-ITS2 sequences; Kimura 2-parameter distance) between con-specific isolates were shallow and a deep divergence between species was generally observed. The NJ trees based on ITS1 or ITS2 rRNA gene sequences had lower statistical support for some internal nodes, we therefore propose ITS1-5.8S-ITS2 rRNA gene as barcode for identifying species of aquatic hyphomycetes.