真核生物原生生物基于 LSU rRNA D1-D5 结构域的 DNA 分类学评估。

An evaluation of the use of the LSU rRNA D1-D5 domain for DNA-based taxonomy of eukaryotic protists.

机构信息

Department of General Ecology, Zoological Institute, Biowissenschaftliches Zentrum, University of Cologne, Otto-Fischer-Str. 6, 50674 Cologne, Germany.

出版信息

Protist. 2010 Jul;161(3):342-52. doi: 10.1016/j.protis.2010.01.003. Epub 2010 Feb 12.

DOI:10.1016/j.protis.2010.01.003

PMID:20153693

Abstract

Diagnostic signature DNA sequences are important tools for the identification of species. There is an active debate in the literature on the choice of the best markers applicable for a broad range of organisms. Protists have seldom been included in these evaluations. Mitochondrial gene sequences are inappropriate for protists since several groups do not possess mitochondria. Here we studied the application of the large subunit (LSU) rRNA gene fragments (D1-D5) regarding their usefulness to discriminate between a wide range of heterotrophic nanoflagellates. Phylogenetic analyses based on the LSU rRNA fragments showed similar results compared to phylogenetic trees based on the small subunit (SSU) rRNA. The data set indicates the power of the use of the D1-D5 region as a marker for a DNA-based taxonomy. Our results, together with the available sequences in Genbank, form a comprehensive database for unicellular eukaryotes, especially heterotrophic flagellates. It is now possible to assign new sequences to the different groups of heterotrophic flagellates which we have tested for different closely related Cercomonas and Paracercomonas strains from groundwater.

摘要

诊断特征 DNA 序列是用于识别物种的重要工具。在文献中，关于适用于广泛生物的最佳标记物的选择存在激烈的争论。原生动物很少被包括在这些评估中。由于某些群体不具有线粒体，因此线粒体基因序列不适用于原生动物。在这里，我们研究了大亚基（LSU）rRNA 基因片段（D1-D5）的应用，以了解其在区分广泛的异养纳米鞭毛虫方面的有用性。基于 LSU rRNA 片段的系统发育分析与基于小亚基（SSU）rRNA 的系统发育树显示出相似的结果。该数据集表明，使用 D1-D5 区域作为基于 DNA 的分类学标记的强大功能。我们的结果与 Genbank 中可用的序列一起，为单细胞真核生物，特别是异养鞭毛虫，形成了一个综合数据库。现在可以将新序列分配给我们已经测试过的不同的异养鞭毛虫群体，这些群体来自地下水的不同密切相关的 Cercomonas 和 Paracercomonas 菌株。