Borrelli Chiara, Hou Yubo, Pawlowski Jan W, Holzmann Maria, Katz Miriam E, Chandler G Thomas, Bowser Samuel S
Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, 12180, New York, USA.
Wadsworth Center, New York State Department of Health, Albany, 12201, New York, USA.
J Eukaryot Microbiol. 2018 Mar;65(2):220-235. doi: 10.1111/jeu.12471. Epub 2017 Oct 4.
The Small Subunit Ribosomal RNA gene (SSU rDNA) is a widely used tool to reconstruct phylogenetic relationships among foraminiferal species. Recently, the highly variable regions of this gene have been proposed as DNA barcodes to identify foraminiferal species. However, the resolution of these barcodes has not been well established, yet. In this study, we evaluate four SSU rDNA hypervariable regions (37/f, 41/f, 43/e, and 45/e) as DNA barcodes to distinguish among species of the genus Bolivina, with particular emphasis on Bolivina quadrata for which ten new sequences (KY468817-KY468826) were obtained during this study. Our analyses show that a single SSU rDNA hypervariable sequence is insufficient to resolve all Bolivina species and that some regions (37/f and 41/f) are more useful than others (43/e and 45/e) to distinguish among closely related species. In addition, polymorphism analyses reveal a high degree of variability. In the context of barcoding studies, these results emphasize the need to assess the range of intraspecific variability of DNA barcodes prior to their application to identify foraminiferal species in environmental samples; our results also highlight the possibility that a longer SSU rDNA region might be required to distinguish among species belonging to the same taxonomic group (i.e. genus).
小亚基核糖体RNA基因（SSU rDNA）是一种广泛用于重建有孔虫物种间系统发育关系的工具。最近，该基因的高变区已被提议作为DNA条形码用于识别有孔虫物种。然而，这些条形码的分辨率尚未得到很好的确立。在本研究中，我们评估了四个SSU rDNA高变区（37/f、41/f、43/e和45/e）作为DNA条形码来区分玻利维纳属的物种，特别关注了四方玻利维纳，在本研究期间获得了其十个新序列（KY468817 - KY468826）。我们的分析表明，单个SSU rDNA高变序列不足以区分所有玻利维纳物种，并且一些区域（37/f和41/f）在区分近缘物种方面比其他区域（43/e和45/e）更有用。此外，多态性分析揭示了高度的变异性。在条形码研究的背景下，这些结果强调在将DNA条形码应用于识别环境样本中的有孔虫物种之前，需要评估其种内变异范围；我们的结果还突出了可能需要更长的SSU rDNA区域来区分属于同一分类组（即属）的物种的可能性。
