Department of Marine Sciences, University of Connecticut, Groton 06340, Connecticut, USA.
Protist. 2013 Jan;164(1):24-36. doi: 10.1016/j.protis.2011.12.002. Epub 2012 Jan 20.
We evaluated the small- and large-subunit rDNA (SSU and LSU, respectively) for their ability to discriminate morphospecies of tintinnid ciliates. Multiple individuals from 29 morphospecies were identified according to microscopically-observed characteristics of the lorica, and then sequenced for both loci (21 new species for SSU and all of them new for LSU). Sequences from public databases were included in our analyses, and two hypervariable SSU regions (V4 and V9) were separately examined. Of the four regions, LSU is the most useful as a potential barcoding tool. It showed a gap in distances within and between species, and discriminated the maximum number of phylotypes (86% at 1% cut-off). SSU and V4 were less consistent, sometimes lumping together very distinctive morphospecies, even at the 1% level of sequence divergence. V9 was the least reliable marker in delimitating morphospecies. The agreement in sequences and morphology suggests that the lorica is useful for species discrimination, even in agglomerated forms. However, the observation of both genetically constant yet polymorphic groups of species, as well as similar morphospecies with divergent sequences, indicates that previous taxonomic schemes are complementary to the emerging molecular database.
我们评估了小亚基 rDNA（SSU）和大亚基 rDNA（LSU）在鉴别纤毛原生动物形态种方面的能力。根据被壳的微观特征，从 29 个形态种中鉴定出了多个个体，然后对这两个基因座进行了测序（SSU 有 21 个新种，LSU 全部是新种）。我们的分析中包括了来自公共数据库的序列，并分别检查了两个超变 SSU 区（V4 和 V9）。在这四个区域中，LSU 作为一种潜在的条形码工具最有用。它在种内和种间显示出距离上的差距，并能区分出最多的系统发育型（1%截断值下为 86%）。SSU 和 V4 不太一致，有时甚至在 1%的序列差异水平上也会将非常独特的形态种聚在一起。V9 是区分形态种的最不可靠的标记。序列和形态的一致性表明，被壳对于物种的鉴别是有用的，即使在聚集的形式下也是如此。然而，观察到遗传上恒定但形态上多态的物种群体，以及具有不同序列的相似形态种，表明以前的分类方案与新兴的分子数据库是互补的。
