A case study to estimate the applicability of secondary structures of SSU‐rRNA gene in taxonomy and phylogenetic analyses of ciliates
A case study to estimate the applicability of secondary structures of SSU‐rRNA gene in taxonomy and phylogenetic analyses of ciliates
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DOI：
10.1111/zsc.12122
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发表时间：
2015-06
影响因子：
2.5
通讯作者：
Pu Wang;F. Gao;Jie Huang;M. Strüder-Kypke;Zhenzhen Yi
中科院分区：
文献类型：
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作者：
Pu Wang;F. Gao;Jie Huang;M. Strüder-Kypke;Zhenzhen Yi
纤毛虫的系统发育研究主要基于核基因的一级结构信息。小亚基核糖体RNA（SSU-rRNA）基因的某些区域具有独特的二级结构，这些二级结构已被证明是系统发育/分类特征的价值。在目前的工作中，我们预测的四个可变区（V2，V4，V7和V9）的二级结构的SSU-rRNA基因的45 urostylids。结构比较表明，V4区域在揭示种间关系方面最有效，而V9区域似乎适合在科水平或更高水平上。V2区也提供了一些分类学信息，但过于保守，不能反映科或更低水平的系统发育关系，至少对尾柱虫来说是这样。V7区域信息量最少。我们构建了几个系统发育树，基于一级序列比对和基于改进的比对，根据二级结构。结果表明，包括二级结构信息的系统发育分析提供了额外的见解系统发育关系。使用urostylid纤毛虫作为一个例子，我们表明，二级结构信息的结果，更好地了解他们的关系，例如家庭内的属关系Pseudokeronopsidae。
Phylogenetic studies of ciliates are mainly based on the primary structure information of the nuclear genes. Some regions of the small subunit ribosomal RNA (SSU‐rRNA) gene have distinctive secondary structures, which have demonstrated value as phylogenetic/taxonomic characters. In the current work, we predict the secondary structures of four variable regions (V2, V4, V7 and V9) in the SSU‐rRNA gene of 45 urostylids. Structure comparisons indicate that the V4 region is the most effective in revealing interspecific relationships, while the V9 region appears suitable at the family level or higher. The V2 region also offers some taxonomic information, but is too conserved to reflect phylogenetic relationships at the family or lower level, at least for urostylids. The V7 region is the least informative. We constructed several phylogenetic trees, based on the primary sequence alignment and based on an improved alignment according to the secondary structures. The results suggest that including secondary structure information in phylogenetic analyses provides additional insights into phylogenetic relationships. Using urostylid ciliates as an example, we show that secondary structure information results in a better understanding of their relationships, for example generic relationships within the family Pseudokeronopsidae.