Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
Plant Biol (Stuttg). 2012 Nov;14(6):987-96. doi: 10.1111/j.1438-8677.2012.00576.x. Epub 2012 May 28.
Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. It is possible to simultaneously infer alignments and phylogenies on the primary sequence and the secondary structure information. For the internal transcribed spacer 2 (ITS2), a phylogenetic RNA transcript marker, two different structure conformations (I or Y shape for helix I) were published for Scenedesmaceae, and a third appeared in the ITS2 database. We contrast the effects on phylogenetic tree reconstruction of different structure sets for a small scenedesmacean subset, using neighbour-joining, maximum parsimony and, for the first time, maximum likelihood, on sequence-structure alignments. Generally our study supports inclusion of secondary structure information. However, we found that any of the three structure conformations is equally fit for phylogenetic studies, but prefer the I shape for helix I. Moreover, our results enable us to give general recommendations on how to build a phylogenetic tree using ITS2 sequence-structure alignments, including different methods to obtain the secondary structures. Thus, we hope to provide a valuable contribution not only for scenedesmacean ITS2 phylogeny, but also for other approaches using RNA transcript markers.
包括 RNA 二级结构可提高系统发育树重建的准确性和稳健性。有可能同时在主要序列和二级结构信息上推断比对和系统发育。对于内部转录间隔区 2（ITS2），一种系统发育 RNA 转录本标记，已经为 Scenedesmaceae 发布了两种不同的结构构象（I 型或 Y 型的螺旋 I），并且在 ITS2 数据库中出现了第三种构象。我们使用邻接法、最大简约法（首次使用最大似然法），对比了在小 Scenedesmaceae 子集的序列-结构比对中，不同结构集对系统发育树重建的影响。总的来说，我们的研究支持包含二级结构信息。然而，我们发现任何三种构象都同样适合系统发育研究，但我们更喜欢 I 型的螺旋 I。此外，我们的结果使我们能够就如何使用 ITS2 序列-结构比对构建系统发育树提供一般性建议，包括获得二级结构的不同方法。因此，我们希望不仅为 Scenedesmaceae 的 ITS2 系统发育，而且为其他使用 RNA 转录本标记的方法提供有价值的贡献。
