Misof Bernhard, Niehuis Oliver, Bischoff Inge, Rickert Andreas, Erpenbeck Dirk, Staniczek Arnold
Zoologisches Forschungsinstitut und Museum A. Koenig Adenauerallee 160, 53113 Bonn, Germany.
J Exp Zool B Mol Dev Evol. 2006 Jan 15;306(1):70-88. doi: 10.1002/jez.b.21040.
RNA molecules and in particular the nuclear SSU RNA play an important role in molecular systematics. With the advent of increasingly parameterized substitution models in systematic research, the incorporation of secondary-structure information became a realistic option compensating interdependence of character variation. As a prerequisite, consensus structures of eukaryotic SSU RNA molecules have become available through extensive comparative analyses and crystallographic studies. Despite extensive research in hexapod phylogenetics, consensus SSU RNA secondary structures focusing on hexapods have not yet been explored. In this study, we compiled a representative hexapod SSU data set of 261 sequences and inferred a specific consensus SSU secondary-structure model. Our search for conserved structural motives relied on a combined approach of thermodynamic and covariation analyses. The hexapod consensus-structure model deviates from the canonical eukaryotic model in a number of helices. Additionally, in several helices the hexapod sequences did not support a single consensus structure. We provide consensus structures of these sections of single less-inclusive taxa, thus facilitating the adaptation of the consensus hexapod model to less-inclusive phylogenetic questions. The secondary-structure catalog will foster the application of RNA structure models in phylogenetic analyses using the SSU rRNA molecule, and it will improve the realism of substitution models and the reliability of reconstructions based on rRNA sequences.
RNA分子，尤其是核小亚基RNA（SSU RNA）在分子系统学中发挥着重要作用。随着系统发育研究中参数化替代模型的日益发展，纳入二级结构信息成为补偿性状变异相互依赖性的一个现实选择。作为前提条件，通过广泛的比较分析和晶体学研究，真核生物SSU RNA分子的共有结构已可得。尽管在六足动物系统发育学方面有广泛研究，但尚未探索专注于六足动物的SSU RNA二级结构共有模型。在本研究中，我们汇编了一个包含261个序列的代表性六足动物SSU数据集，并推断出一个特定的SSU二级结构共有模型。我们对保守结构基序的搜索依赖于热力学分析和共变分析相结合的方法。六足动物共有结构模型在多个螺旋方面偏离了典型的真核生物模型。此外，在几个螺旋中，六足动物序列并不支持单一的共有结构。我们提供了这些单系分类群较少部分的共有结构，从而便于将六足动物共有模型应用于涵盖范围较小的系统发育问题。二级结构目录将促进RNA结构模型在使用SSU rRNA分子进行系统发育分析中的应用，并将提高替代模型的真实性以及基于rRNA序列的重建的可靠性。
