Molecular Morphology: Deep Phylogeny Using RNA Structures and Related Markers

我们建议继续重新评估现有的核糖体RNA数据，以及其他非编码RNA类别，使用二级结构感知方法，重点关注由其他参与DMP的研究小组进行的EST调查所检索到的数据。在此背景下，我们将继续开发和完善算法，以推导新的rRNA序列和其他合适的ncRNA类别的可靠二级结构模型，并开发利用二级结构本身的进化来重建系统发育的方法。将探索进化枝特异性“分子形态特征”的自主衍生，例如序列特征，例如特别保守的模式或插入，来自多个序列比对，以及系统发育信息结构特征。将ncRNA二级结构的特征演化作为一种实用的结构比对工具，并考虑“现实的”突变事件的模型的开发和应用将会引起人们的兴趣。此外，区分保守和“其他”区域的核苷酸替代模型，以及结合结构元件本身的较慢进化，将被开发出来。将探讨基于结构和增强结构的系统发育方法是否可以扩展到氨基酸序列。新的和改进的基于rRNA系统发育的软件将提供给研究界。

We propose a continued re-evaluation of the existing ribosomal RNA data, and other non-coding RNA classes, with secondary-structure-aware methods, focusing on data that will be retrieved by the EST surveys performed by other participating research groups in the DMP. In this context, we will continue to develop and refine algorithms for the derivation of reliable secondary structure models of novel rRNA sequences and other suitable ncRNA classes, as well as develop methods for utilizing the evolution of the secondary structures themselves for reconstructing phylogenies. The autonomous derivation of clade-specific “molecular morphological characters”, such as sequence features, e.g. particularly wellconserved patterns or insertions, from multiple sequence alignments, and phylogenetically informative structural features will be explored. The development and application of a model that accounts for the character evolution of ncRNA secondary structure as a practical structural alignment tool and the consideration of “realistic” mutational events will be of interest. Additionally, nucleotide substitution models that distinguish between conserved and “other” regions, as well as incorporate the slower evolution of the structural elements themselves will be developed. It will be explored whether the structure-based and structure-enhanced phylogenetic methods can be extended to amino acid sequences. Novel and improved software for rRNA based phylogeny will be provided to the research community.