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Fine-scale phylogeny using a mathematical model of the dynamics of rDNA repeat sequence evolution

使用 rDNA 重复序列进化动力学数学模型进行精细系统发育

基本信息

批准号：
BB/G00045X/1
负责人：
Joanne Dicks
金额：
$ 0.31万
依托单位：
John Innes Centre
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2008
资助国家：
英国
起止时间：
2008 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FG00045X%2F1
关键词：
Fine scale phylogeny using mathematical

项目摘要

Ever since Charles Darwin introduced his theory for evolution, biologists have been interested in reconstructing the Tree of Life, the tree representing the evolutionary history of all present-day species (http://www.phylo.org/). This is an extremely ambitious goal, and so biologists usually concentrate on constructing evolutionary trees for small sub-collections of present-day species. In the past, the construction of such trees was based on particular characteristics of the species, such as properties of their skeleton or anatomy. However, now that we are able to sequence parts of genomes, or in some cases whole genomes, it is now commonplace for biologists to construct evolutionary trees using DNA data. Consequently, in recent years a whole new theory, called 'Phylogenetics', has grown around building such trees. The most important DNA sequence used in phylogenetics is that of the ribosomal DNA repeat unit (or rDNA), a section of DNA which is present in all species, and which has been used to construct the 'universal' tree-of-life. Thanks to recent large-scale genome sequencing projects, which have revealed the DNA codes of many organisms, including very closely related ones such as various yeast strains (or sub-species), we now have data available to construct far more detailed phylogenies. In particular some DNA sequences, such the rDNA sequences that we plan to use in this project, vary within genomes and well as between them. These DNA sequences will enable us to uncover the relationships between closely related organisms, such as our yeast strains, much more clearly than we have been able to do before now. However, new tools will be required to carry out the analytical processes involved. Recent advances in computational biology mean we now have the ability to build rapid and efficient tools to achieve this goal. The aim of this project is to build a new mathematical tool to analyse rDNA sequence variation and dynamics at the most basic level. The tool will be applied to yeast and, if possible, plant data, allowing much more detailed phylogenies to be constructed than hitherto possible. Yeast genomes provide excellent models for understanding genome dynamics in plants and in other eukaryotic genomes, including humans. Therefore, our new tool can also be used by scientists who wish to analyse datsets of other species groups.

自从查尔斯·达尔文提出他的进化论以来，生物学家一直对重建生命之树感兴趣，这棵树代表了所有现代物种的进化历史（http：//www.tag.org/）。这是一个非常雄心勃勃的目标，因此生物学家通常专注于为现代物种的小子集构建进化树。在过去，这种树的构建是基于物种的特定特征，例如它们的骨骼或解剖学特性。然而，现在我们能够对部分基因组，或者在某些情况下对整个基因组进行测序，生物学家使用DNA数据构建进化树现在已经司空见惯。因此，近年来，一个全新的理论，称为“系统发生学”，已经围绕建立这样的树。遗传学中最重要的DNA序列是核糖体DNA重复单位（或rDNA），这是存在于所有物种中的DNA片段，并已被用于构建“通用”生命树。多亏了最近的大规模基因组测序项目，这些项目揭示了许多生物体的DNA密码，包括非常密切相关的生物体，如各种酵母菌株（或亚种），我们现在有数据可以构建更详细的遗传学。特别是一些DNA序列，例如我们计划在本项目中使用的rDNA序列，在基因组内以及基因组之间存在差异。这些DNA序列将使我们能够揭示密切相关的生物体之间的关系，例如我们的酵母菌株，比我们以前能够做的更清楚。然而，需要新的工具来进行有关的分析过程。计算生物学的最新进展意味着我们现在有能力构建快速有效的工具来实现这一目标。该项目的目的是建立一个新的数学工具来分析rDNA序列变异和动态在最基本的水平。该工具将应用于酵母，如果可能的话，植物数据，允许更详细的遗传学构建比迄今为止可能的。酵母基因组为理解植物和包括人类在内的其他真核生物基因组中的基因组动态提供了极好的模型。因此，我们的新工具也可以被希望分析其他物种组数据集的科学家使用。