Detecting footprints of selection at duplicated genes in cultivated and wild flowering plant species using population genetics tools

大量研究表明，基因复制和保留在基因组进化中起着重要作用。一些研究复制和保留动态的模型试图在基因复制和适应之间建立理论联系。事实上，正选择作用于不同植物类群的重复基因的许多情况下，可以使用系统发育的方法来确定。这些方法为长期和/或反复出现的积极选择提供了坚实的证据。将这种方法应用于被子植物（开花植物）基因组，我和我的同事提供了经验证据，证明与单拷贝基因相比，正选择更频繁地作用于重复基因。然而，最近的选择足迹在重复的基因使用群体遗传工具的研究是稀缺的。其主要原因是很难区分等位基因和基因组中的基因拷贝，尤其是转录组数据。然而，一个可靠的分类等位基因和基因重复是必不可少的群体遗传分析。在这个项目中，我首先计划开发一个管道来区分等位基因和基因拷贝。这将通过开发以前的程序来完成，这些程序用于进一步区分重复和单拷贝基因。在下一步中，我计划应用合适的群体遗传学方法来分析这些重复。具体来说，我想分析ARCAD数据集，其中包含栽培植物及其野生姐妹物种的转录组。该数据集允许识别负责适应的基因。这项工作将在Nathalie Chantret博士的小组中进行，作为ARCAD项目的一部分，该项目提供数据集。ARCAD项目有一个独特的结构，因为它是与来自各个领域（例如生物信息学，人口遗传学，比较基因组学）的许多科学家合作进行的。因此，我将能够建立一个广泛的科学网络，这将有助于开展这个项目。此外，我将有机会与ARCAD生物信息学团队合作，提高我的编程技能，这对我未来的研究很有用。这个项目无疑将帮助我进一步发展我的知识和技能，以便继续研究植物基因复制和基因家族进化这一有趣的话题。

Numerous studies revealed that gene duplication and retention play an important role in genome evolution. Some models dealing with duplication and retention dynamics tried to establish a theoretical link between gene duplication and adaptation. Indeed, many cases of positive selection acting at duplicated genes from different plant taxa could be identified using phylogenetic approaches. These approaches give solid evidence for long term and/or recurring positive selection. Applying such an approach to angiosperm (flowering plant) genomes, my colleagues and I provided empirical evidence that positive selection is acting far more frequently on duplicated genes compared to single-copy genes. However, studies searching for recent selection footprints at duplicated genes using population genetic tools are scarce. The main reason for this is that it is very difficult to distinguish alleles from gene copies in genome and especially transcriptome data. However, a reliable classification of alleles and gene duplicates is essential for population genetic analysis. In this project, I first plan to develop a pipeline to distinguish alleles and gene copies. This will be done by developing previous programs which were used to differentiate between duplicated and single-copy genes further. In the next step, I plan to apply suitable population genetic methods to analyse these duplicates. Specifically, I want to analyse the ARCAD dataset which contains transcriptomes of cultivated plants and populations of their wild sister species. This dataset allows identifying genes responsible for adaptation. This work will be carried out in the group of Dr Nathalie Chantret as part of the ARCAD project, which provides the dataset. The ARCAD project has a unique structure as it is conducted in collaboration with many scientists from various fields (e.g. bioinformatics, population genetics, comparative genomics). Therefore, I will be able to establish a broad scientific network which will be helpful for conducting this project. Additionally, I will have the opportunity to improve my programing skills in collaboration with the ARCAD bioinformatics team which will be useful for my future research. This project will undoubtedly help me to develop my knowledge and skills further in order to continue investigating the interesting topic of gene duplication and gene family evolution in plants.