PostDoctoral Research Fellowship in Biological Informatics FY2006

项目名称：了解转座因子在禾本科植物核基因组中的水平转移本项目获得2006年生物信息学博士后研究奖学金。植物线粒体基因组跨物种边界交换基因（一种称为水平转移的过程），但植物核基因组是否以类似的规模交换DNA仍然是一个悬而未决的问题。成功的水平转移需要DNA从一个生物体到另一个生物体，然后被整合到受体基因组中。转座因子（Transposable elements，TE）是一种能够在宿主中增加拷贝数的自私遗传因子，具有主动插入基因组新位点的机制，是水平转移的良好候选者。本项目将通过从公开数据库中识别和收集TE序列并分析序列来发现具有水平转移历史的那些元素，从而调查不同物种草之间的TE交换。该项目旨在确定共享DNA的草和受转移的TE家族，并在此过程中，澄清一般植物中DNA水平转移背后的机制。该研究员将在格鲁吉亚大学的Susan Wessler实验室工作，在那里他将获得编程复杂和灵活的搜索算法，复杂的主题搜索技术，以及指导本科生独立研究或研究生轮换项目的经验。该项目建立在该研究员在植物线粒体基因组进化方面的背景之上，通过扩展到植物核基因组，这是一个数量级更大，基因丰富和复杂的基因组。这项研究将导致职业和植物比较基因组学。

Project Title: Understanding the Horizontal Transfer of Transposable elements in Grass Nuclear GenomesThis project is awarded under the Postdoctoral Research Fellowships in Biological Informatics Program for 2006. Plant mitochondrial genomes exchange genes across species boundaries (a process known as horizontal transfer), but whether plant nuclear genomes exchange DNA on a similar scale remains an open question. Successful horizontal transfer requires that DNA physically travels from one organism to another and then is incorporated into the recipient genome. Transposable elements (TEs), selfish genetic elements capable of increasing in copy number in their hosts, are good candidates for horizontal transfer because they have active mechanisms to insert themselves into new sites in a genome. This project will survey the exchange of TEs among different species of grasses by identifying and collecting TE sequences from publicly available databases and analyzing the sequences to uncover those elements with a history of horizontal transfer. This project aims to identify both the grasses that share DNA and the families of TEs that are subject to transfer, and in so doing, clarify the mechanisms behind the horizontal transfer of DNA in plants in general. The fellow will work in the lab of Susan Wessler at the University of Georgia where he will gain experience in programming complex and flexible search algorithms, sophisticated motif searching techniques, and mentoring undergraduate independent research or graduate student rotation projects. The project builds on the fellow's background in the evolution of plant mitochondrial genomes by scaling to the plant nuclear genome, which is orders of magnitude larger, gene-rich, and complex. The research will lead to a career and plant comparative genomics.