Functional and evolutionary roles of co-opted transposable elements

我研究的中心主题是了解转座因子在进化中的作用和影响，特别是它们对宿主的有益功能。自生命诞生以来，转座因子可能一直是基因组的基本组成部分。它们长期的进化持久性反映在真核生物基因组中的高拷贝数上，从面包酵母基因组中的几个百分比到构成绝大多数基因组，例如，玉米到我们自己的基因组。转座因子明显不同于“宿主”基因，因为它们是可移动的，而宿主基因是在表型选择下进化的，而转座因子是在自私选择下进化的。这提供了一个场景，表明转座因子与宿主基因不一致；事实上，转座因子通常被认为是寄生的、有害的，或者充其量是垃圾DNA。尽管这种范式可能仍然占主导地位，但现在越来越多的证据表明，转座因子可能为宿主提供了好处，并支持了转座因子作为基因组和基因网络塑造者的观点。******这种益处的一个重要例子是转座因子进化成宿主基因。增选转座因子的重要性是不可否认的，主要的进化创新包括脊椎动物适应性免疫系统、哺乳动物胎盘和植物发育。事实上，越来越多的报告记录了房东从适应移动的生活方式中脱离出来，获得了新的、但在很大程度上未知的适应性角色。作为Genome Quebec/Canada资助项目的一部分，我们从拟南芥（Arabidopsis thaliana）基因组序列中发现了67个增选转座因子。为了确认宿主的功能，我们对每个增选转座因子使用了多个突变系，以揭示与非生物胁迫（盐、低磷酸盐、砷和冷冻）相关的表型。利用加拿大创新基金会资助的高通量表型组学平台，我们能够将表型与增选的转座因子联系起来。******这些是许多经过验证的增选转座因子，第一次了解它们的功能，并为后续研究打开了大门，例如这些表型的进化意义和分子基础是什么，它们是否有其他表型，以及我们如何利用这些表型进行作物改良？寻找这些问题的答案是我目前研究计划的核心，将需要功能和进化基因组学、生物信息学、遗传学、分子和发育生物学、表型组学和翻译生物学等技术。这不仅将为HQP的培训提供一个良好的环境，而且还将允许利用我从nserc资助的活动中获得的发现，以确保为影响加拿大利益的大型合作项目提供资金

The central theme of my research is to understand the role and impact of transposable elements in evolution especially their beneficial functions for the host. Transposable elements have likely been fundamental components of genomes since the inception of life. Their long evolutionary persistence is reflected in their high copy number in eukaryotic genomes, from a few percent in the genome of baker's yeast to making up the vast majority of the genomes of, for example, maize to our own. Transposable elements are distinctly different than "host" genes in that they are mobile and, whereas host genes evolve under phenotypic selection, transposable elements evolve under selfish selection. This provides a scenario suggesting transposable elements are at odds with host genes; in fact, transposable elements are commonly viewed as parasitic, detrimental, or, at best, junk DNA. Though this paradigm may still reign, increasing evidence now suggests that transposable elements may provide a benefit for the host and supports the view of transposable elements as shapers of genomes and gene networks.******An important example of such a benefit is when transposable elements evolve into host genes. The importance of co-opted transposable elements is undeniable, with major evolutionary innovations including the vertebrate adaptive immune system, the mammalian placenta, and plant development. In fact, there are a growing number of reports documenting the departure from a mobile adapted lifestyle and attaining new, but largely unknown and adaptive roles for the host. As part of a Genome Quebec/Canada funded project, we uncovered 67 co-opted transposable elements from the genome sequence of Arabidopsis thaliana. In order to confirm a host function we used multiple mutant lines for each of the co-opted transposable elements to reveal a phenotype associated with abiotic stresses (salt, low phosphate, arsenic and freezing). Using our Canada Foundation for Innovation funded high-throughput phenomics platform, we were able to associate phenotypes to the co-opted transposable elements.******These are for many of the validated co-opted transposable elements, the first glimpse into their function and opens the door to several follow up studies, such as what are the evolutionary significance and molecular underpinnings of these phenotypes, do they have other phenotypes, and how can we exploit these phenotypes for crop improvement? Finding answers to these questions are at the heart of my current research program and will require techniques in functional and evolutionary genomics, bioinformatics, genetics, molecular and developmental biology, phenomics, and translational biology. This will not only be an excellent environment for the training of HQP but will also allow leveraging discoveries from my NSERC-funded activities to secure funding of collaborative larger scale projects impacting Canadian interests.**