Functional and evolutionary roles of co-opted transposable elements

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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.**