Genome structural variation and gene regulation discovery in complex plant genomes using bioinformatics and microgenomics

基因组是成千上万个基因的惊人集合，由不同水平的调控精心安排，导致功能性生物适应其生活条件。我的NSERC发现资助的研究计划侧重于调控DNA基序和植物基因调控，使用生物信息学（计算方法）与基因组学（分子方法）相结合的方法。长期目标是了解不同的基因调控机制，以及它们如何有助于植物功能解剖。 北极的植物已经适应了恶劣的天气条件和突然的极端温度波动。在生长季节，根和地上部分经常暴露在明显的温差下，土壤温度低于冰点，地面温度高出20度或更多。为了能够抵御恶劣的气候，北极植物在新陈代谢、物候和解剖学上都做出了适应性的调整，比如防冻分子、常年缓慢生长、浓密的毛发和矮小的身材。这种多样性被认为部分得益于多倍化（染色体内容加倍），部分基因区域复制（增加关键基因的拷贝数）以及关键基因的多层基因调控。人们的共识是，北极植物是通过组成型（恒定）表达专门的基因准备压力。然而，随着气候的变化，迫切需要更多的研究来阐明该基因表达的调控，以及多倍体化对其可能产生的影响。拟议的研究旨在对棘豆属中北极和温带物种之间的基因调控差异进行令人兴奋的发现（在豆科或豆科中），组装二倍体和多倍体棘豆属物种的第一个基因组序列，开发全基因组调控基序发现生物信息学工具和植物中基序的验证。对适应北极条件的植物以及使这种适应成为可能的分子机制进行这项研究具有非常宝贵的影响：作为对恶劣条件下生命的知识的增加，我们对植物发育和功能的基本知识的增加，生物技术和作物改良策略的潜在创新的提供者，以及用于植物序列分析的更好的生物信息学工具的提供者。也许最重要的是，我们处于一个非常有利的位置，在这个令人兴奋和迅速发展的领域培养高素质的人才。 通过拟议的研究在现代分子遗传学，基因组学和生物信息学方面接受培训的高素质人员将在高影响力期刊上发表论文，他们将拥有关键技能，知识，科学思维以及对作物改良应用的观点，以适应不断变化的气候-使他们在学术界具有竞争力的特征，以及加拿大和世界各地的工业。

The genome, an amazing collection of tens of thousands of genes, orchestrated by different levels of regulation, leads to functional organisms adapted to their living conditions. My NSERC Discovery funded research program focuses on regulatory DNA motifs and plant gene regulation using an approach that integrates bioinformatics (computational methods) with genomics (molecular methods). The long-term objective is to understand different gene regulating mechanisms and how they contribute to plant functional anatomy. Plants in the Arctic have adapted to harsh weather conditions and sudden, extreme temperature fluctuations. During the growing season, roots and aerial parts are often exposed to a significant difference in temperatures, with soil temperatures below freezing, and above ground temperatures being 20 or more degrees higher. To be able to withstand the elements, arctic plants have assumed metabolic, phenological and anatomical adaptations, such as anti-freeze molecules, perennial slow growth, and thick hairs and low stature. This diversification is thought to partially be helped by polyploidization (doubling of the chromosome content), partial gene region duplications (increasing number of copies of key genes), as well as by several layers of gene regulation of key genes. The consensus is that arctic plants are prepared for stress through constitutive (constant) expression of specialized genes. However, with the changing climate more studies are urgently required to clarify the regulation of this gene expression, and what impact polyploidization may have on it. The proposed research pursues exciting findings on gene regulatory differences between arctic and temperate species in the Oxytropis genus (in the Fabaceae or legume family), assembling the first genome sequences for both diploid and polyploid Oxytropis species, developing a whole genome regulatory motif discovery bioinformatics tool and validation of motifs in planta. Embarking on this research into plants adapted to arctic conditions, and the molecular mechanisms that enable this adaptation, has invaluable impact: as an increase in knowledge of life in harsh conditions, an increase in our basic knowledge of plant development and function, a provider of potential innovations for biotechnology and crop improvement strategies, and a provider of better bioinformatics tools for plant sequence analysis. Maybe most importantly, we are in an excellent position to train Highly Qualified Personnel for a future in this exciting and rapidly expanding field. Highly Qualified Personnel trained in modern molecular genetics, genomics and bioinformatics through the proposed research will have publications in high impact journals, they will have in demand key skills, knowledge, scientific thinking, as well as a perspective on applications of crop improvement for resilience under a changing climate - traits which make them competitive in academia as well as industry in Canada and worldwide.