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

基因组是由数以万计的基因组成的惊人集合，由不同水平的调控编排，导致功能有机体适应它们的生活条件。我的NSERC发现资助的研究计划专注于调控DNA基序和植物基因调控，使用一种将生物信息学(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及其对植物功能解剖的贡献。 北极的植物已经适应了恶劣的天气条件和突如其来的极端温度波动。在生长季节，根和地上部分经常暴露在显著的温度差异中，土壤温度低于冰点，而地上温度高于20摄氏度或更高。为了能够抵抗这些因素，北极植物在代谢、物候和解剖方面都有适应能力，比如抗冻分子，常年生长缓慢，毛发浓密，身材矮小。这种多样性被认为部分得益于多倍化(染色体含量加倍)、部分基因区域复制(关键基因拷贝数增加)，以及关键基因的多层基因调控。人们的共识是，北极植物通过特定基因的结构性(恒定)表达为应对压力做好了准备。然而，随着气候的变化，迫切需要更多的研究来阐明该基因的表达调控，以及多倍化对其可能产生的影响。这项拟议的研究在北极和温带棘豆属(豆科或豆科)物种之间的基因调控差异方面取得了令人兴奋的发现，组装了二倍体和多倍体棘豆物种的第一个基因组序列，开发了一个全基因组调控基序发现生物信息学工具，并验证了植物中的基序。 开展对适应北极条件的植物的研究，以及使这种适应得以实现的分子机制，具有宝贵的影响：随着对严酷条件下生命的了解的增加，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战略的潜在创新的提供者，以及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，我们处于极佳的地位，可以在这个令人兴奋且迅速扩张的领域为未来培养高素质的人才。 通过拟议的研究培训的现代分子遗传学、基因组学和生物信息学方面的高素质人员将在影响较大的期刊上发表文章，他们将拥有急需的关键技能、知识、科学思维以及在变化的气候特征下应用作物改良恢复能力的观点，这些特征使他们在加拿大和世界各地的学术界和工业界具有竞争力。

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.