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

基因组是由成千上万个基因组成的惊人集合，由不同水平的调控精心编排，导致适应其生活条件的功能性生物体。我的NSERC发现资助的研究项目侧重于使用整合生物信息学（计算方法）和基因组学（分子方法）的方法来调节DNA基序和植物基因调控。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学的贡献。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，根和地面部分经常暴露在明显不同的温度下，土壤温度低于冰点，地面温度高于20度或更多。为了能够承受这些因素，北极植物已经具备了代谢、物候和解剖学上的适应性，比如抗冻分子、常年缓慢生长、浓密的毛发和矮小的身材。这种多样化被认为部分得益于多倍体化（染色体内容加倍）、部分基因区域复制（关键基因拷贝数增加）以及关键基因的几层基因调控。人们一致认为，北极植物是通过组成性（恒定）表达专门基因来应对压力的。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，以及多倍体化可能对其产生的影响。本研究旨在研究棘豆属植物（豆科或豆科）北极和温带物种间基因调控差异，构建二倍体和多倍体棘豆属植物的首个基因组序列，开发全基因组调控基序发现生物信息学工具，并验证植物基序。开展对适应北极条件的植物及其分子机制的研究具有不可估量的影响：增加了对恶劣条件下生命的认识，增加了我们对植物发育和功能的基本知识，为生物技术和作物改良策略提供了潜在的创新，为植物序列分析提供了更好的生物信息学工具。也许最重要的是，我们在这个令人兴奋和快速发展的领域具有培养高素质人才的优势。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培训的高素质人才将在高影响力的期刊上发表文章，他们将需要关键技能、知识、科学思维，以及对作物改良应用的看法，以提高气候变化下的抗逆性——这些特征使他们在加拿大和全世界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.