Arabidopsis 2010: Collaborative Research: Evolution of gene position and function in Arabidopsis using outgroup genomes

拟南芥 2010：合作研究：利用外群基因组研究拟南芥基因位置和功能的进化

• 批准号: 0821096
• 负责人: Andrew Paterson
• 金额: $ 61.91万
• 依托单位: University of Georgia Research Foundation Inc
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-02-15 至 2014-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0821096&HistoricalAwards=false
• 关键词: Arabidopsis; 2010; Collaborative; Research; Evolution

Abstract Over time, the position of a gene in its genome often changes, but the functional consequences of such gene movements are largely unknown. To help fill this gap, these three investigators are not only exploiting the wealth of research tools and resources available for the model plant Arabidopsis, along with the genome sequences for papaya, grape, and poplar, they are also creating new ones. Focusing on Arabidopsis's 26,500 non-transposon, non-tandem genes, and using a new top-down, multi-alignment algorithm to infer gene order in the last common ancestor of Arabidopsis and papaya, grape, and poplar, the investigators have found evidence for an ancient hexaploidy shared by all dicots and perhaps all plants. Additional preliminary data show that about 40% of Arabidopsis genes are no longer ancestral, either because they (1) have diverged rapidly; (2) exhibit a high birth-and-death behavior in the phylogenetic tree; (3) are positioned in rearrangement-prone regions of the chromosome; or (4) have transposed to new locations in the genome. Interestingly, a "flanking gene test" has shown that certain gene families contain genes that are almost always newly transposed. The investigators also show that conserved noncoding sequences sometimes subfunctionalize among homeologs. Over 4,000 deeply conserved noncoding sequences (CNSs) are shared between papaya and Arabidopsis. These regulatory sites will be sorted to gene, made into a database, and evaluated for subfunctionalization at the level of sequence, gene expression, and fitness (reproductive output) through the use of knockout mutations and phenotypic analyses. In addition, using microarray data normalized by The Arabidopsis Information Resource (TAIR), the investigators will test, in silico, hypotheses concerning issues such as the relationship between genes' positions and their coregulation. Broader Impacts of Project. This project provides exciting training opportunities at both pre- and postgraduate levels. The investigators will continue their long-established partnerships with Chevron on the SEED project, and with Berkeley High School on improving biology training for promising, underserved minority high school students. The Freeling laboratory provides these students with paid summer research experiences tailored to the needs of the students and their families. The University of Georgia ranks sixth in the US in percentage of minorities, and research there is closely tied to strong outreach programs. This project will contribute to the development and implementation of research-based educational materials to improve comprehension and mastery of scientific concepts by middle and high school students through training of one teacher per year in the GIFT (Georgia Internships for Teachers) program. Together with GIFT, the investigators seek to nucleate a "teachers-teach-teachers" program that uses metaphorical examples and dialogue to portray key scientific concepts without becoming ensnarled in the debate on creationism, an issue prominent in many areas, including Georgia and South Carolina. In addition, exchanges between the three institutions will enhance the scientific and cultural experiences of these investigators students and add further to the bonds formed by research collaboration. The investigators on this project will communicate with the public and provide data and applications for download at their NSF 2010 project-specific website, http://www.plantgenome.uga.edu/outgroup.html .

随着时间的推移，基因在基因组中的位置经常发生变化，但这种基因运动的功能后果在很大程度上是未知的。为了填补这一空白，这三位研究人员不仅利用了模式植物拟南芥的丰富研究工具和资源，以及木瓜、葡萄和杨树的基因组序列，他们还创造了新的基因组序列。研究人员关注拟南芥的26500个非转座子、非串联基因，并使用一种新的自顶向下、多对齐算法来推断拟南芥与木瓜、葡萄和杨树的最后共同祖先的基因顺序，他们发现了所有薯蓣甚至所有植物共有的古老六倍体的证据。额外的初步数据显示，大约40%的拟南芥基因不再来自祖先，要么是因为它们(1)迅速分化；(2)在系统发育树上表现出较高的生灭行为；(3)位于染色体重排易发区域；或者(4)已经转移到基因组中的新位置。有趣的是，一项“侧翼基因测试”表明，某些基因家族包含的基因几乎总是新转位的。研究人员还表明，保守的非编码序列有时会在同源物中发生亚功能化。木瓜和拟南芥共有4000多个深度保守的非编码序列。这些调控位点将被分类到基因中，建立一个数据库，并通过使用基因敲除突变和表型分析来评估序列、基因表达和适应性（生殖输出）水平的亚功能化。此外，利用由拟南芥信息资源（The Arabidopsis Information Resource， TAIR）标准化的微阵列数据，研究人员将在计算机上验证有关基因位置与其协同调节之间关系等问题的假设。项目的广泛影响。该项目提供了令人兴奋的培训机会，在预科和研究生水平。研究人员将继续与雪佛龙公司在SEED项目上建立长期的合作关系，并与伯克利高中合作，为有前途的、服务不足的少数民族高中生提供更好的生物培训。自由实验室为这些学生提供暑期有偿研究经验，以满足学生及其家庭的需求。佐治亚大学（University of Georgia）的少数族裔比例在全美排名第六，该校的研究与强大的外展项目密切相关。该项目将通过每年培训一名乔治亚州教师实习计划的教师，促进以研究为基础的教材的开发和实施，以提高初高中学生对科学概念的理解和掌握。与GIFT一起，研究人员试图建立一个“教师-教师-教师”项目，该项目使用隐喻性的例子和对话来描述关键的科学概念，而不会陷入关于神创论的争论中，神创论在包括乔治亚州和南卡罗来纳州在内的许多地区都很突出。此外，三所院校之间的交流，将提升这些研究人员和学生的科学和文化经验，并进一步加强研究合作所形成的联系。该项目的研究人员将与公众沟通，并在他们的国家科学基金会2010年项目特定网站http://www.plantgenome.uga.edu/outgroup.html上提供数据和应用程序下载。