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 .

随着时间的流逝，基因在其基因组中的位置经常会发生变化，但是这种基因运动的功能后果在很大程度上是未知的。为了帮助填补这一空白，这三位调查人员不仅利用了模型植物拟南芥可用的大量研究工具和资源，以及用于木瓜，葡萄和杨树的基因组序列，而且还在创造新的研究工具和资源。专注于拟南芥的26,500种非倾斜基因，并使用一种新的自上而下的多键式算法来推断拟南芥和帕帕亚木瓜，葡萄和Poplar的最后一个共同祖先，调查人员发现了所有DICOTS和所有Dicticots和所有Dicticots共享的古代六核酸酯的证据。其他初步数据表明，大约40％的拟南芥基因不再是祖先，因为它们（1）迅速差异。 （2）在系统发育树中表现出高出生和死亡的行为； （3）位于染色体的重排容易区域；或（4）已转移到基因组中的新位置。有趣的是，“侧翼基因测试”表明，某些基因家族几乎始终始终被新地转化。研究人员还表明，保守的非编码序列有时在同源物之间实功能。木瓜和拟南芥之间共享了超过4,000多个深层保守的非编码序列（CNSS）。这些调节位点将被分类为基因，制成数据库，并通过使用基因敲除突变和表型分析来评估在序列，基因表达和适应性（生殖输出）的水平上进行亚功能化。此外，使用拟南芥信息资源（TAIR）归一化的微阵列数据，研究人员将在计算机中测试，假设有关基因位置与其核心测量之间关系的问题。项目的更广泛影响。该项目在研究生和研究生级别都提供了令人兴奋的培训机会。调查人员将继续与雪佛龙（Chevron）在种子项目上建立悠久的伙伴关系，并与伯克利高中（Berkeley High School）改善生物学培训，以实现有前途的，服务不足的少数民族高中生。自由职业实验室为这些学生提供了针对学生及其家人需求量身定制的夏季研究经验。佐治亚大学在美国的少数族裔百分比中排名第六，研究与强大的外展计划紧密相关。该项目将有助于开发和实施基于研究的教育材料，以通过每年在礼物（Georgia for Teachers实习）计划中培训中学和高中生对科学概念的理解和掌握。调查人员与礼物一起，寻求将“教师教师教师”的计划定为核定，该计划使用隐喻的例子和对话来描绘关键的科学概念，而不会在关于神灵论的辩论中陷入困境，这是在包括佐治亚州和南卡罗来纳州在内的许多领域中突出的问题。此外，这三个机构之间的交流将增强这些研究者学生的科学和文化经验，并进一步增加研究合作所形成的纽带。该项目的调查人员将与公众通信，并在其NSF 2010特定网站http://www.plantgenome.uga.uga.edu/outgroup.html上提供数据和应用程序。