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: 0820821
• 负责人: Michael Freeling
• 金额: $ 89.31万
• 依托单位: University of California-Berkeley
• 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 2013-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0820821&HistoricalAwards=false
• 关键词: Arabidopsis; 2010; Collaborative; Research; Evolution

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，基因在其基因组中的位置经常会发生变化，但这种基因运动的功能后果在很大程度上是未知的。为了帮助填补这一空白，这三名研究人员不仅在利用模式植物拟南芥可用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，他们还在创造新的基因组序列。研究人员聚焦于拟南芥的26,500个非转座子、非串联基因，并使用一种新的自上而下的多比对算法来推断拟南芥与木瓜、葡萄和杨树最后一个共同祖先的基因顺序，研究人员发现了所有双子叶植物甚至所有植物共享的古老六倍体的证据。更多的初步数据表明，大约40%的拟南芥基因不再是祖先，要么是因为它们(1)迅速分化；(2)在系统发育树上表现出高度的生死行为；(3)位于染色体上易重排的区域；或者(4)已经转座到基因组中的新位置。有趣的是，一项“侧翼基因测试”显示，某些基因家族含有几乎总是新转位的基因。研究人员还表明，保守的非编码序列有时在同源基因中具有亚功能。番木瓜和拟南芥共有4000多个高度保守的非编码序列。这些调控位点将被分类到基因，制成一个数据库，并通过使用敲除突变和表型分析在序列、基因表达和适合度(生殖输出)水平上评估亚功能。此外，使用由拟南芥信息资源(TAIR)标准化的微阵列数据，研究人员将以电子计算机测试关于基因位置之间的关系及其协同调节等问题的假说。该项目提供了令人兴奋的预科和研究生培训机会。调查人员将继续与雪佛龙在SEED项目上建立长期合作伙伴关系，并与伯克利高中在改善有前途的、服务不足的少数族裔高中学生的生物培训方面继续建立合作伙伴关系。弗里林实验室为这些学生提供根据学生及其家庭的需求量身定做的有偿暑期研究体验。佐治亚大学的少数民族比例在美国排名第六，该校的研究与强大的外展项目密切相关。该项目将通过在GIFT(佐治亚州教师实习)方案中每年培训一名教师，促进编写和实施研究型教材，以提高中学生对科学概念的理解和掌握。与GIFT一起，调查人员试图启动一个“教师-教师-教师”项目，该项目使用隐喻的例子和对话来描绘关键的科学概念，而不会陷入关于神创论的辩论中，这是一个在许多地区都很突出的问题，包括佐治亚州和南卡罗来纳州。此外，这三个机构之间的交流将增进这些研究人员学生的科学和文化体验，并进一步加强研究合作形成的纽带。该项目的调查人员将与公众交流，并在他们的NSF2010项目特定网站http://www.plantgenome.uga.edu/outgroup.html上提供数据和应用程序供下载。