The Geraniaceae genomes project: Accelerated and coordinated evolution across the three plant genomes

PI: Robert K. Jansen（德克萨斯大学奥斯汀分校）合作PI: Jeffrey P. Mower（内布拉斯加州大学）和Jeffrey D. Palmer（印第安纳大学）资深科学家：Tracey A. Ruhlman（德克萨斯大学奥斯汀分校）植物细胞的基因组包含在三个不同的区室中，线粒体，细胞核和质体。线粒体和质体基因组起源于早期细菌细胞与另一个细菌细胞的结合。随着时间的推移，成千上万的基因在这些基因组之间转移，现在这些隔室之间有广泛的交流。这种相互作用导致了植物进化树中基因组的相当大的保守性和稳定性。开花植物天竺葵科，包括天竺葵和其他常见植物，代表了这种高度保守的一个新的例外，因为线粒体和质体基因组在基因含量、顺序和核苷酸替换率方面都经历了显著加快的变化速度。这些加速速率的原因尚不清楚，但可能是由细胞核中编码的基因指导的。该项目调查了这种加速进化的基础，目的是了解单个细胞内的基因组如何相互影响并随着时间的推移共同进化。该项目将对线粒体基因组中的DNA进行测序，并将对16个天竺葵科成员和两个相关家族的细胞核和线粒体中表达的基因进行测序。这些数据将与同一物种的质体数据进行比较，以阐明植物细胞隔室间串扰和共同进化的机制。该项目的目标是确定天竺葵科的线粒体和质体基因组的基因组剧变程度，并确定核基因组中导致这种不稳定性的相关变化。该结果有望显著提高我们对所有植物细胞中基因在不同区室之间交换机制的理解。细胞内基因组进化的主题是教学生基因组如何进化，相互作用和促进植物生长和发育的理想选择。该项目将通过在每个机构提供暑期研究实习的方式，与高中理科学生合作。在教师培训方面，每年将举办讲习班，并将与公共服务团体合作开发具体的教师培训模块，如德克萨斯州自然科学中心和印第安纳州布卢明顿的Wonderlab科学博物馆。该项目所产生的基因组资源将对进一步开展这一具有园艺价值的植物家族的遗传工作至关重要，据估计，这一植物家族每年在全球范围内产生40亿美元的销售额。最终，确定天竺葵科植物快速进化的来源可以为理解和潜在地操纵其他作物植物的细胞器基因组提供基因组工具。通过建立一个项目网站（可通过http://www.biosci.utexas.edu/ib/faculty/jansen.htm访问）和将数据存入GenBank的长期序列数据库，这些资源将提供给科学界和公众。

PI: Robert K. Jansen (University of Texas at Austin)Co-PIs: Jeffrey P. Mower (University of Nebraska)and Jeffrey D. Palmer (Indiana University)Senior Scientist: Tracey A. Ruhlman (University of Texas at Austin)Plant cells contain genomes in three distinct compartments, the mitochondrion, nucleus and plastid. The mitochondrial and plastid genomes originated by incorporation of an earlier bacterial cell into another. Over time, thousands of genes transferred among these genomes and now there is extensive communication among the compartments. This interaction has resulted in considerable conservation and stability of the genomes across the evolutionary tree of plants. The flowering plant family Geraniaceae, which includes Geranium and other common plants, represents a novel exception to this high level of conservation because both mitochondrial and plastid genomes have experienced remarkably accelerated rates of change in both gene content and order and rates of nucleotide substitutions. The cause of these accelerated rates is unknown, but may be directed by genes encoded in the nucleus. This project investigates the basis for this accelerated evolution with the aim of understanding how genomes within a single cell can influence one another and co-evolve over time. The project will sequence the DNA in mitochondrial genomes and will sequence the genes expressed in the nucleus and mitochondria of 16 members of the Geraniaceae and two related families. These data will be compared to plastid data for the same species to elucidate the mechanisms of inter-compartmental crosstalk and co-evolution in plant cells. The goals of this project are to determine the extent of genomic upheaval in the mitochondrial and plastid genomes of the Geraniaceae and to identify the correlated changes in the nuclear genome that have driven this instability. The results are expected to improve significantly our understanding of the mechanisms of how genes are exchanged across different compartments within all plant cells. The topic of genome evolution within cells is ideal for teaching students about how genomes evolved, interact and contribute to plant growth and development. The project will work with high school science students by offering summer research internships at each institution. For teacher training, workshops will be offered each year and specific teacher training modules will be developed in cooperation with public service groups, such as the Texas Natural Science Center and the Wonderlab Museum of Science in Bloomington, IN. The genomic resources generated by this project will be important for further genetic work with this horticulturally valuable plant family, which is estimated to generate $4 billion in sales annually on a worldwide basis. Ultimately, identifying the sources of rapid evolution in the Geraniaceae could provide genomic tools for understanding and potentially manipulating organelle genomes in other crop plants. These resources will be made available to the scientific community and the public through the creation of a project website (accessible via http://www.biosci.utexas.edu/ib/faculty/jansen.htm) and by depositing the data in long-term sequence databases at GenBank.