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)共同PI：Jeffrey P.Mower(内布拉斯加州大学)和Jeffrey D.Palmer(印第安纳大学)高级科学家：Tracey A.Ruhlman(德克萨斯大学奥斯汀分校)植物细胞包含三个不同部分的基因组，即线粒体、细胞核和质体。线粒体和叶绿体基因组起源于将一个较早的细菌细胞合并到另一个细胞中。随着时间的推移，数以千计的基因在这些基因组之间转移，现在这些隔间之间有了广泛的交流。这种相互作用导致了植物进化树上基因组的相当大的保守性和稳定性。开花植物家族天竺葵科，包括天竺葵科和其他常见植物，代表了这种高度保护的一个新的例外，因为线粒体和叶绿体基因组都经历了显著加快的基因含量和核苷酸替换顺序和速率的变化速度。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决定的。这个项目研究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随着时间的推移相互影响和共同进化。该项目将对线粒体基因组中的DNA进行测序，并对香草科16个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叶绿体数据进行比较，以阐明植物细胞间串扰和共同进化的机制。该项目的目标是确定香茅科植物线粒体和叶绿体基因组中基因组突变的程度，并确定导致这种不稳定的核基因组的相关变化。这些结果有望显著提高我们对基因如何在所有植物细胞内的不同隔间交换的机制的理解。细胞内基因组进化的主题是教授学生基因组如何进化、相互作用并对植物生长和发育做出贡献的理想主题。该项目将与高中理科学生合作，在每个机构提供暑期研究实习机会。在教师培训方面，将每年举办讲习班，并与德克萨斯州自然科学中心和位于印第安纳州布鲁明顿的WonderLab科学博物馆等公共服务团体合作开发具体的教师培训模块。该项目产生的基因组资源将对进一步开展这种具有园艺价值的植物家族的基因工作非常重要，据估计，这种植物家族每年在全球范围内产生40亿美元的销售额。最终，确定香草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的细胞器基因组提供基因组学工具。这些资源将通过创建一个项目网站(可通过http://www.biosci.utexas.edu/ib/faculty/jansen.htm)获取，并将数据存放在基因银行的长期序列数据库中)向科学界和公众提供。

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.