Phylogeny and Chloroplast Genome Evolution in Geraniaceae

这项研究将利用多个基因为开花植物科天竺葵科植物生成进化树，这将使根据进化历史对该科进行第一次分类成为可能。天竺葵科为研究叶绿体基因组进化提供了一个模式系统，这将极大地提高在序列和全基因组水平上对分子进化现象的理解。天竺葵科植物由5属800种组成，广泛分布于南北半球的温带和热带地区，有几个属被广泛种植作为观赏植物，包括广受欢迎的园林天竺葵属。在香草科植物中，叶绿体DNA中通常保守的基因排列高度重排，DNA序列的变化率在基因和物种之间表现出相当大的差异。该项目的第一个目标是利用四个叶绿体和两个核基因的序列以及来自五个属和四个近缘科的所有主要类群的110种香叶科植物的叶绿体基因组重排，构建一个全科进化树。为这项调查获取植物材料将涉及两次前往地中海和南非的采集旅行，这将涉及来自这些地区的几名科学家。第二个目标是对四种天竺葵科植物的整个叶绿体基因组进行测序，以添加到詹森博士的实验室中已经测序或正在进行的九个基因组中。这些数据将被用来评估香茅科的亲缘关系，这将为研究与其高度重排的叶绿体基因组相关的各种进化现象提供一个框架。这项研究也将在香叶科的系统学和进化之外做出重要的科学贡献。这项工作将为了解植物叶绿体基因组变化的机制提供重要的新见解，特别是因为以前的大多数研究都集中在基因组上，几乎没有重排。这一结果将对叶绿体基因组的遗传学和分子生物学等相关领域具有重要意义。本科生和研究生将在广泛的不同领域得到支持和培训，包括开花植物系统学、基因组学、分子生物学和计算生物学。

This study will generate an evolutionary tree for the flowering plant family Geraniaceae using multiple genes, which will enable the development of the first classification for the family based on evolutionary history. The Geraniaceae provides a model system for investigating chloroplast genome evolution, which will greatly enhance the understanding of molecular evolutionary phenomena at both the sequence and whole genome levels. The Geraniaceae comprises five genera and 800 species that are distributed broadly in temperate and tropical regions of the Northern and Southern Hemispheres, and several genera are widely cultivated as ornamentals, including the popular garden geranium. The normally conserved arrangement of genes in chloroplast DNA is highly rearranged in the Geraniaceae, and rates of DNA sequence change show considerable variation among genes and species. The first goal of this project is to construct a family-wide evolutionary tree using sequences of four chloroplast and two nuclear genes and chloroplast genome rearrangements for 110 species of Geraniaceae from all major groups within each of the five genera and from four related families. Acquisition of plant material for this investigation will involve two collecting trips to the Mediterranean and South Africa that will involve several scientists from these regions. The second goal involves sequencing entire chloroplast genomes for four species of Geraniaceae to add to the nine genomes sequenced or in progress in Dr. Jansen's lab. These data will be used to estimate relationships within the Geraniaceae, which will provide a framework for examining various evolutionary phenomena associated with their highly rearranged chloroplast genomes.This study will also make important scientific contributions beyond the systematics and evolution of the Geraniaceae. The work will provide important new insights into mechanisms of chloroplast genome change in plants, especially since most previous studies have focused on genomes with few if any rearrangements. The results will have important implications for related fields, such as genetics and molecular biology of chloroplast genomes. Undergraduate and graduate students will be supported and trained in a wide diversity of fields, including flowering plant systematics, genomics, molecular biology, and computational biology.