Phylogeny and Chloroplast Genome Evolution in Geraniaceae

本研究将利用多基因生成开花植物天竺葵科的进化树，这将使天竺葵科的第一个基于进化历史的分类成为可能。天竺葵科植物为研究叶绿体基因组进化提供了一个模型系统，这将大大提高对分子进化现象在序列和全基因组水平上的认识。天竺葵科包括5属800种，广泛分布于北半球和南半球的温带和热带地区，其中一些属作为观赏植物被广泛种植，包括流行的园林天竺葵。在天竺葵科植物中，叶绿体DNA中通常保守的基因排列被高度重排，DNA序列变化率在基因和物种之间表现出相当大的差异。本项目的第一个目标是利用4个叶绿体和2个核基因的序列和叶绿体基因组的重排，对天竺葵科5属、4个相关科的110个主要类群进行全家族进化树的构建。为这项调查收集植物材料将涉及两次前往地中海和南非的收集旅行，这些旅行将涉及来自这些地区的几位科学家。第二个目标是对四个天竺葵科物种的整个叶绿体基因组进行测序，以添加到詹森博士实验室已经测序或正在进行的九个基因组中。这些数据将用于估计天竺葵科内的关系，这将为研究与它们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。这项研究还将对天竺葵科植物的系统学和进化做出重要的科学贡献。这项工作将为植物叶绿体基因组变化的机制提供重要的新见解，特别是因为大多数先前的研究都集中在很少重排的基因组上。研究结果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.