Comparative plastid genomics and phylogenetics of land plants

我的研究计划旨在对陆地植物“生命树”的主要分支产生可靠的估计。系统发育树在生物学的各个领域都有巨大的影响。它们为进化生物学家、系统学家和遗传学家提供了研究植物生物多样性的历史框架，使我们能够测试关于植物及其基因组如何进化的假设，并创建反映进化史的地球生命分类方案。他们还确定了以前没有被认为是深层系统发育谱系的群体，标志着他们需要更详细的研究和更多的保护关注。我们对植物系统发育的许多了解都来自于绿色体(叶绿体)的基因组，这是绿色植物中执行光合作用的细胞器。我们将利用DNA测序技术的进步，恢复多个植物物种的整个叶绿体基因组。这些数据集将提供更多的力量来解决系统发育问题，使我们能够解决以前太难解决的问题，包括生命树几个主要分支的有问题的根节点。在一个测试案例--水葫芦家族中，我们将平衡这一叶绿体系统发育信息和来自核基因组的多个单拷贝基因。一些植物从参与绿色植物地下食物网的真菌中窃取养分，从而失去或降低了它们的光合作用能力。我们将对这些真菌异养植物的叶绿体基因组进行测序，并将它们与它们的绿色近亲进行比较，以研究这种重大的营养转变如何影响基因的保留和丢失模式，以及分子进化的速度。这些新的数据将使我们能够检验这样的预测，即一些基因组变化先于完全的真菌异质营养进化，并将为了解叶绿体基因组的非光合作用功能提供新的见解。

My research program is aimed at generating reliable estimates of major branches of the land plant 'Tree of Life'. Phylogenetic trees have a tremendous impact in diverse fields of biology. They provide evolutionary biologists, systematists and geneticists with historical frameworks for studying plant biodiversity, allowing us to test hypotheses on how plants and their genomes evolved, and to create classification schemes for life on earth that reflect evolutionary history. They also identify groups that were previously unrecognized as deep phylogenetic lineages, flagging them for more detailed study and increased conservation attention. Much of what we know about plant phylogeny comes from the genomes of plastids (chloroplasts), which are the organelles that perform photosynthesis in green plants. We will take advantage of advances in DNA sequencing technology to recover the whole plastid genomes of multiple plant species. These data sets will provide additional power to resolve phylogenies, allowing us to tackle problems that were previously too difficult to address, including problematic root nodes of several major branches of the Tree of Life. In one test case, the water-hyacinth family, we will balance this plastid phylogenetic information with multiple single-copy genes from the nuclear genome. Some plants steal nutrients from fungi involved in an underground food web with green plants, and consequently have lost or reduced their ability to photosynthesize. We will sequence the plastid genomes of these mycoheterotrophic plants and compare them to their green relatives, to examine how this major nutritional shift affects patterns of gene retention and loss, and the rate of molecular evolution. These new data will allow us to test the prediction that some genomic changes precede the evolution of full-blown mycoheterotrophy, and will provide novel insights into the non-photosynthetic functions of plastid genomes.