反映进化历史关系的生命之树是生物学各项研究的基础，以系统发育基因组学为手段的系统关系重建是当前进化生物学领域的主要研究内容之一。禾本目（Poales）共包括16科近2万种植物，是一个高度分化具有广泛适应性的类群，具有重要经济生态价值，然而其系统关系仍存在亟待解决的问题如基部类群和禾本科（Poaceae）姐妹群的确定。已有研究表明禾本目叶绿体基因组具有特殊结构组成变异，本项目将依据该目各科的大小选取代表种，包括外类群共80-100种，开展基因组浅层测序，拼接组装叶绿体和线粒体基因组序列。基于两套独立遗传的基因组数据构建禾本目科级水平的系统树，澄清关键进化节点的系统关系；解析其特有叶绿体基因组结构变异式样与进化路线，检测分子进化速率的快慢变化与分子水平的自然选择，揭示其发生的内在机制和外在动因。该项目将在基因组层面上加深对禾本目适应性进化的理解，为重建被子植物目内科级水平生命之树提供重要参考。

The reconstruction of Tree of Life representing the evolutionary history of species plays a basic role in the field of biology, and phylogenetic reconstruction with a phylogenomic approach is one of the main research topics in the current evolutionary biology. The Poales is a highly diversified order of flowering plants, encompassing 16 families and around 20,000 species due to rapid adaptive evolution. The order is economic and ecological important, however, its backbone phylogeny such as the most basal group of it and the sister group to the core family Poaceae within it has long been in dispute. The variations of the plastid genomes have been previously suggested for the Poales. This project plans to sample representative species from each family of the order according to the total number of species within it, amounting to 80-100 taxa including the outgroups for genome skimming. We will assemble the complete plastid genome sequences and partial mitochondrial genome sequences of these taxa, and use these plastid and mitochondrial genome-scale data to reconstruct the family-level phylogeny of Poales to clarify the evolutionary history of it. The organizational variability of plastid genomes in Poales will be revealed and mapped onto its phylogeny. We will analyze the evolution of plastid DNA sequences and determine the substitutions under positive/negative selection. In the end, the mechanisms underlying these genomic variations and the external conditions will be investigated in the Poales. This project will provide novel insights into the understanding of the adaptive evolution of Poales from the organelle genomes and will be an example study in building the Tree of Life at the family-level within the angiosperms.