Brassicaceae,as many vegetable crops and important model plants,is one of the most successful and economically valuable angiosperm families. Recent phylogenetic studies revealed that plants of Brassicaceae were classified into 3 major lineages(I,II,and III), however,detailed evolutionary relationships among them and intra-lineage still remain unknown. In order to quickly and accurately understand the phylogeny of Brassicaceae species,39 Brassicaceae species and two species of other family were chosen as research materials,and a set of low copy orthologous genes covering all the selected species was acquired via phylogenetic genomics. Further,the composition characteristics of low copy nuclear genes were analyzed by CVTree,the phylogeny of Brassicaceae in highly supported and stable relationship was obtained. The results revealed that Brassicaceae could be classified into 6 major lineages,and 3 of which agreed well with the classification by the priors, and 2 new major lineages were defined. Moreover,lineage II that was in dispute in previous studies was confirmed as the single lineage with stable supports. This indicated that a large number of low copy orthologous genes set combined with the analysis of composition vector may more accurately reflect phylogeny of Brassicaceae species. Therefore,CVTree not only is suitable for studying the phylogeny of microorganisms such as prokaryotic organisms and fungi,but also for exploring the genetic relationship of higher organisms such as Brassicaceae plants.%近年来人们在十字花科物种系统发生关系方面开展了大量工作，研究发现十字花科可分为3个主要类群，但是这些类群内部以及类群间的进化关系还不明确。旨在快速准确地解决十字花科物种系统发生关系，通过选取39个十字花科物种及两个外类群物种作为研究材料，使用系统发生基因组学方法获得了覆盖所选物种的低拷贝同源基因集合。进一步通过 CVTree 方法分析低拷贝核基因的组分特征，得到了高度支持与稳定的十字花科系统发育关系。结果显示，十字花科被分为6个主要的类群，其中3个主要类群的划分与前人的分类结果高度一致，并且增加了两个新类群，此外，前人研究中存在争议的第二类群在本研究结果中成为有稳定支持的单系群。表明基于大量低拷贝同源基因集合并结合组分矢量分析，可以较为准确地反映十字花科物种的系统发生关系。因此，CVTree 方法不仅适用于研究原核生物、真菌等微生物的系统发生关系，也可以用来探究十字花科植物等高等生物的亲缘关系。
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