Angiosperms (flowering plants) are the most diverse and species-rich group of plants. The vast majority (∼99.95%) of angiosperms form a clade called Mesangiospermae, which is subdivided into five major groups: eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales. The relationships among these Mesangiospermae groups have been the subject of long debate. In this study, we assembled a phylogenomic dataset of 1594 genes from 151 angiosperm taxa, including representatives of all five lineages, to investigate the phylogeny of major angiosperm lineages under both coalescent- and concatenation-based methods. We dissected the phylogenetic signal and found that more than half of the genes lack phylogenetic information for the backbone of angiosperm phylogeny. We further removed the genes with weak phylogenetic signal and showed that eudicots, Ceratophyllales, and Chloranthales form a clade, with magnoliids and monocots being the next successive sister lineages. Similar frequencies of gene tree conflict are suggestive of incomplete lineage sorting along the backbone of the angiosperm phylogeny. Our analyses suggest that a fully bifurcating species tree may not be the best way to represent the early radiation of angiosperms. Meanwhile, we inferred that the crown-group angiosperms originated approximately between 255.1 and 222.2 million years ago, and Mesangiospermae diversified into the five extant groups in a short time span (∼27 million years) at the Early to Late Jurassic.

被子植物（开花植物）是最多样化、物种最丰富的植物群。绝大多数（~99.95%）被子植物形成一个称为中子植物科（Mesangiospermae）的分支，该分支又分为五个主要类群：真双子叶植物、单子叶植物、木兰科、金粟兰目和金鱼藻目。这些中子植物群之间的关系一直是长期争论的话题。在这项研究中，我们收集了来自 151 个被子植物类群的 1594 个基因的系统发育数据集，包括所有五个谱系的代表，以研究基于合并和串联方法的主要被子植物谱系的系统发育。我们剖析了系统发育信号，发现超过一半的基因缺乏被子植物系统发育骨架的系统发育信息。我们进一步去除了系统发育信号较弱的基因，并发现真双子叶植物、金鱼藻目和金粟兰目形成了一个分支，木兰科和单子叶植物是接下来的姐妹谱系。基因树冲突的相似频率表明沿着被子植物系统发育主干的谱系排序不完整。我们的分析表明，完全分叉的物种树可能不是代表被子植物早期辐射的最佳方式。同时，我们推测冠群被子植物起源于约255.1至2.222亿年前，中子植物在早侏罗世至晚侏罗世的短时间内（约2700万年）分化为现存的5个类群。