Plastid phylogenomic insights into relationships of all flowering plant families

<b>Background:</b> Flowering plants (angiosperms) are dominant components of the global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our understanding of their evolution and early diversification. The plastome, typically mapped as a ring-shaped genome, has been the most important molecular data source for plant phylogenetic reconstruction for decades. <b>Results:</b> Here we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4,792 plastomes of 4,660 species in 2,024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient radiation. <b>Conclusions:</b> We provide the most comprehensive dataset of plastome to date and robust phylogenetic relationships, which will serve as a firm basis for future evolutionary studies of flowering plants.

<b>研究背景：</b> 被子植物（angiosperms）是全球陆地生态系统的优势类群，但其科级及以上水平的系统发育关系仍仅部分得以解析，极大阻碍了我们对其演化与早期分化的认知。质体基因组（plastome）通常被组装为环状基因组，数十年来一直是植物系统发育重建的核心分子数据来源。<b>研究结果：</b> 本研究构建了迄今为止规模最大的被子植物质体基因组数据集，涵盖了隶属于2024个属、4660个物种的4792个质体基因组，包含80个基因，且代表了当前所有已被认可的被子植物科。本研究构建的系统发育树（PPA II）与既往质体基因组系统发育分析得到的树结构基本一致，但整体上为各分支提供了更高的支持度。在PPA II树中，75%的目级及以上节点和78%的科级及以上节点获得了高自展支持率（BP≥90）。本研究为核心真双子叶植物（core eudicots）中既往分辨率较差的诸多目间、科间亲缘关系提供了强支持，例如：五桠果目（Dilleniales）、虎耳草目（Saxifragales）和葡萄目（Vitales）依次作为其余蔷薇类（rosids）的姐妹群得到解析；檀香目（Santalales）、小檗丝藤目（Berberidopsidales）和石竹目（Caryophyllales）依次作为菊类（asterids）的姐妹群得到解析。然而，尽管木兰类（magnoliids）的系统位置被解析为所有其他中生被子植物（Mesangiospermae）的姐妹群，但其支持度并不高，且与基于核基因组数据推断的拓扑结构不一致。尽管增加了采样量，中生被子植物五大主要分支间的亲缘关系仍难以解析，这可能源于一次古老的辐射演化事件。<b>研究结论：</b> 本研究构建了迄今为止最全面的质体基因组数据集，并得到了可靠的被子植物系统发育关系，将为未来被子植物演化研究提供坚实的基础。