Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets

Angiosperms dominate the Earth’s ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different ge..., ,被子植物（Angiosperms）在地球生态系统中占据主导地位，可为人类提供绝大多数基本生存必需物资。依据被子植物系统发育群第四版（APG IV）分类系统的界定，被子植物的主要演化支涵盖64个目。然而，被子植物的系统发育关系仍未明确：不同的序列数据集（从靶向基因到转录组）会重建出拓扑结构各异的系统发育树，进而导致研究结果存在差异。本研究利用现有从头（de novo）组装基因组数据，基于同一物种细胞核、质体与线粒体基因组中的直系同源基因（orthologous gene），结合兼容数据集，对隶属于64个目中43个目、97个科的241个属的366种被子植物开展系统发育重建。结果显示，基于各基因组类型序列变异构建的系统发育关系，大体与既往研究得到的结果一致；但针对5个中生被子植物类群（Mesangiospermae）的系统发育关系，当采用不同的[原文此处截断]