The genomes of flowering plants reveal contrasting evolutionary paths in monocots and eudicots

Abstract Flowering plants (angiosperms) emerged over 150 million years ago¹–⁴, leading to the origin of two major groups, the monocots and eudicots. Accompanying this rapid species diversification was a period of dynamic genome evolution, as evidenced by their conflicting evolutionary relationships⁵,⁶. However, the genomic trends governing the evolution of flowering plants remain poorly understood. Here, starting with 1,181 genomes, we have selected and analysed 273 archaeplastid genomes, to produce a novel, robustly supported angiosperm phylogeny. With this phylogeny, our analyses identify unprecedented rates of gene loss and duplication. The origin of monocots was accompanied by a period of reductive genome evolution while the first eudicot genomes experienced modest rates of gene duplication. Lost genes in the first monocots support the morphological simplification of the cotyledon, leaf venation patterning and root system architecture. Contrastingly, genome expansion in eudicots were associated to floral development and plant reproduction. Individual orders were characterised by pervasive gene loss, coupled with modest gene duplication. This suggests that angiosperms reached a core genomic diversity early in their evolutionary history, corresponding to their high floral diversity. This work highlights the importance of loss as well as gain of function in the diversification of the most speciose plant group.