Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution

Abstract

Angiosperms represent one of the most spectacular terrestrial radiations on the planet, but their early diversification and phylogenetic relationships remain uncertain. A key reason for this impasse is due to the paucity of complete genomes representing early-diverging angiosperms. Here, we present high-quality, chromosomal-level genome assemblies of two species, prickly waterlily (Euryale ferox; Nymphaeales) and the rigid hornwort (Ceratophyllum demersum; Ceratophyllales), thus expanding genomic representation for key sectors of the angiosperm tree of life. We identify multiple independent polyploidization events in each of the five major clades (i.e., Nymphaeales, magnoliids, monocots, Ceratophyllales, and eudicots). In addition, our phylogenomic analyses spanning multiple data sets and diverse methods confirm that Amborella and Nymphaeales are successively sister to all other angiosperms. Furthermore, these genomes help elucidate the relationships among the major subclades within Mesangiospermae, which contain about 350,000 species. In particular, the species-poor lineage Ceratophyllales is supported as sister to eudicots, and monocots and magnoliids are placed as successively sister to Ceratophyllales + eudicots. Finally, our analyses indicate that incomplete lineage sorting may well account for the incongruent placement of magnoliids between nuclear and plastid genomes.