Abstract
Angiosperms represent one of the most spectacular terrestrial radiations on the planet1, but their early diversification and phylogenetic relationships remain uncertain2–5. A key reason for this impasse is the paucity of complete genomes representing early-diverging angiosperms. Here, we present high-quality, chromosomal-level genome assemblies of two aquatic species—prickly waterlily (Euryale ferox; Nymphaeales) and the rigid hornwort (Ceratophyllum demersum; Ceratophyllales)—and expand the genomic representation for key sectors of the angiosperm tree of life. We identify multiple independent polyploidization events in each of the five major clades (that is, Nymphaeales, magnoliids, monocots, Ceratophyllales and eudicots). Furthermore, our phylogenomic analyses, which spanned multiple datasets and diverse methods, confirm that Amborella and Nymphaeales are successively sister to all other angiosperms. Furthermore, these genomes help to elucidate 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 and eudicots. Finally, our analyses indicate that incomplete lineage sorting may account for the incongruent phylogenetic placement of magnoliids between nuclear and plastid genomes.
Highlights
The angiosperms, or flowering plants, represent one of the most diverse and species-rich clades on Earth
A total of 31.7 Gb of Oxford Nanopore Technologies (ONT) long reads and 47.4 Gb of Illumina short reads were generated for Euryale, and 80.5 Gb of ONT long reads and 46.4 Gb of short reads were generated for Ceratophyllum (Supplementary Fig. 3, Supplementary Table 2)
On the basis of the syntenic relationships between and within each species, our analyses collectively demonstrate that Euryale underwent an ancient whole-genome duplication (WGD) followed by one whole-genome triplication, and Ceratophyllum has undergone three WGDs
Summary
The angiosperms, or flowering plants, represent one of the most diverse and species-rich clades on Earth. NAture PlAnts genome size of 777.2 Mb), which are representatives of the two aquatic lineages Nymphaeales and Ceratophyllales, respectively (Supplementary Fig. 2, Supplementary Table 1). Assembled contigs were clustered into 29 and 12 pseudochromosomes for Euryale and Ceratophyllum, respectively, using LACHESIS27 (Fig. 1a, Supplementary Tables 2 and 4).
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