Nymphaeales are the most species-rich lineage of the earliest diverging angiosperms known as the ANA grade (Amborellales, Nymphaeales, Austrobaileyales), and they have received considerable attention from morphological, physiological, and ecological perspectives. Although phylogenetic relationships between these three lineages of angiosperms are mainly well resolved, insights at the whole genome level are still limited because of a dearth of information. To address this, genome sizes and chromosome numbers in 34 taxa, comprising 28 species were estimated and analysed together with previously published data to provide an overview of genome size and chromosome diversity in Nymphaeales. Overall, genome sizes were shown to vary 10-fold and chromosome numbers and ploidy levels ranged from 2n = 2x = 18 to 2n = 16x = ∼224. Distinct patterns of genome diversity were apparent, reflecting the differential incidence of polyploidy, changes in repetitive DNA content, and chromosome rearrangements within and between genera. Using model-based approaches, ancestral genome size and basic chromosome numbers were reconstructed to provide insights into the dynamics of genome size and chromosome number evolution. Finally, by combining additional data from Amborellales and Austrobaileyales, a comprehensive overview of genome sizes and chromosome numbers in these early diverging angiosperms is presented.

Genome-wide discovery of candidate genes for functional traits within a species typically involves the sequencing of large samples of phenotyped individuals 1 , or linkage analysis through multiple generations 2 . When a trait occurs repeatedly among phylogenetically independent lineages within a genus, a more efficient approach may be to identify genes via detection of amino acid residues shared by species possessing that trait 3,4 . Here, by taking this approach, we identify candidate loci in the genus Fraxinus (ash trees) for resistance to the emerald ash borer beetle (EAB; Agrilus planipennis), a pest species that appears innocuous to otherwise healthy ash in its native East Asian range 5 but is highly destructive in North America 6 and poses a threat to ash trees in Europe 7 . Assembling whole genome sequences for 24 diploid species and subspecies of ash, and estimating resistance to EAB for 26 taxa from egg bioassays, we find 53 genes containing amino acid variants shared between two or more independent Fraxinus lineages with EABresistant species, that are unlikely to be due to chance or undetected paralogy. Of these, seven genes have putative roles relating to the phenylpropanoid biosynthesis pathway and 17 are potentially connected to herbivore recognition, defence signalling or programmed cell death. We also find that possible loss-of-function mutations among our 53 candidate genes are more frequent in susceptible species, 2 than in resistant ones. Patterns of polymorphism for the EAB-associated amino acid variants in ash trees representing different European populations suggest that selection may be able to enhance their resistance to EAB.