Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms 1-3. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms. Many water lily species, particularly from Nymphaea (Nymphaeaceae), have large and showy flowers and belong to the angiosperms (also called flowering plants). Their aesthetic beauty has captivated notable artists such as the French impressionist Claude Monet. Water lily flowers have limited differentiation in perianths (outer floral organs), but they possess both male and female organs and have diverse scents and colours, similar to many mesangiosperms (core angiosperms, including eudicots, monocots, and magnoliids) (Supplementary Note 1). In addition, some water lilies have short life cycles and enormous numbers of seeds 4 , which increase their potential as a model plant to represent the ANA-grade of angiosperms and to study early evolutionary events within the angiosperms. In particular, N. colorata Peter has a relatively small genome size (2n = 28 and approximately 400 Mb) and blue petals that make it popular in breeding programs (Supplementary Note 1). We report here the genome sequence of N. colorata, obtained using PacBio RSII single-molecule real-time (SMRT) sequencing technology. The genome was assembled into 1,429 contigs (with a contig N50 of 2.1 Mb) and total length of 409 Mb with 804 scaffolds, 770 of which were anchored onto 14 pseudo-chromosomes (Extended Data Fig. 1 and Extended Data Table 1). Genome completeness was estimated to be 94.4% (Supplementary Note 2). We annotated 31,580 protein-coding genes and predicted repetitive elements with a collective length of 160.4 Mb, accounting for 39.2% of the genome (Supplementary Note 3). The N. colorata genome provides an opportuni...

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1. Poyang Lake is the largest freshwater lake in China and is of global importance for the conservation of migratory waterbirds of the East Asian -Australasian Flyway. Recent dam construction on the Yangtze River and its tributaries for agriculture and hydroelectric power has affected the hydrological regimes in downstream lakes. The Three Gorges Dam changed the hydrological regime of downstream lakes by reducing wet season flooding and expanding water storage in the dry season. 2. Despite the critical role of Poyang Lake in regional and global biodiversity conservation and the potential adverse ecological impacts of the Three Gorges Dam on downstream lakes, there have been few studies of the hydrological requirements of wintering waterbirds in the middle Yangtze floodplains. 3. We assembled a predictor matrix including three hydrological variables (annual inflow, maximum water level in high water season or MaxWL and minimum water level in low water season or MinWL) and two climatic variables (annual rainfall and biological cumulative temperature or BioT). Using the predictor matrix and annual waterbird census, we built group-specific generalised additive models (GAM) to investigate how waterbird population variations were related to climatic and hydrological factors in the Poyang Lake National Natural Reserve. We then used the modelled predictor-response curves to identify the optimal lake water levels for each waterbird group. 4. The community-level model selected group and the group-varying-coefficient term of BioT, Inflow and MaxWL as explanatory variables. At group level, tuber eaters and sedge foragers responded positively to BioT and MinWL. Seed eaters, invertebrate eaters and fish eaters responded positively to Inflow and negatively to MaxWL and MinWL. Based on the modelled predictor-response curves, we propose the following optimal water level ranges for Poyang Lake wintering waterbird conservation: a) maximum high water season level should be less than 17.4 m; and b) minimum low water level should be between 8.2 m and 8.8 m.