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...

This study investigates the effect of roughness on interfacial properties of an n-alkanethiolate self-assembled monolayer (SAM) and uses hydrophobicity to demonstrate the existence of upper and lower limits. This article also sheds light on the origin of the previously unexplained gradual increase in contact angles with increases in the size of the molecule making the SAM. We prepared Au surfaces with a root-mean-square (RMS) roughness of ∼0.2-0.5 nm and compared the wetting properties of n-alkanethiolate (C10-C16) SAMs fabricated on these surfaces. Static contact angles, θ(s), formed between the SAM and water, diethylene glycol, and hexadecane showed an odd-even effect irrespective of the solvent properties. The average differences in subsequent SAM(E) and SAM(O) are Δθ(s|n  – (n+1)|) ≈ 1.7° (n = even) and Δθ(s|n – (n+1)|) ≈ 3.1° (n = odd). A gradual increase in θ(s) with increasing length of the molecule was observed, with values ranging from water 104.7-110.7° (overall Δθ(s) = 6.0° while for the evens Δθ(s)(E) = 4.4° and odds Δθ(s)(O) = 3.5°) to diethylene glycol 72.9-80.4° (overall Δθ(s) = 7.5° while for the evens Δθ(s)(E) = 2.9° and odds Δθ(s)(O) = 2.4°) and hexadecane 40.4–49.4° (overall Δθ(s) = 9.0° while for the evens Δθ(s)(E) = 3.7° and odds Δθ(s)(O) = 2.1°). This article establishes that the gradual increase in θ(s) with increasing molecular size in SAMs is due to asymmetry in the zigzag oscillation in the odd-even effect. Comparison of the magnitude and proportion differences in this asymmetry allows us to establish the reduction in interfacial dispersive forces, due to increasing SAM crystallinity with increasing molecular size, as the origin of this asymmetry. By comparing the dependence of θ(s) on surface roughness we infer that (i) RMS roughness ≈ 1 nm is a theoretical limit beyond which the odd-even effect cannot be observed and (ii) on a hypothetically flat surface the maximum difference in hydrophobicity, as expressed in θ(s), is ∼3°.

Self-assembled monolayers (SAMs) are widely used in surface modifications, specifically in tuning the surface chemistry of materials. The structure and properties of SAMs have been extensively studied often with sophisticated tools, even for the simplest n -alkanethiolate SAMs. In SAMs, especially in linear n -alkanethiolates, the properties are dependent on the chain length, which is best manifested in the so-called odd–even effect, a simple yet not fully understood phenomenon. One main challenge is fully delineating the origin of length-dependent properties, which can be due to the structure (ideal SAMs), defect evolution, or substrate-molecule effects. This study demonstrates that utilizing the wetting behavior of polar (water) and nonpolar (hexadecane (HD)) solvents on n -alkanethiolate SAMs formed on ultraflat gold and silver surfaces, the evolution of chain-length-dependent gauche defects can be revealed and parameterized through a newly defined dimensionless number (χ). The observation of the odd–even effect in hydrophobicity, however, depends on the thiol chain length, and it was only observed on longer-chain (>C 8 ) molecules. The trend in this odd–even effect demonstrates that there are three main transitions in the nature of wetting, hence structure, across n -alkanethiols. From wetting with HD, the role of dispersive components in wetting reveal that the SAMs are dynamic, which we attribute to rotations associated with previously reported evolution in gauche defects and changes in packing density. Therefore, from re-expression of the Young–Dupre equation, we define a new dimensionless number associated with molecular conformations, whose periodicity mirrors the energetics of Goodman’s conformations of n -alkanes in unbound states and associated four- or two-twist turns. Therefore, we infer that the evolution in surface energy is largely due to molecular conformations and associated relaxations of the bound thiolates.

Substrate roughness influences the wetting properties of self-assembled monolayers (SAMs), but details on this dependency at the sub-nanometer level are still lacking. This study investigates the effect of surface roughness on interfacial properties of n-alkanethiolate SAMs, specifically wetting, and confirms the predicted limit to the observation of the odd-even effect in hydrophobicity. This article studies static contact angles of polar and nonpolar probe liquids on a series of n-alkanethiolate SAMs on surfaces with tunable roughness. We prepared Ag surfaces with root-mean-square roughness (Rrms) of ∼0.6-2.2 nm and compared the wetting properties of n-alkanethiolate SAMs fabricated on these surfaces. We measured the static contact angles, θs, formed between SAM and probe liquids [water, glycerol, and hexadecane]. Hexadecane showed an odd-even effect on all surfaces irrespective of the degree of roughness. Polar liquids (water and glycerol), however, showed a dependency on the roughness of the substrate with an odd-even effect observable only on smooth, but not rougher (Rrms ≥ 1.15 nm), surfaces. These results confirm that the previously predicted limit to observation of the odd-even effect in hydrophobicity (here extended to polar liquids) is real. From the results with glycerol, we infer that this limit is not limited just to hydrophobicity but may extend to other polar liquids. Results from hexadecane, however, suggest that this limit may not be a universal property of the SAM.

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

Background Pecan ( Carya illinoinensis ) and Chinese hickory ( C. cathayensis ) are important commercially cultivated nut trees in the genus Carya (Juglandaceae), with high nutritional value and substantial health benefits. Results We obtained >187.22 and 178.87 gigabases of sequence, and ∼288× and 248× genome coverage, to a pecan cultivar (“Pawnee”) and a domesticated Chinese hickory landrace (ZAFU-1), respectively. The total assembly size is 651.31 megabases (Mb) for pecan and 706.43 Mb for Chinese hickory. Two genome duplication events before the divergence from walnut were found in these species. Gene family analysis highlighted key genes in biotic and abiotic tolerance, oil, polyphenols, essential amino acids, and B vitamins. Further analyses of reduced-coverage genome sequences of 16 Carya and 2 Juglans species provide additional phylogenetic perspective on crop wild relatives. Conclusions Cooperative characterization of these valuable resources provides a window to their evolutionary development and a valuable foundation for future crop improvement.

Self-assembled monolayers (SAMs) have emerged as a simple platform technology and hence have been broadly studied. With advances in state-of-the-art fabrication and characterization methods, new insights into SAM structure and related properties have been delineated, albeit with some discrepancies and/or incoherencies. Some discrepancies, especially between experimental and theoretical work, are in part due to the misunderstanding of subtle structural features such as phase evolution and SAM quality. Recent work has, however, shown that simple techniques, such as the measurement of static contact angles, can be used to delineate otherwise complex properties of the SAM, especially when complemented by other more advanced techniques. In this article, we highlight the effect of nanoscale substrate asperities and molecular chain length on the SAM structure and associated properties. First, surfaces with tunable roughness are prepared on both Au and Ag, and their corresponding n-alkanethiolate SAMs are characterized through wetting and spectroscopy. From these data, chain-length- and substrate-morphology-dependent limits to the odd-even effect (structure and properties vary with the number of carbons in the molecules and the nature of the substrate), parametrization of gauche defect densities, and structural phase evolution (liquidlike, waxy, crystalline interfaces) are deduced. An evaluation of the correlation between the effect of roughness and the components of surface tension (polar-γ and dispersive-γ) reveals that wetting, at nanoscale rough surfaces, evolves proportionally with the ratio of the two components of surface tension. The evolution of conformational order is captured over a range of molecular lengths and parametrized through a dimensionless number, χ. By deploying a well-known tensiometry technique (herein the liquid is used to characterize the solid, hence the term inverse tensiometry) to characterize SAMs, we demonstrate that complex molecular-level phenomena in SAMs can be understood through simplicity.

Delineating the role of dipoles in large area junctions that are based on self-assembled monolayers (SAMs) is challenging due to molecular tilt, surface defects, and interchain coupling among other features. To mitigate SAM-based effects in study of dipoles, we investigated tunneling rates across carboranesisostructural molecules that orient along the surface normal on Au (but bear different dipole moments) without changing the thickness, packing density, or morphology of the SAM. Using the Au-SAM//Ga2O3-EGaIn junction (where “//” = physisorption, “–” = chemisorption, and EGaIn is eutectic gallium–indium), we observe that molecules with dipole moments oriented along the surface normal (with dipole moment, p = 4.1D for both M9 and 1O2) gave lower currents than when the dipole is orthogonal (p = 1.1 D, M1) at ±0.5 V applied bias. Similarly, from transition voltage spectroscopy, the transition voltages, V T (volt), are significantly different. (0.5, 0.43, and 0.4 V for M1, M9, and 1O2, respectively). We infer that the magnitude and direction of a dipole moments significantly affect the rate of charge transport across large area junctions with Δ log|J| ≅ 0.4 per Debye. This difference is largely due to effect of the dipole moment on the molecule-electrode coupling strength, Γ, hence effect of dipoles is likely to manifest in the contact resistance, J o, although in conformational flexible molecules field-induced effects are expected.