Deep strong light-matter coupling in plasmonic nanoparticle crystals.

In the regime of deep strong light-matter coupling, the coupling strength exceeds the transition energies of the material1-3, fundamentally changing its properties4,5; for example, the ground state of the system contains virtual photons and the internal electromagnetic field gets redistributed by photon self-interaction1,6. So far, no electronic excitation of a material has shown such strong coupling to free-space photons. Here we show that three-dimensional crystals of plasmonic nanoparticles can realize deep strong coupling under ambient conditions, if the particles are ten times larger than the interparticle gaps. The experimental Rabi frequencies (1.9 to 3.3 electronvolts) of face-centred cubic crystals of gold nanoparticles with diameters between 25 and 60 nanometres exceed their plasmon energy by up to 180 per cent. We show that the continuum of photons and plasmons hybridizes into polaritons that violate the rotating-wave approximation. The coupling leads to a breakdown of the Purcell effect-the increase of radiative damping through light-matter coupling-and increases the radiative polariton lifetime. The results indicate that metallic and semiconducting nanoparticles can be used as building blocks for an entire class of materials with extreme light-matter interaction, which will find application in nonlinear optics, the search for cooperative effects and ground states, polariton chemistry and quantum technology4,5.

Testing hypotheses of a coevolutionary key innovation reveals a complex suite of traits involved in defusing the mustard oil bomb.

Coevolutionary interactions are responsible for much of the Earth's biodiversity, with key innovations driving speciation bursts on both sides of the interaction. One persistent question is whether macroevolutionary traits identified as key innovations accurately predict functional performance and selection dynamics within species, as this necessitates characterizing their function, investigating their fitness consequences, and exploring the selection dynamics acting upon them. Here, we used CRISPR-Cas9 mediating nonhomologous end joining (NHEJ) in the butterfly species Pieris brassicae to knock out and directly assess the function and fitness impacts of nitrile specifier protein (NSP) and major allergen (MA). These are two closely related genes that facilitate glucosinolate (GSL) detoxification capacity, which is a key innovation in mustard feeding Pierinae butterflies. We find NSP and MA are both required for survival on plants containing GSLs, with expression differences arising in response to variable GSL profiles, concordant with detoxification performance. Importantly, this concordance was only observed when using natural host plants, likely reflecting the complexity of how these enzymes interact with natural plant variation in GSLs and myrosinases. Finally, signatures of positive selection for NSP and MA were detected across Pieris species, consistent with these genes' importance in recent coevolutionary interactions. Thus, the war between these butterflies and their host plants involves more than the mere presence of chemical defenses and detoxification mechanisms, as their regulation and activation represent key components of complex interactions. We find that inclusion of these dynamics, in ecologically relevant assays, is necessary for coevolutionary insights in this system and likely others.

Metabolic novelty originating from horizontal gene transfer is essential for leaf beetle survival.

Horizontal gene transfer (HGT) provides an evolutionary shortcut for recipient organisms to gain novel functions. Although reports of HGT in higher eukaryotes are rapidly accumulating, in most cases the evolutionary trajectory, metabolic integration, and ecological relevance of acquired genes remain unclear. Plant cell wall degradation by HGT-derived enzymes is widespread in herbivorous insect lineages. Pectin is an abundant polysaccharide in the walls of growing parts of plants. We investigated the significance of horizontally acquired pectin-digesting polygalacturonases (PGs) of the leaf beetle Phaedon cochleariae. Using a CRISPR/Cas9-guided gene knockout approach, we generated a triple knockout and a quadruple PG-null mutant in order to investigate the enzymatic, biological, and ecological effects. We found that pectin-digestion 1) is exclusively linked to the horizontally acquired PGs from fungi, 2) became fixed in the host genome by gene duplication leading to functional redundancy, 3) compensates for nutrient-poor diet by making the nutritious cell contents more accessible, and 4) facilitates the beetles development and survival. Our analysis highlights the selective advantage PGs provide to herbivorous insects and demonstrate the impact of HGT on the evolutionary success of leaf-feeding beetles, major contributors to species diversity.

Genome sequencing provides insights into the evolution of gene families encoding plant cell wall-degrading enzymes in longhorned beetles.

With more than 36,000 species, the longhorned beetles (family Cerambycidae) are a mega-diverse lineage of mostly xylophagous insects, all of which are represented by the sole sequenced genome of the Asian longhorned beetle (Anoplophora glabripennis; Lamiinae). Their successful radiation has been linked to their ability to degrade plant cell wall components using a range of so-called plant cell wall-degrading enzymes (PCWDEs). Our previous analysis of larval gut transcriptomes demonstrated that cerambycid beetles horizontally acquired genes encoding PCWDEs from various microbial donors; these genes evolved through multiple duplication events to form gene families. To gain further insights into the evolution of these gene families during the Cerambycidae radiation, we assembled draft genomes for four beetle species belonging to three subfamilies using long-read nanopore sequencing. All the PCWDE-encoding genes we annotated from the corresponding larval gut transcriptomes were present in these draft genomes. We confirmed that the newly discovered horizontally acquired glycoside hydrolase family 7 (GH7), subfamily 26 of GH43 (GH43_26), and GH53 (all of which are absent from the A. glabripennis genome) were indeed encoded by these beetles' genome. Most of the PCWDE-encoding genes of bacterial origin gained introns after their transfer into the beetle genome. Altogether, we show that draft genome assemblies generated from nanopore long-reads offer meaningful information to the study of the evolution of gene families in insects. We anticipate that our data will support studies aiming to better understand the biology of the Cerambycidae and other beetles in general.

Microevolution of Pieris butterfly genes involved in host plant adaptation along a host plant community cline.

Herbivorous insects have evolved counteradaptations to overcome the chemical defences of their host plants. Several of these counteradaptations have been elucidated at the molecular level, in particular for insects specialized on cruciferous host plants. While the importance of these counteradaptations for host plant colonization is well established, little is known about their microevolutionary dynamics in the field. In particular, it is not known whether and how host plant diversity shapes diversity in insect counteradaptations. In this study, we examine patterns of host plant use and insect counteradaptation in three Pieris butterfly species across Japan. The larvae of these butterflies express nitrile-specifier protein (NSP) and its paralogue major allergen (MA) in their gut to overcome the highly diversified glucosinolate-myrosinase defence system of their cruciferous host plants. Pieris napi and Pieris melete colonize wild Brassicaceae whereas Pieris rapae typically uses cultivated Brassica as a host, regardless of the local composition of wild crucifers. As expected, NSP and MA diversity was independent of the local composition of wild Brassicaceae in P. rapae. In contrast, NSP diversity correlated with local host plant diversity in both species that preferred wild Brassicaceae. Both P. melete and P. napi revealed two distinct major NSP alleles, which shaped diversity among local populations, albeit with different evolutionary trajectories. In comparison, MA showed no indication for local adaptation. Altogether, MA appeared to be evolutionary more conserved than NSP, suggesting that both genes play different roles in diverting host plant chemical defence.

Molecular signatures of selection associated with host plant differences in Pieris butterflies.

Adaptive traits that enable organisms to conquer novel niches and experience subsequent diversification are ecologically and evolutionarily important. The larvae of Pieris butterflies express nitrile-specifier proteins (NSPs), a key innovation for overcoming the glucosinolate (GLS)-myrosinase-based defence system of their Brassicales host plants. Nitrile-specifier proteins are a member of the NSP-like gene family, which includes the major allergen (MA) protein, a paralog of NSP with a GLS-disarming function, and a single domain major allergen (SDMA) protein, whose function is unknown. The arms-race between GLS-based defences and the NSP-like gene family is suggested to mediate diversification in both Pierid butterflies and Brassicales plants. Here, we tested whether the expected strong selection on NSP-like gene family correlates with shifts in host plant spectra among Pierid butterflies. We combined feeding experiments using 25 Brassicaceae plants and five Pieris species with larval transcriptome data to investigate the patterns of selection acting on NSP-like gene family members. Although we observed significantly elevated nonsynonymous to synonymous substitution rate ratios in NSPs on branches associated with changes in patterns of host plant usage, no such pattern was observed in MAs or SDMAs. Furthermore, we found evidence for positive selection of NSP at a phylogenetic branch which reflects different host plant spectra. Our data indicate that the NSP-related gene members have evolved differently: NSPs have accumulated more amino acid changes in response to shifting preferences for host plants, whereas MAs and SDMAs appear to be more conserved. Further detailed functional assays of these genes would provide important insights to understand their role in the chemical arms-race between Pieris butterflies and their Brassicales host plants.

Interspecific Differences in the Larval Performance of Pieris Butterflies (Lepidoptera: Pieridae) Are Associated with Differences in the Glucosinolate Profiles of Host Plants.

The tremendous diversity of plants and herbivores has arisen from a coevolutionary relationship characterized by plant defense and herbivore counter adaptation. Pierid butterfly species feed on Brassicales plants that produce glucosinolates as a chemical deterrent against herbivory. In turn, the larvae of pierids have nitrile specifier proteins (NSPs) that are expressed in their gut and disarm glucosinolates. Pierid butterflies are known to have diversified in response to glucosinolate diversification in Brassicales. Therefore, each pierid species is expected to have a spectrum of host plants characterized by specific glucosinolate profiles. In this study, we tested whether the larval performance of different Pieris species, a genus in Pieridae (Lepidoptera: Pieridae), was associated with plant defense traits of putative host plants. We conducted feeding assays using larvae of three Pieris species and 10 species of the Brassicaceae family possessing different leaf physical traits and glucosinolate profile measurements. The larvae of Pieris rapae responded differently in the feeding assays compared with the other two Pieris species. This difference was associated with differences in glucosinolate profiles but not with variations in physical traits of the host plants. This result suggests that individual Pieris species are adapted to a subset of glucosinolate profiles within the Brassicaceae. Our results support the idea that the host ranges of Pieris species depend on larval responses to glucosinolate diversification in the host species, supporting the hypothesis of coevolution between butterflies and host plants mediated by the chemical arms race.

De Novo Genome Assembly and Annotation of Leptosia nina Provide New Insights into the Evolutionary Dynamics of Genes Involved in Host-Plant Adaptation of Pierinae Butterflies.

In interactions between plants and herbivorous insects, the traits enabling phytophagous insects to overcome chemical defenses of their host plants have evolved multiple times. A prominent example of such adaptive key innovations in herbivorous insects is nitrile specifier proteins (NSPs) that enabled Pierinae butterflies to colonize Brassicales host plants that have a glucosinolate-myrosinase defense system. Although the evolutionary aspects of NSP-encoding genes have been studied in some Pierinae taxa (especially among Pieris butterflies), the ancestral evolutionary state of NSPs is unclear due to the limited genomic information available for species within Pierinae. Here, we generate a high-quality genome assembly and annotation of Leptosia nina, a member of a small tribe, Leptosiaini. L. nina uses as its main host Capparaceae plants, one of the ancestral hosts within Pierinae. By using ∼90-fold coverage of Oxford Nanopore long reads and Illumina short reads for subsequent polishing and error correction, we constructed a final genome assembly that consisted of 286 contigs with a total of 225.8 Mb and an N50 of 10.7 Mb. Genome annotation with transcriptome hints predicted 16,574 genes and covered 98.3% of BUSCO genes. A typical NSP gene is composed of three tandem domains found in Pierinae butterflies; unexpectedly, we found a new NSP-like gene in Pierinae composed of only two tandem domains. This newly found NSP-like gene in L. nina provides important insights into the evolutionary dynamics of domain and gene duplication events relating to host-plant adaptation in Pierinae butterflies.

Phenylphenalenones and Linear Diarylheptanoid Derivatives Are Biosynthesized via Parallel Routes in Musella lasiocarpa, the Chinese Dwarf Banana.

Here, we use transcriptomic data from seeds of Musella lasiocarpa to identify five enzymes involved in the formation of dihydrocurcuminoids. Characterization of the substrate specificities of the enzymes reveals two distinct dihydrocurcuminoid pathways leading to phenylphenalenones and linear diarylheptanoid derivatives, the major seed metabolites. Furthermore, we demonstrate the stepwise conversion of dihydrobisdemethoxycurcumin to the phenylphenalenone 4'-hydroxylachnanthocarpone by feeding intermediates to M. lasiocarpa root protein extract.

A radiation of Psylliodes flea beetles on Brassicaceae is associated with the evolution of specific detoxification enzymes.

Flea beetles of the genus Psylliodes have evolved specialized interactions with plant species belonging to several distantly related families, mainly Brassicaceae, Solanaceae, and Fagaceae. This diverse host use indicates that Psylliodes flea beetles are able to cope with different chemical defense metabolites, including glucosinolates, the characteristic defense metabolites of Brassicaceae. Here we investigated the evolution of host use and the emergence of a glucosinolate-specific detoxification mechanism in Psylliodes flea beetles. In phylogenetic analyses, Psylliodes species clustered into four major clades, three of which contained mainly species specialized on either Brassicaceae, Solanaceae, or Fagaceae. Most members of the fourth clade have broader host use, including Brassicaceae and Poaceae as major host plant families. Ancestral state reconstructions suggest that Psylliodes flea beetles were initially associated with Brassicaceae and then either shifted to Solanaceae or Fagaceae, or expanded their host repertoire to Poaceae. Despite a putative ancestral association with Brassicaceae, we found evidence that the evolution of glucosinolate-specific detoxification enzymes coincides with the radiation of Psylliodes on Brassicaceae, suggesting that these are not required for using Brassicaceae as hosts but could improve the efficiency of host use by specialized Psylliodes species.

Observation of Multi-Directional Energy Transfer in a Hybrid Plasmonic-Excitonic Nanostructure.

Hybrid plasmonic devices involve a nanostructured metal supporting localized surface plasmons to amplify light-matter interaction, and a non-plasmonic material to functionalize charge excitations. Application-relevant epitaxial heterostructures, however, give rise to ballistic ultrafast dynamics that challenge the conventional semiclassical understanding of unidirectional nanometal-to-substrate energy transfer. Epitaxial Au nanoislands are studied on WSe2 with time- and angle-resolved photoemission spectroscopy and femtosecond electron diffraction: this combination of techniques resolves material, energy, and momentum of charge-carriers and phonons excited in the heterostructure. A strong non-linear plasmon-exciton interaction that transfers the energy of sub-bandgap photons very efficiently to the semiconductor is observed, leaving the metal cold until non-radiative exciton recombination heats the nanoparticles on hundreds of femtoseconds timescales. The results resolve a multi-directional energy exchange on timescales shorter than the electronic thermalization of the nanometal. Electron-phonon coupling and diffusive charge-transfer determine the subsequent energy flow. This complex dynamics opens perspectives for optoelectronic and photocatalytic applications, while providing a constraining experimental testbed for state-of-the-art modelling.

A high-quality functional genome assembly of Delia radicum L. (Diptera: Anthomyiidae) annotated from egg to adult.

Belowground herbivores are overseen and underestimated, even though they can cause significant economic losses in agriculture. The cabbage root fly Delia radicum (Anthomyiidae) is a common pest in Brassica species, including agriculturally important crops, such as oilseed rape. The damage is caused by the larvae, which feed specifically on the taproots of Brassica plants until they pupate. The adults are aboveground-living generalists feeding on pollen and nectar. Female flies are attracted by chemical cues in Brassica plants for oviposition. An assembled and annotated genome can elucidate which genetic mechanisms underlie the adaptation of D. radicum to its host plants and their specific chemical defences, in particular isothiocyanates. Therefore, we assembled, annotated and analysed the D. radicum genome using a combination of different next-generation sequencing and bioinformatic approaches. We assembled a chromosome-level D. radicum genome using PacBio and Hi-C Illumina sequence data. Combining Canu and 3D-DNA genome assembler, we constructed a 1.3 Gbp genome with an N50 of 242 Mbp and 6 pseudo-chromosomes. To annotate the assembled D. radicum genome, we combined homology-, transcriptome- and ab initio-prediction approaches. In total, we annotated 13,618 genes that were predicted by at least two approaches. We analysed egg, larval, pupal and adult transcriptomes in relation to life-stage specific molecular functions. This high-quality annotated genome of D. radicum is a first step to understanding the genetic mechanisms underlying host plant adaptation. As such, it will be an important resource to find novel and sustainable approaches to reduce crop losses to these pests.

The Genome of the Margined White Butterfly (Pieris macdunnoughii): Sex Chromosome Insights and the Power of Polishing with PoolSeq Data.

We report a chromosome-level assembly for Pieris macdunnoughii, a North American butterfly whose involvement in an evolutionary trap imposed by an invasive Eurasian mustard has made it an emerging model system for studying maladaptation in plant-insect interactions. Assembled using nearly 100× coverage of Oxford Nanopore long reads, the contig-level assembly comprised 106 contigs totaling 316,549,294 bases, with an N50 of 5.2 Mb. We polished the assembly with PoolSeq Illumina short-read data, demonstrating for the first time the comparable performance of individual and pooled short reads as polishing data sets. Extensive synteny between the reported contig-level assembly and a published, chromosome-level assembly of the European butterfly Pieris napi allowed us to generate a pseudochromosomal assembly of 47 contigs, placing 91.1% of our 317 Mb genome into a chromosomal framework. Additionally, we found support for a Z chromosome arrangement in P. napi, showing that the fusion event leading to this rearrangement predates the split between European and North American lineages of Pieris butterflies. This genome assembly and its functional annotation lay the groundwork for future research into the genetic basis of adaptive and maladaptive egg-laying behavior by P. macdunnoughii, contributing to our understanding of the susceptibility and responses of insects to evolutionary traps.

Surface-Enhanced Raman Scattering and Surface-Enhanced Infrared Absorption by Plasmon Polaritons in Three-Dimensional Nanoparticle Supercrystals.

Surface-enhanced vibrational spectroscopy strongly increases the cross section of Raman scattering and infrared absorption, overcoming the limited sensitivity and resolution of these two powerful analytic tools. While surface-enhanced setups with maximum enhancement have been studied widely in recent years, substrates with reproducible, uniform enhancement have received less attention although they are required in many applications. Here, we show that plasmonic supercrystals are an excellent platform for enhanced spectroscopy because they possess a high density of hotspots in the electric field. We describe the near field inside the supercrystal within the framework of plasmon polaritons that form due to strong light-matter interaction. From the polariton resonances we predict resonances in the far-field enhancement for Raman scattering and infrared absorption. We verify our predictions by measuring the vibrations of polystyrene molecules embedded in supercrystals of gold nanoparticles. The intensity of surface-enhanced Raman scattering is uniform within 10% across the crystal with a peak integrated enhancement of up to 300 and a peak hotspot enhancement of 105. The supercrystal polaritons induce pairs of incoming and outgoing resonances in the enhanced cross section as we demonstrate experimentally by measuring surface-enhanced Raman scattering with multiple laser wavelengths across the polariton resonance. The infrared absorption of polystyrene is likewise enhanced inside the supercrystals with a maximum enhancement of 400%. We show with a coupled oscillator model that the increase originates from the combined effects of hotspot formation and the excitation of standing polariton waves. Our work clearly relates the structural and optical properties of plasmonic supercrystals and shows that such crystals are excellent hosts and substrates for the uniform and predictable enhancement of vibrational spectra.

Diversification and selection pattern of CYP6B genes in Japanese Papilio butterflies and their association with host plant spectra.

Herbivorous insects are thought to have evolved counteradaptations to conquer chemical defenses in their host plants in a stepwise co-evolutionary process. Papilio butterflies use CYP6B gene family members to metabolize furanocoumarins in their Rutaceae or Apiaceae host plants. CYP6Bs have functionally diverged among Papilio species to be able to metabolite diverse types of furanocoumarins in their host plants. In this study, we examined the diversification and selection patterns of CYP6B among nine Papilio species in Japan (eight Rutaceae specialists and one Apiaceae specialist) and their association with host plant spectra and furanocoumarin profiles. We compared host plant spectrum of eight Rutaceae feeding Papilio species and also performed a furanocoumarin profiling of their host plants. In addition, we reconstructed CYP6B gene phylogeny and performed selection analysis based on the transcriptome data of those nine Papilio species. Among Rutaceae-feeding Papilio species, host plant spectrum differences were correlated with their furanocoumarin profiles. However, all tested Papilio species had similar duplicated sets of CYP6B, with no apparent lineage-specific or host plant-specific pattern of CYP6B diversification. Selection analysis showed a signature of positive selection on a CYP6B branch. The positively selected sites located at predicted substrate recognition sites and we also found that these CYP6B genes were observed only in Rutaceae-feeding species. These findings indicate that most CYP6B diversification occurred in ancestral species of these Papilio species, possibly in association with specific host plant chemical defenses and subsequent gene loss due to host specialization. These processes would have shaped the complex diversification patterns of the CYP6B gene family in Papilio butterflies. Our results also show potentially important CYP6B clades among Papilio species which likely to have diverged functions and associated with host plant phytochemicals in ancestral Papilio species.

Structural order in plasmonic superlattices.

The assembly of plasmonic nanoparticles into ordered 2D- and 3D-superlattices could pave the way towards new tailored materials for plasmonic sensing, photocatalysis and manipulation of light on the nanoscale. The properties of such materials strongly depend on their geometry, and accordingly straightforward protocols to obtain precise plasmonic superlattices are highly desirable. Here, we synthesize large areas of crystalline mono-, bi- and multilayers of gold nanoparticles >20 nm with a small number of defects. The superlattices can be described as hexagonal crystals with standard deviations of the lattice parameter below 1%. The periodic arrangement within the superlattices leads to new well-defined collective plasmon-polariton modes. The general level of achieved superlattice quality will be of benefit for a broad range of applications, ranging from fundamental studies of light-matter interaction to optical metamaterials and substrates for surface-enhanced spectroscopies.

Differential regulation of host plant adaptive genes in Pieris butterflies exposed to a range of glucosinolate profiles in their host plants.

Specialist herbivores have often evolved highly sophisticated mechanisms to counteract defenses mediated by major plant secondary-metabolites. Plant species of the herbivore host range often display high chemical diversity and it is not well understood how specialist herbivores respond to this chemical diversity. Pieris larvae overcome toxic products from glucosinolate hydrolysis, the major chemical defense of their Brassicaceae hosts, by expressing nitrile-specifier proteins (NSP) in their gut. Furthermore, Pieris butterflies possess so-called major allergen (MA) proteins, which are multi-domain variants of a single domain major allergen (SDMA) protein expressed in the guts of Lepidopteran larvae. Here we show that Pieris larvae fine-tune NSP and MA gene expression depending on the glucosinolate profiles of their Brassicaceae hosts. Although the role of MA is not yet fully understood, the expression levels of NSP and MA in larvae that fed on plants whose glucosinolate composition varied was dramatically changed, whereas levels of SDMA expression remained unchanged. In addition, we found a similar regulation pattern among these genes in larvae feeding on Arabidopsis mutants with different glucosinolate profiles. Our results demonstrate that Pieris larvae appear to use different host plant adaptive genes to overcome a wide range of glucosinolate profiles in their host plants.

Diffracted X-ray Blinking Tracks Single Protein Motions.

Single molecule dynamics studies have begun to use quantum probes. Single particle analysis using cryo-transmission electron microscopy has dramatically improved the resolution when studying protein structures and is shifting towards molecular motion observations. X-ray free-electron lasers are also being explored as routes for determining single molecule structures of biological entities. Here, we propose a new X-ray single molecule technology that allows observation of molecular internal motion over long time scales, ranging from milliseconds up to 103 seconds. Our method uses both low-dose monochromatic X-rays and nanocrystal labelling technology. During monochromatic X-ray diffraction experiments, the intensity of X-ray diffraction from moving single nanocrystals appears to blink because of Brownian motion in aqueous solutions. X-ray diffraction spots from moving nanocrystals were observed to cycle in and out of the Bragg condition. Consequently, the internal motions of a protein molecule labelled with nanocrystals could be extracted from the time trajectory using this diffracted X-ray blinking (DXB) approach. Finally, we succeeded in distinguishing the degree of fluctuation motions of an individual acetylcholine-binding protein (AChBP) interacting with acetylcholine (ACh) using a laboratory X-ray source.