Search

The chalcone synthase superfamily consists of type III polyketidesynthases (PKSs), enzymes responsible for producing plant secondary metabolites with various biological and pharmacological activities. Anther-specific chalcone synthase-like enzymes (ASCLs) represent an ancient group of type III PKSs involved in the biosynthesis of sporopollenin, the main component of the exine layer of moss spores and mature pollen grains of seed plants. In the latter, ASCL proteins are localized in the tapetal cells of the anther where they participate in sporopollenin biosynthesis and exine formation within the locule. It is thought that the enzymes responsible for sporopollenin biosynthesis are highly conserved, and thus far, each angiosperm species with a genome sequenced has possessed two ASCL genes, which in Arabidopsis thaliana are PKSA and PKSB. The Gerbera hybrida (gerbera) PKS protein family consists of three chalcone synthases (GCHS1, GCHS3 and GCHS4) and three 2-pyrone synthases (G2PS1, G2PS2 and G2PS3). In previous studies we have demonstrated the functions of chalcone synthases in flavonoid biosynthesis, and the involvement of 2-pyrone synthases in the biosynthesis of antimicrobial compounds found in gerbera. In this study we expanded the gerbera PKS-family by functionally characterizing two gerbera ASCL proteins. In vitro enzymatic studies using purified recombinant proteins showed that both GASCL1 and GASCL2 were able to use medium and long-chain acyl-CoA starters and perform two to three condensation reactions of malonyl-CoA to produce tri- and tetraketide 2-pyrones, usually referred to as alpha-pyrones in sporopollenin literature. Both GASCL1 and GASCL2 genes were expressed only floral organs, with most expression observed in anthers. In the anthers, transcripts of both genes showed strict tapetum-specific localization. (C) 2016 Elsevier Ltd. All rights reserved.

Significance The avocado is a nutritious, economically important fruit species that occupies an unresolved position near the earliest evolutionary branchings of flowering plants. Our nuclear genome sequences of Mexican and Hass variety avocados inform ancient evolutionary relationships and genome doublings and the admixed nature of Hass and provide a look at how pathogen interactions have shaped the avocado’s more recent genomic evolutionary history., The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced 2 lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent “tuning knobs” in the genome adaptive landscapes of given species.

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.

We investigate novel protocols for entanglement purification of qubit Bell pairs. Employing genetic algorithms for the design of the purification circuit, we obtain shorter circuits achieving higher success rates and better final fidelities than what is currently available in the literature. We provide a software tool for analytical and numerical study of the generated purification circuits, under customizable error models. These new purification protocols pave the way to practical implementations of modular quantum computers and quantum repeaters. Our approach is particularly attentive to the effects of finite resources and imperfect local operations - phenomena neglected in the usual asymptotic approach to the problem. The choice of the building blocks permitted in the construction of the circuits is based on a thorough enumeration of the local Clifford operations that act as permutations on the basis of Bell states.

Quantum error-correcting codes are constructed embedding a finite-dimensional codespace in the infinite-dimensional state space of rotational degrees of freedom of rigid bodies. Such codes protect against orientational diffusion and kicks in the body’s angular momentum.

We derive an effective equation of motion within the steady-state subspace of a large family of Markovian open systems (i.e., Lindbladians) subject to perturbations of their Hamiltonians and system-bath couplings. © 2019 The Author(s)

Crassulacean acid metabolism (CAM) photosynthesis is a modification of the core C3 photosynthetic pathway that improves the ability of plants to assimilate carbon in water-limited environments. CAM plants fix CO2 mostly at night, when transpiration rates are low. All of the CAM pathway genes exist in ancestral C3 species, but the timing and magnitude of expression are greatly altered between C3 and CAM species. Understanding these regulatory changes is key to elucidating the mechanism by which CAM evolved from C3. Here we use two closely related species in the Orchidaceae, Erycina pusilla (CAM) and Erycina crista-galli (C3), to conduct comparative transcriptomic analyses across multiple time points. Clustering of genes with expression variation across the diel cycle revealed some canonical CAM pathway genes similarly expressed in both species, regardless of photosynthetic pathway. However, gene network construction indicated that 149 gene families had significant differences in network connectivity and were further explored for these functional enrichments. Genes involved in light sensing and ABA signaling were some of the most differently connected genes between the C3 and CAM Erycina species, in agreement with the contrasting diel patterns of stomatal conductance in C3 and CAM plants. Our results suggest changes to transcriptional cascades are important for the transition from C3 to CAM photosynthesis in Erycina.

Carnivorous plant genome research has focused on members of the Lamiales and Oxalidales; the most complete sequences are for Utricularia gibba and Cephalotus follicularis. The size-limited U. gibba genome highlights the importance of small-scale tandem duplications, which likely play roles in this species’ carnivorous adaptation. Sequencing of the C. follicularis genome detected adaptive changes that may explain the evolution of traits associated with attraction, trapping, digestion, and absorption. Functional consequences of genes putatively missing in the U. gibba genome, yet present in other angiosperms, may have influenced the evolution of polyploidy, physiology, and a rootless Bauplan. Additional draft nuclear genomes and transcriptomes are available for carnivorous Caryophyllales, Ericales, Lamiales, and Poales, but are limited in quantity and quality. Chloroplast genomes of carnivorous Lentibulariaceae have revealed interesting patterns of gene loss, alterations in the proportion of repeat DNA, and plastome-wide increases in substitution rates.

This work derives an analytical formula for the asymptotic state---the quantum state resulting from an infinite number of applications of a general quantum channel on some initial state. For channels admitting multiple fixed or rotating points, conserved quantities---the left fixed/rotating points of the channel---determine the dependence of the asymptotic state on the initial state. The formula stems from a Noether-like theorem stating that, for any channel admitting a full-rank fixed point, conserved quantities commute with that channel's Kraus operators up to a phase. The formula is applied to adiabatic transport of the fixed-point space of channels, revealing cases where the dissipative/spectral gap can close during any segment of the adiabatic path. The formula is also applied to calculate expectation values of noninjective matrix product states (MPS) in the thermodynamic limit, revealing that those expectation values can also be calculated using an MPS with reduced bond dimension and a modified boundary., Comment: 18 pages, 1 figure, 1 table; previous results strengthened, new channel adiabaticity result

Utricularia gibba is an aquatic carnivorous plant with highly specialized morphology, featuring fibrous floating networks of branches and leaf-like organs, no recognizable roots, and bladder traps that capture and digest prey. We recently described the compressed genome of U. gibba as sufficient to control the development and reproduction of a complex organism. We hypothesized intense deletion pressure as a mechanism whereby most noncoding DNA was deleted, despite evidence for three independent whole-genome duplications (WGDs). Here, we explore the impact of intense genome fractionation in the evolutionary dynamics of U. gibba's functional gene space. We analyze U. gibba gene family turnover by modeling gene gain/death rates under a maximum-likelihood statistical framework. In accord with our deletion pressure hypothesis, we show that the U. gibba gene death rate is significantly higher than those of four other eudicot species. Interestingly, the gene gain rate is also significantly higher, likely reflecting the occurrence of multiple WGDs and possibly also small-scale genome duplications. Gene ontology enrichment analyses of U. gibba-specific two-gene orthogroups, multigene orthogroups, and singletons highlight functions that may represent adaptations in an aquatic carnivorous plant. We further discuss two homeodomain transcription factor gene families (WOX and HDG/HDZIP-IV) showing conspicuous differential expansions and contractions in U. gibba. Our results 1) reconcile the compactness of the U. gibba genome with its accommodation of a typical number of genes for a plant genome, and 2) highlight the role of high gene family turnover in the evolutionary diversification of U. gibba's functional gene space and adaptations to its unique lifestyle and highly specialized body plan.

We provide a basic introduction to discrete-variable, rotor, and continuous-variable quantum phase spaces, explaining how the latter two can be understood as limiting cases of the first. We extend the limit-taking procedures used to travel between phase spaces to a general class of Hamiltonians (including many local stabilizer codes) and provide six examples: the Harper equation, the Baxter parafermionic spin chain, the Rabi model, the Kitaev toric code, the Haah cubic code (which we generalize to qudits), and the Kitaev honeycomb model. We obtain continuous-variable generalizations of all models, some of which are novel. The Baxter model is mapped to a chain of coupled oscillators and the Rabi model to the optomechanical radiation pressure Hamiltonian. The procedures also yield rotor versions of all models, five of which are novel many-body extensions of the almost Mathieu equation. The toric and cubic codes are mapped to lattice models of rotors, with the toric code case related to U(1) lattice gauge theory., 22 pages, 3 figures; part of special issue on Rabi model; v2 minor changes

Efficient long distance quantum communication with quantum repeaters is discussed. We show that quantum repeater protocols can be classified into three generations, each performs optimally in different parameter regimes. The application of cat codes as a single-mode encoding to one-way quantum repeaters is analyzed.

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A., published version, peerReviewed

Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains a tiny nuclear genome despite at least two rounds of whole genome duplication (WGD) since common ancestry with grapevine and other species. We used a third-generation genome assembly with several complete chromosomes to reconstruct the two most recent lineage-specific ancestral genomes that led to the modern U. gibba genome structure. Patterns of subgenome dominance in the most recent WGD, both architectural and transcriptional, are suggestive of allopolyploidization, which may have generated genomic novelty and led to instantaneous speciation. Syntenic duplicates retained in polyploid blocks are enriched for transcription factor functions, whereas gene copies derived from ongoing tandem duplication events are enriched in metabolic functions potentially important for a carnivorous plant. Among these are tandem arrays of cysteine protease genes with trap-specific expression that evolved within a protein family known to be useful in the digestion of animal prey. Further enriched functions among tandem duplicates (also with trap-enhanced expression) include peptide transport (intercellular movement of broken-down prey proteins), ATPase activities (bladder-trap acidification and transmembrane nutrient transport), hydrolase and chitinase activities (breakdown of prey polysaccharides), and cell-wall dynamic components possibly associated with active bladder movements. Whereas independently polyploid Arabidopsis syntenic gene duplicates are similarly enriched for transcriptional regulatory activities, Arabidopsis tandems are distinct from those of U. gibba, while still metabolic and likely reflecting unique adaptations of that species. Taken together, these findings highlight the special importance of tandem duplications in the adaptive landscapes of a carnivorous plant genome.

Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption. Analysis of digestive fluid proteins from C. follicularis and three other carnivorous plants with independent carnivorous origins revealed repeated co-options of stress-responsive protein lineages coupled with convergent amino acid substitutions to acquire digestive physiology. These results imply constraints on the available routes to evolve plant carnivory.

Exactly solvable models have played an important role in establishing the sophisticated modern understanding of equilibrium many-body physics. And conversely, the relative scarcity of solutions for non-equilibrium models greatly limits our understanding of systems away from thermal equilibrium. We study a family of non-equilibrium models, some of which can be viewed as dissipative analogues of the transverse-field Ising model, in that an effectively classical Hamiltonian is frustrated by dissipative processes that drive the system toward states that do not commute with the Hamiltonian. Surprisingly, a broad and experimentally relevant subset of these models can be solved efficiently in any number of spatial dimensions. We leverage these solutions to prove a no-go theorem on steady-state phase transitions in a many-body model that can be realized naturally with Rydberg atoms or trapped ions, and to compute the effects of decoherence on a canonical trapped-ion-based quantum computation architecture., Comment: 8 pages, 3 figures

We introduce a driven-dissipative two-mode bosonic system whose reservoir causes simultaneous loss of two photons in each mode and whose steady states are superpositions of pair-coherent/Barut-Girardello coherent states. We show how quantum information encoded in a steady-state subspace of this system is exponentially immune to phase drifts (cavity dephasing) in both modes. Additionally, it is possible to protect information from arbitrary photon loss in either (but not simultaneously both) of the modes by continuously monitoring the difference between the expected photon numbers of the logical states. Despite employing more resources, the two-mode scheme enjoys two advantages over its one-mode cat-qubit counterpart with regards to implementation using current circuit QED technology. First, monitoring the photon number difference can be done without turning off the currently implementable dissipative stabilizing process. Second, a lower average photon number per mode is required to enjoy a level of protection at least as good as that of the cat-codes. We discuss circuit QED proposals to stabilize the code states, perform gates, and protect against photon loss via either active syndrome measurement or an autonomous procedure. We introduce quasiprobability distributions allowing us to represent two-mode states of fixed photon number difference in a two-dimensional complex plane, instead of the full four-dimensional two-mode phase space. The two-mode codes are generalized to multiple modes in an extension of the stabilizer formalism to non-diagonalizable stabilizers. The $M$-mode codes can protect against either arbitrary photon losses in up to $M-1$ modes or arbitrary losses and gains in any one mode., 29 pages, 9 figures, 2 tables; added a numerical comparison

It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of wholegenome duplications (WGDs) and mobile element proliferation 1 . However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism. Like other carnivorous plants, Utricularia (Lentibulariaceae) species derive nitrogen and phosphorus supplements by trapping and digesting prey organisms 2,3 . Lentibulariaceae are asterid angiosperms closely related to the model plants snapdragon (Antirrhinum) and monkey

We investigate cat codes that can correct multiple excitation losses and identify two types of logical errors: bit-flip errors due to excessive excitation loss and dephasing errors due to quantum back-action from the environment. We show that selected choices of logical subspace and coherent amplitude can efficiently reduce dephasing errors. The trade-off between the two major errors enables optimized performance of cat codes in terms of minimized decoherence. With high coupling efficiency, we show that one-way quantum repeaters with cat codes feature drastically boosted secure communication rate per mode compared with conventional encoding schemes, and thus showcase the promising potential of quantum information processing with continuous variable quantum codes.

A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.

The growing number of genome sequences completed during the last few years has made necessary the development of bioinformatics tools for the easy access and retrieval of sequence data, as well as for downstream comparative genomic analyses. Some of these are implemented as online platforms that integrate genomic data produced by different genome sequencing initiatives with data mining tools as well as various comparative genomic and evolutionary analysis possibilities.Here, we use the online comparative genomics platform CoGe ( http://www.genomevolution.org/coge/ ) (Lyons and Freeling. Plant J 53:661-673, 2008; Tang and Lyons. Front Plant Sci 3:172, 2012) (1) to retrieve the entire complement of orthologous and paralogous genes belonging to the SUMO-Activating Enzymes 1 (SAE1) gene family from a set of species representative of the Brassicaceae plant eudicot family with genomes fully sequenced, and (2) to investigate the history, timing, and molecular mechanisms of the gene duplications driving the evolutionary expansion and functional diversification of the SAE1 family in Brassicaceae.

Molecular evolutionary analysis of gene families commonly involves a sequence of steps including multiple sequence alignment (MSA) and reconstructing phylogenetic trees, using any of the multiple algorithms available. SeaView is a multiplatform program that integrates different methods for performing the above tasks, and others, within a friendly and simple-to-use graphical user interface (Gouy et al. Mol Biol Evol 27(2):221-224, 2010). By using SeaView, we will investigate the evolutionary relationships among SAE1 genes in Brassicaceae species by means of two alternative methods of phylogenetic reconstruction: Maximum Likelihood (ML) and Neighbor-Joining (NJ). Prior to ML phylogenetic analysis (Guindon and Gascuel. Syst Biol 52(5):696-704, 2003), we will use ProtTest to select the best-fit evolutionary model of amino acid substitution for the MSA of SAE1 proteins (Abascal et al. Bioinformatics 21(9):2104-2105, 2005).

We construct a new class of quantum error-correcting codes for a bosonic mode which are advantageous for applications in quantum memories, communication, and scalable computation. These 'binomial quantum codes' are formed from a finite superposition of Fock states weighted with binomial coefficients. The binomial codes can exactly correct errors that are polynomial up to a specific degree in bosonic creation and annihilation operators, including amplitude damping and displacement noise as well as boson addition and dephasing errors. For realistic continuous-time dissipative evolution, the codes can perform approximate quantum error correction to any given order in the timestep between error detection measurements. We present an explicit approximate quantum error recovery operation based on projective measurements and unitary operations. The binomial codes are tailored for detecting boson loss and gain errors by means of measurements of the generalized number parity. We discuss optimization of the binomial codes and demonstrate that by relaxing the parity structure, codes with even lower unrecoverable error rates can be achieved. The binomial codes are related to existing two-mode bosonic codes but offer the advantage of requiring only a single bosonic mode to correct amplitude damping as well as the ability to correct other errors. Our codes are similar in spirit to 'cat codes' based on superpositions of the coherent states, but offer several advantages such as smaller mean number, exact rather than approximate orthonormality of the code words, and an explicit unitary operation for repumping energy into the bosonic mode. The binomial quantum codes are realizable with current superconducting circuit technology and they should prove useful in other quantum technologies, including bosonic quantum memories, photonic quantum communication, and optical-to-microwave up- and down-conversion., Published version

Universal computation of a quantum system consisting of superpositions of well-separated coherent states of multiple harmonic oscillators can be achieved by three families of adiabatic holonomic gates. The first gate consists of moving a coherent state around a closed path in phase space, resulting in a relative Berry phase between that state and the other states. The second gate consists of "colliding" two coherent states of the same oscillator, resulting in coherent population transfer between them. The third gate is an effective controlled-phase gate on coherent states of two different oscillators. Such gates should be realizable via reservoir engineering of systems which support tunable nonlinearities, such as trapped ions and circuit QED., 6 pages, 3 figures + 4 page supplement; (v3 scheme now universal; v4 title changed to match published version); gate animations available at http://dancingblobs.krastanov.org/

The growing number of genome sequences completed during the last few years has made necessary the development of bioinformatics tools for the easy access and retrieval of sequence data, as well as for downstream comparative genomic analyses. Some of these are implemented as online platforms that integrate genomic data produced by different genome sequencing initiatives with data mining tools as well as various comparative genomic and evolutionary analysis possibilities.Here, we use the online comparative genomics platform CoGe ( http://www.genomevolution.org/coge/ ) (Lyons and Freeling. Plant J 53:661-673, 2008; Tang and Lyons. Front Plant Sci 3:172, 2012) (1) to retrieve the entire complement of orthologous and paralogous genes belonging to the SUMO-Activating Enzymes 1 (SAE1) gene family from a set of species representative of the Brassicaceae plant eudicot family with genomes fully sequenced, and (2) to investigate the history, timing, and molecular mechanisms of the gene duplications driving the evolutionary expansion and functional diversification of the SAE1 family in Brassicaceae.

Quantum channels can describe all transformations allowed by quantum mechanics. We provide an explicit universal protocol to construct all possible quantum channels, using a single qubit ancilla with quantum non-demolition readout and adaptive control. Our construction is efficient in both physical resources and circuit depth, and can be demonstrated using superconducting circuits and various other physical platforms. There are many applications of quantum channel construction, including system stabilization and quantum error correction, Markovian and exotic channel simulation, implementation of generalized quantum measurements and more general quantum instruments. Efficient construction of arbitrary quantum channels opens up exciting new possibilities for quantum control, quantum sensing and information processing tasks., Comment: 16 pages, 8 figures

Molecular evolutionary analysis of gene families commonly involves a sequence of steps including multiple sequence alignment (MSA) and reconstructing phylogenetic trees, using any of the multiple algorithms available. SeaView is a multiplatform program that integrates different methods for performing the above tasks, and others, within a friendly and simple-to-use graphical user interface (Gouy et al. Mol Biol Evol 27(2):221-224, 2010). By using SeaView, we will investigate the evolutionary relationships among SAE1 genes in Brassicaceae species by means of two alternative methods of phylogenetic reconstruction: Maximum Likelihood (ML) and Neighbor-Joining (NJ). Prior to ML phylogenetic analysis (Guindon and Gascuel. Syst Biol 52(5):696-704, 2003), we will use ProtTest to select the best-fit evolutionary model of amino acid substitution for the MSA of SAE1 proteins (Abascal et al. Bioinformatics 21(9):2104-2105, 2005).

Plant-specific TCP domain transcription factors have been shown to regulate morphological novelties during plant evolution, including the complex architecture of the Asteraceae inflorescence that involves different types of flowers. We conducted comparative analysis of the CYCLOIDEA/TEOSINTE BRANCHED1 (CYC/TB1) gene family in Gerbera hybrida (gerbera) and Helianthus annuus (sunflower), two species that represent distant tribes within Asteraceae. Our data confirm that the CYC/TB1 gene family has expanded in Asteraceae, a condition that appears to be connected with the increased developmental complexity and evolutionary success of this large plant family. Phylogenetic analysis of the CYC/TB1 gene family revealed both shared and lineage-specific duplications in gerbera and sunflower, corresponding to the three gene lineages previously identified as specific to core eudicots: CYC1, CYC2, and CYC3. Expression analyses of early stages of flower primordia development indicated that especially within the CYC2 clade, with the greatest number of secondary gene duplications, gene expression patterns are conserved between the species and associated with flower and inflorescence development. All sunflower and gerbera CYC2 clade genes showed differential expression between developing flower types, being upregulated in marginal ray (and trans) flowers. One gene in gerbera (GhCYC3) and two in sunflower (HaCYC2d and HaCYC2c) were indicated to be strong candidates as regulators of ray flower identity, a function that is specific for Asteraceae. Our data further showed that other CYC2 clade genes are likely to have more specialized functions at the level of single flowers, including the late functions in floral reproductive organs that may be more conserved across plant families. The expression patterns of CYC1 and CYC3 clade genes showed more differences between the two species but still pointed to possible conserved functions during vegetative plant development. Pairwise protein– protein interaction assays gave the first molecular evidence that CYC/TB1-like proteins function in complexes. Compared with sunflower, the gerbera proteins showed higher capacity for dimerization, between as well as within CYC clades. Our data from two distant species within the Asteraceae suggest that the expansion and the apparent conservation of especially the CYC2 clade CYC/TB1-like genes are associated with the evolution of the increased complexity of the Asteraceae inflorescence architecture.

Electronic excitation energies and wavefunctions are calculated for Ru ( bpy ) 3 + 2 ( bpy = 2 , 2 ′ ‐ bipyridine ) and its two derivatives, where one or two bpy ligands are functionalized with carboxyl and methyl groups. We show that the structure of these molecules allows one to express their excitations in terms of wavefunctions localized on individual ligands via the Frenkel exciton model. The model is based on three parameters – effective single-ligand excitation energy, inter-ligand interaction coupling, and energy shift brought by the ligand functionalization – that are extracted from time-dependent density functional theory (TDDFT). This simple model is able to accurately explain the optical intensity, localization properties, and splitting patterns of the low-energy excited states not only in molecules with a high degree of symmetry, but also in non-symmetrically functionalized Ru(II) complexes in vacuum and in solvent. Such reduced description of the excited states provides better understanding and interpretation of experimental data on Ru–polypyridine complexes, and allows for description of excited-state structure in a large ensemble of interacting molecules and treatment of possible charge and energy transfer phenomena in the material.

Simulations of ligated semiconductor quantum dots (QDs) and their physical properties, such as morphologies, QD–ligand interactions, electronic structures, and optical transitions, are expected to be very sensitive to computational methodology. We utilize Density Functional Theory (DFT) and systematically study how the choice of density functional, atom-localized basis set, and a solvent affects the physical properties of the Cd33Se33 cluster ligated with a trimethylphosphine oxide ligand. We have found that qualitative performance of all exchange-correlation (XC) functionals is relatively similar in predicting strong QD–ligand binding energy (∼1 eV). Additionally, all functionals predict shorter Cd–Se bond lengths on the QD surface than in its core, revealing the nature and degree of QD surface reconstruction. For proper modeling of geometries and QD–ligand interactions, however, augmentation of even a moderately sized basis set with polarization functions (e.g., LANL2DZ* and 6-31G*) is very important. A...

The family of MADS box genes is involved in a number of processes besides controlling floral development. In addition to supplying homeotic functions defined by the ABC model, they influence flowering time and transformation of vegetative meristem into inflorescence meristem, and have functions in roots and leaves. Three Gerbera hybrida At-SOC1-like genes (Gh-SOC1-Gh-SOC3) were identified among gerbera expressed sequence tags.Evolutionary relationships between SOC1-like genes from gerbera and other plants were studied by phylogenetic analysis. The function of the gerbera gene Gh-SOC1 in gerbera floral development was studied using expression analysis, protein-protein interaction assays and reverse genetics. Transgenic gerbera lines over-expressing or downregulated for Gh-SOC1 were obtained using Agrobacterium transformation and investigated for their floral phenotype.Phylogenetic analysis revealed that the closest paralogues of At-SOC1 are Gh-SOC2 and Gh-SOC3. Gh-SOC1 is a more distantly related paralogue, grouping together with a number of other At-SOC1 paralogues from arabidopsis and other plant species. Gh-SOC1 is inflorescence abundant and no expression was seen in vegetative parts of the plant. Ectopic expression of Gh-SOC1 did not promote flowering, but disturbed the development of floral organs. The epidermal cells of ray flower petals appeared shorter and their shape was altered. The colour of ray flower petals differed from that of the wild-type petals by being darker red on the adaxial side and greenish on the abaxial surface. Several protein-protein interactions with other gerbera MADS domain proteins were identified.The At-SOC1 paralogue in gerbera shows a floral abundant expression pattern. A late petal expression might indicate a role in the final stages of flower development. Over-expression of Gh-SOC1 led to partial loss of floral identity, but did not affect flowering time. Lines where Gh-SOC1 was downregulated did not show a phenotype. Several gerbera MADS domain proteins interacted with Gh-SOC1.

This paper presents a phylogenetic analysis of Lamiaceae subfam. Lamioideae (including subfamily Pogostemonoideae) based on sequences of the trnL intron, trnL-trnF intergenic spacer, and rps16 intron of the plastid genome. It is the first analysis that includes all major lamioid and pogostemonoid genera. Monophyly of Lamioideae s.l. (i.e., including Pogostemonoideae) is strongly supported, with Cymaria Benth. as its sister group, and Pogostemonoideae, which sometimes has been recognized as a subfamily, is subsumed in Lamioideae. On the basis of the phylogenetic hypothesis, Lamioideae is divided into nine tribes. Three new tribes are established: Gomphostemmateae Scheen & Lindqvist, Phlomideae Mathiesen, and Leucadeae Scheen & Ryding. The other six tribes are: Pogostemoneae Briq., Synandreae Raf., Stachydeae Dumort., Leonureae Dumort., Lamieae Coss. & Germ., and Marrubieae Vis. The genus Betonica L. is reestablished. The results also strongly suggest that the genera Stachys L., Sideritis L., Ballota L., and Leucas R. Br. are polyphyletic or paraphyletic. The results were used to examine evolution of non-molecular characters.

Carnivorous plants inhabit nutrient-poor environments, where prominent targets of prey capture are organic nitrogen and phosphorus. Some carnivorous plants also acquire carbon from their victims. A new report focusing on Utricularia, the bladderwort, demonstrates that carbon assimilated from photosynthesis is paradoxically secreted into the trapping environment, where it may help to support a mutualistic bacterial community. This bacterial community may also secrete allelochemicals that attract microcrustaceans which bear a strong overt resemblance to bladderwort traps. Furthermore, Utricularia and its sister genus Genlisea share anomalous molecular evolutionary features, such as highly increased rates of nucleotide substitution and dynamic evolution of genome size, from approximately 60-1500 megabases depending on the species or even population. A mechanistic hypothesis, based on the mutagenic action of reactive oxygen species (ROS) is proposed to underlie these phenomena, involving error-prone repair at the level of DNA bases and double-strand breaks. It is argued that these plants are prime candidates for further research on the complexities of plant physiology associated with carnivory, metagenomic surveys of trap microbial communities, novel plant nitrogen/nutrient utilization pathways, the ecology of prey attraction, whole-plant and trap comparative development, and, finally, evolution of the minimal angiosperm genome.

Compact, but relatively accurate wavefunctions for the ground state of the Li atom were obtained through the use of a limited basis of exponentially correlated functions with optimized nonlinear parameters. In contrast to our earlier work, the basis contains pre-exponential factors that improve the rate of convergence of the basis-set expansion. The matrix elements needed in the present work were evaluated analytically using recursive methods reported recently by one of us; a check on the programming was provided by comparison with numerical evaluations carried out by Turbiner and Guevara. The rate of convergence of the expansion is compared with those of Hylleraas-basis computations, and a comparison is also made with exponentially correlated studies of He-like systems. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

According to the classical ABC model, B-function genes are involved in determining petal and stamen development. Most core eudicot species have B class genes belonging to three different lineages: the PI ,e uAP3, and TM6 lineages, although both Arabidopsis and Antirrhinum appear to have lost their TM6-like gene. Functional studies were performed for three gerbera (Gerbera hybrida) B class MADS-box genes—PI/GLO-like GGLO1 ,e uAP3 class GDEF2, and TM6-like GDEF1—and data are shown for a second euAP3-like gene, GDEF3. In phylogenetic analysis, GDEF3 is a closely related paralogue of GDEF2, and apparently stems from a duplication common to all Asteraceae. Expression analysis and transgenic phenotypes confirm that GGLO1 and GDEF2 mediate the classical B-function since they determine petal and stamen identities. However, based on assays in yeast, three B class heterodimer combinations are possible in gerbera. In addition to the interaction of GGLO1 and GDEF2 proteins, GGLO1 also pairs with GDEF1 and GDEF3. This analysis of GDEF1 represents the first functional characterization of a TM6-like gene in a core eudicot species outside Solanaceae. Similarly to its relatives in petunia and tomato, the expression pattern and transgenic phenotypes indicate that GDEF1 is not involved in determination of petal identity, but has a redundant role in regulating stamen development.

The debate on the origin and evolution of flowers has recently entered the field of developmental genetics, with focus on the design of the ancestral floral regulatory program. Flowers can differ dramatically among angiosperm lineages, but in general, male and female reproductive organs surrounded by a sterile perianth of sepals and petals constitute the basic floral structure. However, the basal angiosperm lineages exhibit spectacular diversity in the number, arrangement, and structure of floral organs, whereas the evolutionarily derived monocot and eudicot lineages share a far more uniform floral ground plan. Here we show that broadly overlapping transcriptional programs characterize the floral transcriptome of the basal angiosperm Persea americana (avocado), whereas floral gene expression domains are considerably more organ specific in the model eudicot Arabidopsis thaliana . Our findings therefore support the “fading borders” model for organ identity determination in basal angiosperm flowers and extend it from the action of regulatory genes to downstream transcriptional programs. Furthermore, the declining expression of components of the staminal transcriptome in central and peripheral regions of Persea flowers concurs with elements of a previous hypothesis for developmental regulation in a gymnosperm “floral progenitor.” Accordingly, in contrast to the canalized organ-specific regulatory apparatus of Arabidopsis , floral development may have been originally regulated by overlapping transcriptional cascades with fading gradients of influence from focal to bordering organs.

We develop criteria to detect neighborhood selection effects on gene loss following whole genome duplication, and apply them to the recently sequenced poplar (Populus trichocarpa) genome. We improve on guided genome halving algorithms so that several thousand gene sets, each containing two paralogs in the descendant T of the doubling event and their single ortholog from an undoubled reference genome R, can be analyzed to reconstruct the ancestor A of T at the time of doubling. At the same time, large numbers of defective gene sets, either missing one paralog from T or missing their ortholog in R, may be incorporated into the analysis in a consistent way. We apply this genomic rearrangement distance-based approach to the poplar and grapevine (Vitis vinifera) genomes, as T and R respectively. We conclude that, after chromosome doubling, the "choice" of which paralogous gene pairs will lose copies is random, but that the retention of strings of single-copy genes on one chromosome versus the other is decidedly non-random.

Parsimony-based phylogenetic analyses of the neotropical tribe Helieae (Gentianaceae) are presented, including 22 of the 23 genera and 60 species. This study is based on data from morphology, palynology, and seed micromorphology (127 structural characters), and DNA sequences (matK, trnL intron, ITS). Phylogenetic reconstructions based on ITS and morphology provided the greatest resolution, morphological data further helping to tentatively place several taxa for which DNA was not available (Celiantha, Lagenanthus, Rogersonanthus, Roraimaea, Senaea, Sipapoantha, Zonanthus). Celiantha, Prepusa and Senaea together appear as the sister clade to the rest of Helieae. The remainder of Helieae is largely divided into two large subclades, the Macrocarpaea subclade and the Symbolanthus subclade. The first subclade includes Macrocarpaea, sister to Chorisepalum, Tachia, and Zonanthus. Irlbachia and Neblinantha are placed as sisters to the Symbolanthus subclade, which includes Aripuana, Calolisianthus, Chelonanthus, Helia, Lagenanthus, Lehmanniella, Purdieanthus, Rogersonanthus, Roraimaea, Sipapoantha, and Symbolanthus. Generic-level polyphyly is detected in Chelonanthus and Irlbachia. Evolution of morphological characters is discussed, and new pollen and seed characters are evaluated for the first time in a combined morphological-molecular phylogenetic analysis.

The genus Leucas R.Br. includes 100 recognized species ranging in distribution from Africa through the Indian subcontinent to Queensland, Australia. Morphological cladistic studies have suggested that several other genera of Lamioideae – Acrotome, Isoleucas, Leonotis, and Otostegia (pro parte) – may be closely related to Leucas, or even nested within it. Here we use phylogenetic analysis of three plastid DNA loci, the trnL–F region, trnS–G spacer, and the rps16 intron and reach similar conclusions. Many of the morphological features used to maintain Leucas since 1810 are shared ancestral (symplesiomorphic) characters. The other genera (or subgeneric group in the case of Otostegia) are therefore defined by apomorphic states. This is particularly apparent in the case of Leonotis, with its highly specialized bird-pollinated flowers, derived within a paraphyletic and insect-pollinated Leucas. Some geographically isolated groups are monophyletic, including all Asian species of Leucas, a Socotran clade, and a large African lineage.

Polyploidy has long been recognized as a major force in angiosperm evolution. Recent genomic investigations not only indicate that polyploidy is ubiquitous among angiosperms, but also suggest several ancient genome-doubling events. These include ancient whole genome duplication (WGD) events in basal angiosperm lineages, as well as a proposed paleohexaploid event that may have occurred close to the eudicot divergence. However, there is currently no evidence for WGD in Amborella, the putative sister species to other extant angiosperms. The question is no longer "What proportion of angiosperms are polyploid?", but "How many episodes of polyploidy characterize any given lineage?" New algorithms provide promise that ancestral genomes can be reconstructed for deep divergences (e.g., it may be possible to reconstruct the ancestral eudicot or even the ancestral angiosperm genome). Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae. However, additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages and to determine when novel genes resulting from polyploidy have enabled adaptive radiations.

Several key processes in plant development are regulated by TCP transcription factors. CYCLOIDEA-like (CYC-like) TCP domain proteins have been shown to control flower symmetry in distantly related plant lineages. Gerbera hybrida , a member of one of the largest clades of angiosperms, the sunflower family (Asteraceae), is an interesting model for developmental studies because its elaborate inflorescence comprises different types of flowers that have specialized structures and functions. The morphological differentiation of flower types involves gradual changes in flower size and symmetry that follow the radial organization of the densely packed inflorescence. Differences in the degree of petal fusion further define the distinct shapes of the Gerbera flower types. To study the role of TCP transcription factors during specification of this complex inflorescence organization, we characterized the CYC-like homolog GhCYC2 from Gerbera . The expression of GhCYC2 follows a gradient along the radial axis of the inflorescence. GhCYC2 is expressed in the marginal, bilaterally symmetrical ray flowers but not in the centermost disk flowers, which are nearly radially symmetrical and have significantly less fused petals. Overexpression of GhCYC2 causes disk flowers to obtain morphologies similar to ray flowers. Both expression patterns and transgenic phenotypes suggest that GhCYC2 is involved in differentiation among Gerbera flower types, providing the first molecular evidence that CYC-like TCP factors take part in defining the complex inflorescence structure of the Asteraceae, a major determinant of the family's evolutionary success.

The five mint genera Brazoria, Macbridea, Physostegia, Synandra and Warnockia (Lamioideae: Lamiaceae) are all North American endemics. Together with the monotypic European genus Melittis and the Asian genus Chelonopsis, these taxa have been classified as subtribe Melittidinae. Previous morphological studies have failed to uncover synapomorphic characters for this group. We sequenced the plastid trnL-trnF region and trnS-trnG spacer and the nuclear ribosomal 5S non-transcribed spacer (5S-NTS) to assess phylogenetic relationships within Melittidinae. Standard parsimony and direct optimization (POY) analyses show Melittis, the type genus of the subtribe, as sister to Stachys. Thus, the monophyly of subtribe Melittidinae is not supported either by molecular or morphological data. However, the North American endemics form a monophyletic group that can be recognized as the recircumscribed tribe Synandreae. The molecular relationships among these genera are corroborated by both morphological and cytological data. The expected close relationship between the south-central endemics Warnockia and Brazoria and their sister relationship to the widespread genus Physostegia is confirmed. Nevertheless, most of the North American endemics are restricted to the south-east of the continent. Dispersal westwards and northwards is correlated with an increase in chromosome numbers. No specific Eurasian origin (i.e., transatlantic or transpacific) can be determined, but Synandreae are clearly distinct from the large Stachys clade, and therefore represent a separate migration into North America. © The Willi Hennig Society 2007.

Collisions between Xe@C60 and sheets of graphite of various dimensions were simulated. A Tersoff many-body potential modeled the interactions between carbon atoms and a Lennard-Jones potential simulated the xenon-carbon interactions. The simulations were compared to experiment and with simulations which implemented other potentials. The results indicate that a relatively small graphite film can be an accurate approximation for a nearly infinite sheet of graphite. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Through multifaceted genome-scale research involving phylogenomics, targeted gene surveys, and gene expression analyses in diverse basal lineages of angiosperms, our studies provide insights into the most recent common ancestor of all extant flowering plants. MADS-box gene duplications have played an important role in the origin and diversification of angiosperms. Furthermore, early angiosperms possessed a diverse tool kit of floral genes and exhibited developmental 'flexibility', with broader patterns of expression of key floral organ identity genes than are found in eudicots. In particular, homologs of B-function MADS-box genes are more broadly expressed across the floral meristem in basal lineages. These results prompted formulation of the 'fading borders' model, which states that the gradual transitions in floral organ morphology observed in some basal angiosperms (e.g. Amborella) result from a gradient in the level of expression of floral organ identity genes across the developing floral meristem.

Within Rauvolfioideae (Apocynaceae), genera have long been assigned to tribes based mainly on only one or two superficial fruit and seed characters. Taxa with drupaceous fruits were included in Alyxieae. To elucidate relationships within Alyxieae, we analyzed phylogenetically a data set of sequences from four plastid DNA regions (RbcL, matK, TrnL intron, and TrnL-F intergenic spacer) and a morphological data set for 33 genera of Apocynaceae, including representatives of all genera previously included in Alyxieae and two non-Apocynaceae species. Results of parsimony analysis indicate that Alyxieae as previously delimited are polyphyletic, with most genera falling into two main clades. The Alyxia clade includes seven genera: Alyxia Banks ex R. Br., Lepinia Decne., Lepiniopsis Valeton, Pteralyxia K. Schum., and Condylocarpon Desf. together with Plectaneia Thouars. (earlier included in Plumerieae) and Chilocarpus Blume (earlier included in Chilocarpeae). The Vinca clade includes eight genera: Cabucal...