We present the results of two exploratory parsimony analyses of DNA sequences from 475 and 499 species of seed plants, respectively, representing all major taxonomic groups. The data are exclusively from the chloroplast gene rbcL, which codes for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO or RuBPCase). We used two different state-transformation assumptions resulting in two sets of cladograms: (i) equal-weighting for the 499-taxon analysis; and (ii) a procedure that differentially weights transversions over transitions within characters and codon positions among characters for the 475-taxon analysis. The degree of congruence between these results and other molecular, as well as morphological, cladistic studies indicates that rbcL sequence variation contains historical evidence appropriate for phylogenetic analysis at this taxonomic level of sampling. Because the topologies presented are necessarily approximate and cannot be evaluated adequately for internal support, these results should be assessed from the perspective of their predictive value and used to direct future studies, both molecular and morphological. In both analyses, the three genera of Gnetales are placed together as the sister group of the flowering plants, and the anomalous aquatic Ceratophyllum (Ceratophyllaceae) is sister to all other flowering plants. Several major lineages identified correspond well with at least some recent taxonomic schemes for angiosperms, particularly those of Dahlgren and Thorne. The basalmost clades within the angiosperms are orders of the apparently polyphyletic subclass Magnoliidae sensu Cronquist. The most conspicuous feature of the topology is that the major division is not monocot versus dicot, but rather one correlated with general pollen type: uniaperturate versus triaperturate. The Dilleniidae and Hamamelidae are the only subclasses that are grossly polyphyletic; an examination of the latter is presented as an example of the use of these broad analyses to focus more restricted studies. A broadly circumscribed Rosidae is paraphyletic to Asteridae and Dilleniidae. Subclass Caryophyllidae is monophyletic and derived from within Rosidae in the 475-taxon analysis but is sister to a group composed of broadly delineated Asteridae and Rosidae in the 499-taxon study.

Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. Although DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honey bee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.BS-Seq | epigenetic profiling | DNA methylation | gene body methylation | UHRF1C ytosine DNA methylation is an epigenetic mark important in many gene regulatory systems, including genomic imprinting, X-chromosome inactivation, silencing of transposons and other repetitive DNA sequences, as well as expression of endogenous genes. Methylation is conserved in most major eukaryotic groups, including many plants, animals, and fungi, although it has been lost from certain model organisms such as the budding yeast Saccharomyces cerevisiae and nematode worm Caenorhabditis elegans (1-3). DNA methylation can be categorized into three types according to the sequence context of the cytosines, namely CG, CHG, and CHH (H = A, C, or T). CG methylation is maintained by conserved Dnmt1 DNA methyltransferase enzymes. CHH methylation, and, to some extent CHG methylation, is generally maintained by the activity of the conserved Dnmt3 methyltransferases, whereas high levels of CHG methylation seen in the model plant Arabidopsis are maintained by the plant-specific methyltransferase CMT3 (2, 3). Generally speaking, DNA methylation is thought to occur "globally" in vertebrates, with CG sites being heavily methylated genome-wide except for those in CpG islands, whereas invertebrates, plants, and fungi have "mosaic" methylation, characterized by interspersed methylated and unmethylated domains (4). These differences are an interesting starting point for studying divergence in methylation pathways and regulatory mechanisms; however, determining precise genomescale methylation patterns has been a challenge for complex genomes until the recent development of high-throughput sequencing technology. In this paper, we generated shotgun bisulfite sequencing data to profile DNA methylation in eight eukaryotic organisms. These organisms display wide variations in methylati...

Forest trees display a perennial growth behavior characterized by a multiple-year delay in flowering and, in temperate regions, an annual cycling between growth and dormancy. We show here that the CO/FT regulatory module, which controls flowering time in response to variations in daylength in annual plants, controls flowering in aspen trees. Unexpectedly, however, it also controls the short-day-induced growth cessation and bud set occurring in the fall. This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe.

Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled .94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.A major opportunity for a sustainable energy and biomaterials economy in many parts of the world lies in a better understanding of the molecular basis of superior growth and adaptation in woody plants. Part of this opportunity involves species of Eucalyptus L'Hér, a genus of woody perennials native to Australia 1 . The remarkable adaptability of eucalypts coupled with their fast growth and superior wood properties has driven their rapid adoption for plantation forestry in more than 100 countries across six continents (.20 million ha) 2 , making eucalypts the most widely planted hardwood forest trees in the world. The subtropical E. grandis and the temperate E. globulus stand out as targets of breeding programmes worldwide. Planted eucalypts provide key renewable resources for the production of pulp, paper, biomaterials and bioenergy, while mitigating human pressures on native forests 3 . Eucalypts also have a large diversity and high concentration of essential oils (mixtures of mono-and sesquiterpenes), many of which have ecological functions as well as medicinal and industrial uses. Predominantly outcrossers 1 with hermaphroditic animal-pollinated flowers, eucalypts are highly heterozygous and display pre-and postzygotic barriers to selfing to reduce inbreeding depression for fitness and survival 4 .To mitigate the challenge of assembling a highly heterozygous genome, we sequenced the genome of 'BRASUZ1', a 17-year-old E. grandis genotype derived from one generation of selfing. The availability of annotated forest tree genomes from two separately evolving rosid lineages, Eucalyptus (order Myrtales) and Populus (order Malpighiales 5 ), in combination with genomes from domesticated woody plants (for example, Vitis, Prunus, Citrus), provides a comparative foundation for addressing

No abstract

Annual plants grow vegetatively at early developmental stages and then transition to the reproductive stage, followed by senescence in the same year. In contrast, after successive years of vegetative growth at early ages, woody perennial shoot meristems begin repeated transitions between vegetative and reproductive growth at sexual maturity. However, it is unknown how these repeated transitions occur without a developmental conflict between vegetative and reproductive growth. We report that functionally diverged paralogs FLOWERING LOCUS T1 (FT1) and FLOWERING LOCUS T2 (FT2), products of whole-genome duplication and homologs of Arabidopsis thaliana gene FLOWERING LOCUS T (FT), coordinate the repeated cycles of vegetative and reproductive growth in woody perennial poplar (Populus spp.). Our manipulative physiological and genetic experiments coupled with field studies, expression profiling, and network analysis reveal that reproductive onset is determined by FT1 in response to winter temperatures, whereas vegetative growth and inhibition of bud set are promoted by FT2 in response to warm temperatures and long days in the growing season. The basis for functional differentiation between FT1 and FT2 appears to be expression pattern shifts, changes in proteins, and divergence in gene regulatory networks. Thus, temporal separation of reproductive onset and vegetative growth into different seasons via FT1 and FT2 provides seasonality and demonstrates the evolution of a complex perennial adaptive trait after genome duplication.ife cycles of higher plants display a great diversity in morphological and seasonal adaptation. Annual plants grow, reproduce, and senesce within a growing season, whereas woody perennials display successive years of vegetative growth before reaching sexual maturity (1-3). After this time, shoot meristems begin cyclical transitions between vegetative and reproductive growth. Consequently, shoots may repeatedly form early vegetative buds (Vegetative Zone I), reproductive buds (Floral Zone), and late vegetative buds (Vegetative Zone II) in a sequential manner (3). However, our understanding of the mechanisms underlying such complex phenotypes, and thus variation in growth habits and adaptation, remain rudimentary. In the herbaceous perennial Arabis alpina, repeated transcriptional repression and activation of PERPETUAL FLOWERING 1 (PEP1), an ortholog of the floral repressor FLOWERING LOCUS C (FLC) in annual Arabidopsis thaliana (4), controls recurring seasonal transitions between reproductive and vegetative phases (5). However, a true functional ortholog of FLC has not been reported in trees, nor does phylogenetic analysis point to a clear structural ortholog of FLC in poplar (Populus spp.) (6).Previous results showed that FLOWERING LOCUS T1 (FT1) (7) and FLOWERING LOCUS T2 (FT2) (8) under the cauliflower mosaic virus 35S (CaMV 35S) constitutive overexpression promoter induce early flowering in poplar. Transcript abundance of both genes gradually increases in the growing season as poplar trees mature....

The frontier orbitals of 22 isolated and characterized C(60)(CF(3))(n) derivatives, including seven reported here for the first time, have been investigated by electronic spectroscopy (n = 2 [1], 4 [1], 6 [2], 8 [5], 10 [6], 12 [3]; the number of isomers for each composition is shown in square brackets) fluorescence spectroscopy (n = 10 [4]), cyclic voltammetry under air-free conditions (all compounds with n

A detailed analysis of the changes in the electronic structure of CO when a proton or a positive charge approaches the carbon or the oxygen atom is reported using quantum mechanical ab initio calculations and several methods to analyze the theoretical data. The C−O bond is shortened by nearly the same amount in HCO+ and QCO+ compared to free CO, while the nearly identical C−O bond lengths of COH+ and COQ+ are longer than in CO. H+ and Q+ have a strong electrostatic effect upon the atom to which they are bonded, which leads to an increased electronegativity of carbon and oxygen, respectively. Inspection of the charge distribution and the natural localized orbitals shows clearly that the shorter C−O distances of HCO+ and QCO+ and the longer C−O bond lengths of COH+ and COQ+ are due to the changes in the polarization of the bonding orbitals which are caused by the positive charge of H+ or Q+ that are bonded to the molecule. The bonding orbitals of CO are polarized toward the more electronegative oxygen end. A proton or a positive charge at carbon attracts electronic charge from the oxygen atom toward the carbon end, which leads to less polarized σ- and π-bonds and to a more covalent C−O bond. A positive charge or a proton at the oxygen atom has the opposite effect. The calculated curve of the C−O bond length in MCO+ (M = Li, Cu, Ag, Au) as a function of the M+−CO distance shows that the C−O bond becomes shorter in the beginning when the metal cation approaches the carbon atom. There is a turning point at shorter M+−CO distances where the C−O bond becomes longer again. The charge decomposition analysis shows that the position of the turning point is determined by the onset of the metal+ → CO back-donation. A relatively small amount of M+ → CO back-donation is sufficient to lengthen the CO bond. The turning point for the curve of the C−O bond length as a function of the M+−CO distance occurs at a M+−CO value that is shorter than the equilibrium distance for M = Li and Ag, while it is longer for M = Cu and Au. The trends of the bond strengths and M+−CO interactions are explained with the radii and orbital energies of the valence ns and (n − 1)d orbitals of the transition metals.