Phylogenetic analysis and molecular evolution of the dormancy associated MADS-box genes from peach

BACKGROUND: Dormancy associated MADS-box (DAM) genes are candidates for the regulation of growth cessation and terminal bud formation in peach. These genes are not expressed in the peach mutant evergrowing, which fails to cease growth and enter dormancy under dormancy-inducing conditions. We analyzed the phylogenetic relationships among and the rates and patterns of molecular evolution within DAM genes in the phylogenetic context of the MADS-box gene family. RESULTS: The peach DAM genes grouped with the SVP/StMADS11 lineage of type II MIKC(C )MADS-box genes. Phylogenetic analyses suggest that the peach SVP/StMADS11-like gene family, which contains significantly more members than annual model plants, expanded through serial tandem gene duplication. We found evidence of strong purifying selection acting to constrain functional divergence among the peach DAM genes and only a single codon, located in the C-terminal region, under significant positive selection. CONCLUSION: Because all DAM genes are expressed in peach and are subjected to strong purifying selection we suggest that the duplicated genes have been maintained by subfunctionalization and/or neofunctionalization. In addition, this pattern of selection suggests that the DAM genes are important for peach growth and development

Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (\u3cem\u3eCastanea mollissima\u3c/em\u3e) and plant reference genomes

Background Chinese chestnut (Castanea mollissima) has emerged as a model species for the Fagaceae family with extensive genomic resources including a physical map, a dense genetic map and quantitative trait loci (QTLs) for chestnut blight resistance. These resources enable comparative genomics analyses relative to model plants. We assessed the degree of conservation between the chestnut genome and other well annotated and assembled plant genomic sequences, focusing on the QTL regions of most interest to the chestnut breeding community. Results The integrated physical and genetic map of Chinese chestnut has been improved to now include 858 shared sequence-based markers. The utility of the integrated map has also been improved through the addition of 42,970 BAC (bacterial artificial chromosome) end sequences spanning over 26 million bases of the estimated 800 Mb chestnut genome. Synteny between chestnut and ten model plant species was conducted on a macro-syntenic scale using sequences from both individual probes and BAC end sequences across the chestnut physical map. Blocks of synteny with chestnut were found in all ten reference species, with the percent of the chestnut physical map that could be aligned ranging from 10 to 39 %. The integrated genetic and physical map was utilized to identify BACs that spanned the three previously identified QTL regions conferring blight resistance. The clones were pooled and sequenced, yielding 396 sequence scaffolds covering 13.9 Mbp. Comparative genomic analysis on a microsytenic scale, using the QTL-associated genomic sequence, identified synteny from chestnut to other plant genomes ranging from 5.4 to 12.9 % of the genome sequences aligning. Conclusions On both the macro- and micro-synteny levels, the peach, grape and poplar genomes were found to be the most structurally conserved with chestnut. Interestingly, these results did not strictly follow the expectation that decreased phylogenetic distance would correspond to increased levels of genome preservation, but rather suggest the additional influence of life-history traits on preservation of synteny. The regions of synteny that were detected provide an important tool for defining and cataloging genes in the QTL regions for advancing chestnut blight resistance research

Underestimated risks of recurrent long-range ash dispersal from northern Pacific Arc volcanoes

Widespread ash dispersal poses a significant natural hazard to society, particularly in relation to disruption to aviation. Assessing the extent of the threat of far-travelled ash clouds on flight paths is substantially hindered by an incomplete volcanic history and an underestimation of the potential reach of distant eruptive centres. The risk of extensive ash clouds to aviation is thus poorly quantified. New evidence is presented of explosive Late Pleistocene eruptions in the Pacific Arc, currently undocumented in the proximal geological record, which dispersed ash up to 8000?km from source. Twelve microscopic ash deposits or cryptotephra, invisible to the naked eye, discovered within Greenland ice-cores, and ranging in age between 11.1 and 83.7 ka b2k, are compositionally matched to northern Pacific Arc sources including Japan, Kamchatka, Cascades and Alaska. Only two cryptotephra deposits are correlated to known high-magnitude eruptions (Towada-H, Japan, ca 15 ka BP and Mount St Helens Set M, ca 28 ka BP). For the remaining 10 deposits, there is no evidence of age- and compositionally-equivalent eruptive events in regional volcanic stratigraphies. This highlights the inherent problem of under-reporting eruptions and the dangers of underestimating the long-term risk of widespread ash dispersal for trans-Pacific and trans-Atlantic flight route

The development and characterisation of a bacterial artificial chromosome library for Fragaria vesca

<p>Abstract</p> <p>Background</p> <p>The cultivated strawberry <it>Fragaria ×ananassa </it>is one of the most economically-important soft-fruit species. Few structural genomic resources have been reported for <it>Fragaria </it>and there exists an urgent need for the development of physical mapping resources for the genus. The first stage in the development of a physical map for <it>Fragaria </it>is the construction and characterisation of a high molecular weight bacterial artificial chromosome (BAC) library.</p> <p>Methods</p> <p>A BAC library, consisting of 18,432 clones was constructed from <it>Fragaria vesca </it>f. <it>semperflorens </it>accession 'Ali Baba'. BAC DNA from individual library clones was pooled to create a PCR-based screening assay for the library, whereby individual clones could be identified with just 34 PCR reactions. These pools were used to screen the BAC library and anchor individual clones to the diploid <it>Fragaria </it>reference map (FV×FN).</p> <p>Findings</p> <p>Clones from the BAC library developed contained an average insert size of 85 kb, representing over seven genome equivalents. The pools and superpools developed were used to identify a set of BAC clones containing 70 molecular markers previously mapped to the diploid <it>Fragaria </it>FV×FN reference map. The number of positive colonies identified for each marker suggests the library represents between 4× and 10× coverage of the diploid <it>Fragaria </it>genome, which is in accordance with the estimate of library coverage based on average insert size.</p> <p>Conclusion</p> <p>This BAC library will be used for the construction of a physical map for <it>F. vesca </it>and the superpools will permit physical anchoring of molecular markers using PCR.</p

Scaling in Small-World Resistor Networks

We study the effective resistance of small-world resistor networks. Utilizing recent analytic results for the propagator of the Edwards-Wilkinson process on small-world networks, we obtain the asymptotic behavior of the disorder-averaged two-point resistance in the large system-size limit. We find that the small-world structure suppresses large network resistances: both the average resistance and its standard deviation approaches a finite value in the large system-size limit for any non-zero density of random links. We also consider a scenario where the link conductance decays as a power of the length of the random links, $l^{-\alpha}$. In this case we find that the average effective system resistance diverges for any non-zero value of $\alpha$.Comment: 15 pages, 6 figure

Self-organized criticality and synchronization in a lattice model of integrate-and-fire oscillators

We introduce two coupled map lattice models with nonconservative interactions and a continuous nonlinear driving. Depending on both the degree of conservation and the convexity of the driving we find different behaviors, ranging from self-organized criticality, in the sense that the distribution of events (avalanches) obeys a power law, to a macroscopic synchronization of the population of oscillators, with avalanches of the size of the system.Comment: 4 pages, Revtex 3.0, 3 PostScript figures available upon request to [email protected]

Z boson production in Pb+Pb collisions at √Snn = 5.02 TeV measured by the ATLAS experiment

The production yield of Z bosons is measured in the electron and muon decay channels in Pb+Pb collisions at √S = 5.02 TeV with the ATLAS detector. Data from the 2015 LHC run corresponding to an integrated luminosity of 0.49 nb are used for the analysis. The Z boson yield, normalised by the total number of minimum-bias events and the mean nuclear thickness function, is measured as a function of dilepton rapidity and event centrality. The measurements in Pb+Pb collisions are compared with similar measurements made in proton-proton collisions at the same centre-of-mass energy. The nuclear modification factor is found to be consistent with unity for all centrality intervals. The results are compared with theoretical predictions obtained at next-to-leading order using nucleon and nuclear parton distribution functions. The normalised Z boson yields in Pb+Pb collisions lie 1-3σ above the predictions. The nuclear modification factor measured as a function of rapidity agrees with unity and is consistent with a next-to-leading-order QCD calculation including the isospin effect. nn -

Measurement of J/ψ production in association with a W ± boson with pp data at 8 TeV

A measurement of the production of a prompt J/ψ meson in association with a W± boson with W± → μν and J/ψ → μ+μ− is presented for J/ψ transverse momenta in the range 8.5–150 GeV and rapidity |yJ/ψ| &lt; 2.1 using ATLAS data recorded in 2012 at the LHC. The data were taken at a proton-proton centre-of-mass energy of s = 8 TeV and correspond to an integrated luminosity of 20.3 fb−1. The ratio of the prompt J/ψ plus W± cross-section to the inclusive W± cross-section is presented as a differential measurement as a function of J/ψ transverse momenta and compared with theoretical predictions using different double-parton-scattering cross-sections. [Figure not available: see fulltext.]