A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research

Nicotiana benthamiana is a widely used model plant species for the study of fundamental questions in molecular plant-microbe interactions and other areas of plant biology. This popularity derives from its well-characterized susceptibility to diverse pathogens and, especially, its amenability to virus-induced gene silencing and transient protein expression methods. Here, we report the generation of a 63-fold coverage draft genome sequence of N. benthamiana and its availability on the Sol Genomics Network for both BLAST searches and for downloading to local servers. The estimated genome size of N. benthamiana is 3 Gb (gigabases). The current assembly consists of approximately 141,000 scaffolds, spanning 2.6 Gb with 50% of the genome sequence contained within scaffolds >89 kilobases. Of the approximately 16,000 N. benthamiana unigenes available in GenBank, >90% are represented in the assembly. The usefulness of the sequence was demonstrated by the retrieval of N. benthamiana orthologs for 24 immunity-associated genes from other species including Ago2, Ago7, Bak1, Bik1, Crt1, Fls2, Pto, Prf, Rar1, and mitogen-activated protein kinases. The sequence will also be useful for comparative genomics in the Solanaceae family as shown here by the discovery of microsynteny between N. benthamiana and tomato in the region encompassing the Pto and Prf genes

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

SolCyc is the entry portal to pathway/genome databases (PGDBs) for major species of the Solanaceae family hosted at the Sol Genomics Network. Currently, SolCyc comprises six organism-specific PGDBs for tomato, potato, pepper, petunia, tobacco and one Rubiaceae, coffee. The metabolic networks of those PGDBs have been computationally predicted by the pathologic component of the pathway tools software using the manually curated multi-domain database MetaCyc (http://www.metacyc.org/) as reference. SolCyc has been recently extended by taxon-specific databases, i.e. the family-specific SolanaCyc database, containing only curated data pertinent to species of the nightshade family, and NicotianaCyc, a genus-specific database that stores all relevant metabolic data of the Nicotiana genus. Through manual curation of the published literature, new metabolic pathways have been created in those databases, which are complemented by the continuously updated, relevant species-specific pathways from MetaCyc. At present, SolanaCyc comprises 199 pathways and 29 superpathways and NicotianaCyc accounts for 72 pathways and 13 superpathways. Curator-maintained, taxon-specific databases such as SolanaCyc and NicotianaCyc are characterized by an enrichment of data specific to these taxa and free of falsely predicted pathways. Both databases have been used to update recently created Nicotiana-specific databases for Nicotiana tabacum, Nicotiana benthamiana, Nicotiana sylvestris and Nicotiana tomentosiformis by propagating verifiable data into those PGDBs. In addition, in-depth curation of the pathways in N.tabacum has been carried out which resulted in the elimination of 156 pathways from the 569 pathways predicted by pathway tools. Together, in-depth curation of the predicted pathway network and the supplementation with curated data from taxon-specific databases has substantially improved the curation status of the species\u2013specific N.tabacum PGDB. The implementation of this strategy will significantly advance the curation status of all organism-specific databases in SolCyc resulting in the improvement on database accuracy, data analysis and visualization of biochemical networks in those species

From manual curation to visualization of gene families and networks across Solanaceae plant species

High-quality manual annotation methods and practices need to be scaled to the increased rate of genomic data production. Curation based on gene families and gene networks is one approach that can significantly increase both curation efficiency and quality. The Sol Genomics Network (SGN; http://solgenomics.net) is a comparative genomics platform, with genetic, genomic and phenotypic information of the Solanaceae family and its closely related species that incorporates a community-based gene and phenotype curation system. In this article, we describe a manual curation system for gene families aimed at facilitating curation, querying and visualization of gene interaction patterns underlying complex biological processes, including an interface for efficiently capturing information from experiments with large data sets reported in the literature. Well-annotated multigene families are useful for further exploration of genome organization and gene evolution across species. As an example, we illustrate the system with the multigene transcription factor families, WRKY and Small Auxin Up-regulated RNA (SAUR), which both play important roles in responding to abiotic stresses in plants

Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

Background Allopolyploids contain genomes composed of more than two complete sets of chromosomes that originate from at least two species. Allopolyploidy has been suggested as an important evolutionary mechanism that can lead to instant speciation. Arabidopsis suecica is a relatively recent allopolyploid species, suggesting that its natural accessions might be genetically very similar to each other. Nonetheless, subtle phenotypic differences have been described between different geographic accessions of A. suecica grown in a common garden. Results To determine the degree of genomic similarity between different populations of A. suecica, we obtained transcriptomic sequence, quantified SNP variation within the gene space, and analyzed gene expression levels genome-wide from leaf material grown in controlled lab conditions. Despite their origin from the same progenitor species, the two accessions of A. suecica used in our study show genomic and transcriptomic variation. We report significant gene expression differences between the accessions, mostly in genes with stress-related functions. Among the differentially expressed genes, there are a surprising number of homoeologs coordinately regulated between sister accessions. Conclusions Many of these homoeologous genes and other differentially expressed genes affect transpiration and stomatal regulation, suggesting that they might be involved in the establishment of the phenotypic differences between the two accessions

Phase Diagram of a Spin Ladder with Cyclic Four Spin Exchange

We present the phase diagram of the $S=1/2$ Heisenberg model on the two leg ladder with cyclic four spin exchange, determined by a combination of Exact Diagonalization and Density Matrix Renormalization Group techniques. We find six different phases and regimes: the rung singlet phase, a ferromagnetic phase, two symmetry broken phases with staggered dimers and staggered scalar chiralities, and a gapped region with dominant vector chirality or collinear spin correlations. We localize the phase transitions and investigate their nature.Comment: 4 pages, 6 figures, REVTeX 4, published versio

The processing, properties and use of the pyrotechnic mixture-titanium subhydride/potassium perchlorate

Development of this pyrotechnic occurred because of the need for a static insensitive material to meet personnel safety requirements and related system safety issues in nuclear weapon energetic material component designs. Ti subhydride materials are made by the thermal dehydrding of commercial Ti hydride powder to the desired equivalent hydrogen composition in the Ti lattice. These Ti subhydrides, when blended with K perchlorate, meet the static insensitivity requirement of not being initiated from an equivalent human body electrostatic discharge. Individual material and blend qualification requirements provide a reproducible material from lot to lot. These pyrotechnic formulations meet the high reliability requirements (0.9995) for initiation and performance parameters and have the necessary stability and compatibility to meet long lived requirements of more than 25 years. Various experiences and problems are also discussed that have led to a mature technology for Ti subhydride/K perchlorate during its use in energetic material component designs

Time-variability in the Interstellar Boundary Conditions of the Heliosphere: Effect of the Solar Journey on the Galactic Cosmic Ray Flux at Earth

During the solar journey through galactic space, variations in the physical properties of the surrounding interstellar medium (ISM) modify the heliosphere and modulate the flux of galactic cosmic rays (GCR) at the surface of the Earth, with consequences for the terrestrial record of cosmogenic radionuclides. One phenomenon that needs studying is the effect on cosmogenic isotope production of changing anomalous cosmic ray fluxes at Earth due to variable interstellar ionizations. The possible range of interstellar ram pressures and ionization levels in the low density solar environment generate dramatically different possible heliosphere configurations, with a wide range of particle fluxes of interstellar neutrals, their secondary products, and GCRs arriving at Earth. Simple models of the distribution and densities of ISM in the downwind direction give cloud transition timescales that can be directly compared with cosmogenic radionuclide geologic records. Both the interstellar data and cosmogenic radionuclide data are consistent with cloud transitions during the Holocene, with large and assumption-dependent uncertainties. The geomagnetic timeline derived from cosmic ray fluxes at Earth may require adjustment to account for the disappearance of anomalous cosmic rays when the Sun is immersed in ionized gas.Comment: Submitted to Space Sciences Review

Parity violating target asymmetry in electron - proton scattering

We analyze the parity-violating (PV) components of the analyzing power in elastic electron-proton scattering and discuss their sensitivity to the strange quark contributions to the proton weak form factors. We point out that the component of the analyzing power along the momentum transfer is independent of the electric weak form factor and thus compares favorably with the PV beam asymmetry for a determination of the strangeness magnetic moment. We also show that the transverse component could be used for constraining the strangeness radius. Finally, we argue that a measurement of both components could give experimental information on the strangeness axial charge.Comment: 24 pages, Latex, 5 eps figures, submitted to Phys.Rev.