The Institute for Genomic Research

Rockville, MD, United States

The Institute for Genomic Research

Rockville, MD, United States
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Wang X.,University of Georgia | Wang X.,Hebei United University | Torres M.J.,University of Georgia | Pierce G.,University of Georgia | And 24 more authors.
BMC Genomics | Year: 2011

Background: Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, Arabidopsis thaliana, provides means to explore their genomic complexity.Results: A genome-wide physical map of a rapid-cycling strain of B. oleracea was constructed by integrating high-information-content fingerprinting (HICF) of Bacterial Artificial Chromosome (BAC) clones with hybridization to sequence-tagged probes. Using 2907 contigs of two or more BACs, we performed several lines of comparative genomic analysis. Interspecific DNA synteny is much better preserved in euchromatin than heterochromatin, showing the qualitative difference in evolution of these respective genomic domains. About 67% of contigs can be aligned to the Arabidopsis genome, with 96.5% corresponding to euchromatic regions, and 3.5% (shown to contain repetitive sequences) to pericentromeric regions. Overgo probe hybridization data showed that contigs aligned to Arabidopsis euchromatin contain ~80% of low-copy-number genes, while genes with high copy number are much more frequently associated with pericentromeric regions. We identified 39 interchromosomal breakpoints during the diversification of B. oleracea and Arabidopsis thaliana, a relatively high level of genomic change since their divergence. Comparison of the B. oleracea physical map with Arabidopsis and other available eudicot genomes showed appreciable 'shadowing' produced by more ancient polyploidies, resulting in a web of relatedness among contigs which increased genomic complexity.Conclusions: A high-resolution genetically-anchored physical map sheds light on Brassica genome organization and advances positional cloning of specific genes, and may help to validate genome sequence assembly and alignment to chromosomes.All the physical mapping data is freely shared at a WebFPC site (http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/; Temporarily password-protected: account: pgml; password: 123qwe123. © 2011 Wang et al; licensee BioMed Central Ltd.


Glasner J.D.,University of Wisconsin - Madison | Yang C.-H.,University of Wisconsin - Milwaukee | Reverchon S.,CNRS Laboratory for Microbiology, Adaptation & Pathogenesis | Hugouvieux-Cotte-Pattat N.,CNRS Laboratory for Microbiology, Adaptation & Pathogenesis | And 44 more authors.
Journal of Bacteriology | Year: 2011

Dickeya dadantii is a plant-pathogenic enterobacterium responsible for the soft rot disease of many plants of economic importance. We present here the sequence of strain 3937, a strain widely used as a model system for research on the molecular biology and pathogenicity of this group of bacteria. © 2011, American Society for Microbiology.


Bogdanove A.J.,Iowa State University | Koebnik R.,CIRAD - Agricultural Research for Development | Lu H.,Iowa State University | Furutani A.,Japan National Institute of Agrobiological Science | And 55 more authors.
Journal of Bacteriology | Year: 2011

Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of Xanthomonas campestris pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology, Arabidopsis thaliana and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete Xanthomonas genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity. © 2011, American Society for Microbiology.


PubMed | The Institute For Genomic Research and University of Warwick
Type: | Journal: Current protocols in pharmacology | Year: 2015

Understanding the physiology, pharmacology, and plasticity associated with synaptic function is a key goal of neuroscience research and is fundamental to identifying the processes involved in the development and manifestation of neurological disease. A diverse range of electrophysiological methodologies are used to study synaptic function. Described in this unit is a technique for recording electrical activity from a single component of the central nervous system that is used to investigate pre- and post-synaptic elements of synaptic function. A strength of this technique is that it can be used on live animals, although the effect of anesthesia must be taken into consideration when interpreting the results. This methodology can be employed not only in nave animals for studying normal physiological synaptic function, but also in a variety of disease models, including transgenic animals, to examine dysfunctional synaptic plasticity associated with neurological pathologies.


Christie G.E.,Virginia Commonwealth University | Matthews A.M.,New York University | King D.G.,Virginia Commonwealth University | Lane K.D.,Virginia Commonwealth University | And 4 more authors.
Virology | Year: 2010

Staphylococcus aureus pathogenicity islands (SaPIs) are mobile elements that are induced by a helper bacteriophage to excise and replicate and to be encapsidated in phage-like particles smaller than those of the helper, leading to high-frequency transfer. SaPI mobilization is helper phage specific; only certain SaPIs can be mobilized by a particular helper phage. Staphylococcal phage 80α can mobilize every SaPI tested thus far, including SaPI1, SaPI2 and SaPIbov1. Phage 80, on the other hand, cannot mobilize SaPI1, and Φ11 mobilizes only SaPIbov1. In order to better understand the relationship between SaPIs and their helper phages, the genomes of phages 80 and 80α were sequenced, compared with other staphylococcal phage genomes, and analyzed for unique features that may be involved in SaPI mobilization. © 2010 Elsevier Inc.


PubMed | The Institute for Genomic Research
Type: | Journal: The Arabidopsis book | Year: 2012

Arabidopsis has been well studied as a model plant for plant pathogen interactions. While a large portion of the literature has been devoted to interactions between Arabidopsis and Pseudomonas and Peronospora species, a small cadre of researchers have been making inroads on the response of Arabidopsis to Xanthomonas. Differential responses of Arabidopsis accessions to isolates of Xanthomonas campestris pv campestris include tolerance, a hypersensitive response, resistance without a hypersensitive response and disease which is characterized by chlorosis and necrosis. Loci that govern the recognition of X. c. campestris have been identified and are the focus of on-going positional cloning efforts. Signaling and other downstream molecules involved in manifestation of resistance to Xanthomonas have been investigated resulting in the identification of many components of the resistance response. Parallel to the characterization of the host response, molecular and genomic efforts focused on the pathogen have the potential to reveal the mechanisms by which this bacterium can invade and colonize host tissues.colony forming units (CFU), Columbia (Col-0), days post inoculation (dpi), hypersensitive response (HR), Landsberg erecta (Ler), pathogenesis-related protein 1 (PR-1), phenylalanine ammonia lyase (PAL), Xanthomonas campestris pv campestris (Xcc).

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