Research Topics
Genomes and GenesSpecies | Ralph DeanSummaryAffiliation: North Carolina State University Country: USA Publications
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Publications
Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzaeYeonyee Oh
North Carolina State University, Center for Integrated Fungal Research, Raleigh, NC 27695 7251, USA
Genome Biol 9:R85. 2008..Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood...
The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzaeMichael R Thon
Department of Plant Pathology and Microbiology, Texas A and M University, College Station, TX 77843, USA
Genome Biol 7:R16. 2006....- Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzaeCristiano C Nunes
Fungal Genomics Laboratory, Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
BMC Genomics 12:288. 2011..Although significant progress has been made towards small RNA discovery and biogenesis in higher eukaryotes and other model organisms, knowledge in simple eukaryotes such as filamentous fungi remains limited... - The evolutionary history of cytochrome P450 genes in four filamentous AscomycetesJixin Deng
Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
BMC Evol Biol 7:30. 2007.... - Alkahest NuclearBLAST : a user-friendly BLAST management and analysis systemStephen E Diener
Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
BMC Bioinformatics 6:147. 2005..However, there are few options available which provide a free and user-friendly solution to the BLAST result storage and data mining needs of biologists... - 'PACLIMS': a component LIM system for high-throughput functional genomic analysisNicole Donofrio
Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC, USA
BMC Bioinformatics 6:94. 2005.... - Fungal biology reaps the benefit of genomicsRalph Dean
Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
Genome Biol 6:336. 2005..A report on the 23rd Fungal Genetics Conference, Pacific Grove, USA, 15-20 March 2005... 
The genome sequence of the rice blast fungus Magnaporthe griseaRalph A Dean
Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina 27695, USA
Nature 434:980-6. 2005..The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation...- MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe griseaStanton L Martin
Fungal Genomics Laboratory, North Carolina State University, 840 Main Campus Drive, Suite 1200, Raleigh, NC 27606, USA
Nucleic Acids Res 30:121-4. 2002..grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm... - BAC end sequences and a physical map reveal transposable element content and clustering patterns in the genome of Magnaporthe griseaMichael R Thon
Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh 27695-7251, USA
Fungal Genet Biol 41:657-66. 2004..This study illustrates the general utility of a physical map and BAC end sequences for the study of genome-wide repetitive DNA content and organization... - Magnaporthe grisea infection triggers RNA variation and antisense transcript expression in riceMalali Gowda
Department of Plant Pathology, Ohio State University, Columbus, OH 43212, USA
Plant Physiol 144:524-33. 2007..These results demonstrate that there is a series of dynamic and complex transcript modifications and changes in the rice transcriptome at the M. grisea early infection stages... - Combining ChIP-chip and expression profiling to model the MoCRZ1 mediated circuit for Ca/calcineurin signaling in the rice blast fungusSoonok Kim
Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
PLoS Pathog 6:e1000909. 2010..We present results from the ChIP-chip and expression analysis along with a refined model of calcium/calcineurin signaling in this important plant pathogen... - Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interactionChatchawan Jantasuriyarat
Department of Plant Pathology, The Ohio State University, Columbus, Ohio 43210, USA
Plant Physiol 138:105-15. 2005..The large cataloged collection of rice ESTs in this study provides a solid foundation for further characterization of the rice defense response and is a useful public genomic resource for rice functional genomics studies... - Insight into Trichoderma reesei's genome content, organization and evolution revealed through BAC library characterizationStephen E Diener
Fungal Genomics Laboratory, North Carolina State University, 840 Main Campus Drive, Suite 1200 Raleigh, NC 27606, USA
Fungal Genet Biol 41:1077-87. 2004..BAC clones were fingerprinted and analyzed using fingerprinted contigs (FPC) software resulting in 334 contigs covering 28 megabases of the genome. The assembly of these FPC contigs was verified by congruence with hybridization results... - Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzaeShaowu Meng
Center for Integrated Fungal Research, North Carolina State University, Raleigh NC 27695, USA
BMC Microbiol 9:S8. 2009..Gene Ontology (GO) annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly... - Novel G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe griseaResham D Kulkarni
Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
Genome Biol 6:R24. 2005..Do fungi contain only this handful or are there more receptors to be discovered? We asked this question using the recently sequenced genome of the fungal plant pathogen Magnaporthe grisea... - The Magnaporthe grisea snodprot1 homolog, MSP1, is required for virulenceJun Seop Jeong
Department of Plant Pathology, Center for Integrated Fungal Research CIFR, North Carolina State University, Raleigh, NC 27695, USA
FEMS Microbiol Lett 273:157-65. 2007..When purified MSP1 protein was applied to wounded leaf tissue, no apparent phytotoxic effects were noted. This is the first report to the authors' knowledge that directly implicates a snodprot1 protein as a virulence factor... - A systematic analysis of T-DNA insertion events in Magnaporthe oryzaeYan Meng
Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
Fungal Genet Biol 44:1050-64. 2007..In addition, we found that the distribution of T-DNA inserts among the M. oryzae chromosomes was not random. The implications of these findings with regard to saturation mutagenesis of the M. oryzae genome are discussed... - The Fusarium wilt resistance locus Fom-2 of melon contains a single resistance gene with complex featuresTarek Joobeur
Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC 27965, USA
Plant J 39:283-97. 2004..The Fom-2 physical region contained retroelement-like sequences and truncated genes, suggesting that this locus is complex... - Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methodsMalali Gowda
Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA
BMC Genomics 7:310. 2006.... - Robust-LongSAGE (RL-SAGE): a substantially improved LongSAGE method for gene discovery and transcriptome analysisMalali Gowda
Department of Plant Pathology, Ohio State University, Columbus, Ohio 43210, USA
Plant Physiol 134:890-7. 2004..5 million tags, within a month. We recently have constructed five libraries from rice (Oryza sativa), one from maize (Zea mays), and one from the rice blast fungus (Magnaporthe grisea)... - An eight-cysteine-containing CFEM domain unique to a group of fungal membrane proteinsResham D Kulkarni
Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
Trends Biochem Sci 28:118-21. 2003..Some CFEM-containing proteins (e.g. Pth11 from Magnaporthe grisea) are proposed to have important roles in fungal pathogenesis... - Common processes in pathogenesis by fungal and oomycete plant pathogens, described with Gene Ontology termsShaowu Meng
Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
BMC Microbiol 9:S7. 2009..This set of standardized GO terms provides a solid base to further compare and contrast the molecular underpinnings of fungal and oomycete pathogenesis... - Fungal gene clustersRalph A Dean
Nat Biotechnol 25:67. 2007 - An integrated physical and genetic map of the rice genomeMingsheng Chen
Clemson University Genomics Institute, 100 Jordan Hall, Clemson, South Carolina 29634-5727, USA
Plant Cell 14:537-45. 2002..Furthermore, the physical map will aid map-based cloning of agronomically important genes and will provide an important tool for the comparative analysis of grass genomes... - Altered patterns of gene duplication and differential gene gain and loss in fungal pathogensAmy J Powell
Department of Computational Systems Biology, Sandia National Laboratories, Albuquerque, NM, USA
BMC Genomics 9:147. 2008..To date, differential gene gain and loss have not been studied at genomic scales in fungal pathogens, despite this phenomenon's known importance in virulence in bacteria and viruses... - Expression of a harpin-encoding gene in rice confers durable nonspecific resistance to Magnaporthe griseaMin Shao
Key Laboratory of Monitoring and Management of Plant Diseases and Pests, Ministry of Agriculture of China, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
Plant Biotechnol J 6:73-81. 2008..These results suggest that harpins may offer new opportunities for generating broad-spectrum disease resistance in other crops... - Transcript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to pathogen (Heterobasidion annosum) invasionAleksandra Adomas
Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, Sweden
Tree Physiol 27:1441-58. 2007.... - Expressed sequence tags from phytophthora sojae reveal genes specific to development and infectionTrudy A Torto Alalibo
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
Mol Plant Microbe Interact 20:781-93. 2007..Sequences identified with putative roles in pathogenesis included avirulence homologs possessing the RxLR motif, elicitins, and hydrolytic enzymes. This large collection of P. sojae ESTs will serve as a valuable public genomic resource... - Cloning, sequencing and functional analysis of Magnaporthe grisea MVP1 gene, a hex-1 homolog encoding a putative 'woronin body' proteinFrederick O Asiegbu
Clemson University Genomics Institute, Clemson, SC, USA
FEMS Microbiol Lett 230:85-90. 2004..The pathological and other phenotypic consequences of gene disruption are discussed... - From genes to genomes: a new paradigm for studying fungal pathogenesis in Magnaporthe oryzaeJin Rong Xu
Department of Botany and Plant Pathology, Purdue University West Lafayette, Indiana 47907, USA
Adv Genet 57:175-218. 2007..The chapter concludes with new prospects in the area of systems biology, such as protein expression profiling, and highlighting remaining crucial information needed to fully appreciate host-pathogen interactions... - Two novel fungal virulence genes specifically expressed in appressoria of the rice blast fungusChaoyang Xue
Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
Plant Cell 14:2107-19. 2002..These two genes may belong to a class of proteins specific for filamentous fungi and function as novel virulence factors in fungal pathogens... - Development of a high throughput transformation system for insertional mutagenesis in Magnaporthe oryzaeMelania F Betts
Department of Plant Sciences, Division of Plant Pathology and Microbiology, University of Arizona, Tucson, AZ 85721 0036, USA
Fungal Genet Biol 44:1035-49. 2007..3% of conidia being transformed. The phenotypic data is accessible via a public database called MGOS and all strains are publicly available. This represents the most comprehensive insertional mutagenesis analysis of a fungal pathogen... - Isolation of a novel antimicrobial peptide gene (Sp-AMP) homologue from Pinus sylvestris (Scots pine) following infection with the root rot fungus Heterobasidion annosumFrederick O Asiegbu
Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, Sweden
FEMS Microbiol Lett 228:27-31. 2003..Southern analyses further confirmed that several copies of the gene are present in the Scots pine genome. The potential significance of Sp-AMP in the H. annosum-conifer pathosystem is discussed... - AFLP analysis of a worldwide collection of Didymella bryoniaeRonald T Kothera
Clemson University, Coastal Research and Education Center, 2865 Savannah Highway, Charleston, South Carolina 29414, USA
Mycol Res 107:297-304. 2003..However, isolates from the northern USA grouped separately from isolates originating from the southern USA... - Cloning of disease-resistance homologues in end sequences of BAC clones linked to Fom-2, a gene conferring resistance to Fusarium wilt in melon (Cucumis melo L.)Yi-Hong Wang
Clemson University Genomics Institute and Department of Plant Pathology and Physiology, Clemson University, SC 29634, USA
Genome 45:473-80. 2002..The sequence information may be useful for identifying NBS-LRR class of R genes in other cucurbits...