Search

Your search keyword '"David DeCaprio"' showing total 10 results
Start Over Author "David DeCaprio" Topic genome
10 results on '"David DeCaprio"'

1. Genome sequence of Aedes aegypti, a major arbovirus vector

Author

Sergio Verjovski-Almeida, James E. Galagan, Ryan C. Kennedy, Zhiyong Xi, Jason R. Miller, Eric Eisenstadt, Kyanne R. Reidenbach, Robert V. Bruggner, Yu-Hui Rogers, Hadi Quesneville, Doreen Werner, Owen White, Alexander S. Raikhel, Mario Stanke, J. Spencer Johnston, Diane D. Lovin, Evgenia V. Kriventseva, Ian T. Paulsen, Kathryn S. Campbell, Norman H. Lee, Ewan Birney, Karyn Megy, Hean Koo, David Kulp, Shelby L. Bidwell, Jingsong Zhu, Philip Montgomery, Paolo Amedeo, Yongmei Zhao, Chinnappa D. Kodira, Javier Costas, Michael C. Schatz, Steven P. Sinkins, Claire M. Fraser-Liggett, Martin Shumway, Kurt LaButti, Akio Mori, Brendan J. Loftus, Manfred Grabherr, Eric O. Stinson, Frank H. Collins, Zhijian Jake Tu, Monique R. Coy, Matt Crawford, Janice P. Vanzee, William M. Gelbart, Joshua Orvis, Peter Arensburger, Chunhong Mao, Evgeny M. Zdobnov, Saul A. Kravitz, Suely Lopes Gomes, David DeCaprio, David G. Hogenkamp, Daniel Lawson, Dennis L. Knudson, David W. Severson, George Dimopoulos, Marcelo B. Soares, Sinéad B. O'Leary, Peter W. Atkinson, David M. Jaffe, Becky deBruyn, Martin Hammond, Ana L. T. O. Nascimento, Jim Biedler, Stefan Wyder, Jose M. C. Tubio, Bruce W. Birren, Catherine A. Hill, Chad Nusbaum, Eduardo Lee, Song Li, Susan E. Brown, Jennifer R. Wortman, James R. Hogan, Hamza El-Dorry, Qi Zhao, Linda Hannick, Carlos Frederico Martins Menck, Vishvanath Nene, Jonathan Crabtree, Steven L. Salzberg, Michael H. Holmes, Maria de Fatima Bonaldo, Quinghu Ren, Mihaela Pertea, Charles Roth, Evan Mauceli, Karin Eiglmeier, Horacio Naveira, Brian J. Haas, Qiandong Zeng, Neil F. Lobo, Jennifer R. Schneider, The Institute for Genomic Research, The Institute for Genomic Research, Rockville, European Bioinformatics Institute [Hinxton] ( EMBL-EBI ), European Molecular Biology Laboratory [Hinxton], Broad Institute of MIT and Harvard ( BROAD INSTITUTE ), Broad Institute of MIT and Harvard, Virginia Polytechnic Institute and State University [Blacksburg], University College Dublin [Dublin] ( UCD ), Bloomberg School of Public Health, Johns Hopkins University ( JHU ) -Bloomberg School of Public Health, University of Geneva Medical School, Swiss Institute of Bioinformatics-University of Geneva Medical School, University of Notre Dame ( UND ), Harvard University [Cambridge], College of Agricultural Sciences Colorado State University, Colorado State University [Fort Collins] ( CSU ) -College of Agricultural Sciences, Northwestern University [Evanston], University of California [Riverside] ( UCR ), Department of Atmospheric, Oceanic and Planetary Physics [Oxford] ( AOPP ), University of Oxford [Oxford], Purdue University [West Lafayette], Centro Nacional de Genotipado Fundación Pública Galega de Medicina Xenómica Hospital Clínico Universitario de Santiago, Centro Nacional de Genotipado-Fundación Pública Galega de Medicina Xenómica-Hospital Clínico Universitario de Santiago, Institut Pasteur [Paris], Universidade de Sao Paulo Instituto de Quimica, Universidade de São Paulo ( USP ) -Instituto de Quimica, Texas A&M University [College Station], Joint Technology Center, University of Massachusetts [Amherst] ( UMass Amherst ), Universidade de Sao Paulo, Institute of Biomedical Sciences, Universidade de São Paulo ( USP ) -Institute of Biomedical Sciences, Instituto Butantan [São Paulo], Universidade da Coruña, University of Maryland [College Park], Institut Jacques Monod ( IJM ), Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), University of California [Santa Cruz] ( UCSC ), Complexo Hospitalario Universitario de Santiago, Universität Göttingen, Georg-August-Universität Göttingen, George Washington University Medical Center, George Washington University ( GW ), The Institute for Genomic Research (TIGR), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], University College Dublin [Dublin] (UCD), Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL)-Université de Lausanne (UNIL)-University of Geneva Medical School, University of Notre Dame [Indiana] (UND), Colorado State University [Fort Collins] (CSU)-College of Agricultural Sciences, University of California [Riverside] (UCR), University of California, Department of Atmospheric, Oceanic and Planetary Physics [Oxford] (AOPP), Universidade de São Paulo (USP)-Instituto de Quimica, University of Massachusetts [Amherst] (UMass Amherst), University of Massachusetts System (UMASS), Universidade de São Paulo (USP)-Institute of Biomedical Sciences (ICB/USP), Universidade de São Paulo (USP), University of Maryland System, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), University of California [Santa Cruz] (UCSC), Georg-August-University [Göttingen], The George Washington University (GW), George Washington University (GW), Université de Lausanne = University of Lausanne (UNIL)-Université de Lausanne = University of Lausanne (UNIL)-University of Geneva Medical School, Harvard University, University of California [Riverside] (UC Riverside), University of California (UC), University of Oxford, Institut Pasteur [Paris] (IP), Universidade de São Paulo = University of São Paulo (USP)-Instituto de Quimica, Universidade de São Paulo = University of São Paulo (USP)-Institute of Biomedical Sciences (ICB/USP), Universidade de São Paulo = University of São Paulo (USP), University of California [Santa Cruz] (UC Santa Cruz), Georg-August-University = Georg-August-Universität Göttingen, Zdobnov, Evgeny, and Wyder, Stefan

Subjects
0106 biological sciences, Male, Transcription, Genetic, Genome, Insect, transposons, receptors, Genes, Insect, Aedes/ genetics/metabolism, MESH: Genes, Insect, Yellow Fever/prevention & control/transmission, MESH: Base Sequence, 01 natural sciences, Dengue/prevention & control/transmission, MESH: Protein Structure, Tertiary, MESH: Arboviruses, MESH : Insect Vectors, MESH: Insect Proteins, MESH : Anopheles gambiae, MESH: Animals, MESH : Arboviruses, insects, MESH: Yellow Fever, superfamily, ddc:616, 0303 health sciences, Anopheles, MESH : Genes, Insect, 3. Good health, yellow-fever mosquito, anopheles-gambiae, drosophila-melanogaster, expression, evolution, organization, Drosophila melanogaster, MESH: DNA Transposable Elements, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Multigene Family, Public Health, MESH : Protein Structure, Tertiary, MESH: Sex Characteristics, Molecular Sequence Data, MESH : Multigene Family, MESH: Sex Determination (Genetics), MESH : Sex Determination (Genetics), Arbovirus, Article, 03 medical and health sciences, Species Specificity, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Anopheles gambiae, Yellow Fever, MESH: Species Specificity, Humans, MESH: Humans, MESH: Molecular Sequence Data, fungi, MESH : Humans, MESH : Sex Characteristics, Membrane Transport Proteins, Sex Determination Processes, medicine.disease, Insect Vectors, Protein Structure, Tertiary, Sex Determination (Genetics), MESH: Multigene Family, MESH: Female, MESH : Sequence Analysis, DNA, MESH: Sequence Analysis, DNA, Drosophila melanogaster/genetics, MESH : Molecular Sequence Data, Odorant binding, Insect Proteins/genetics, Anopheles gambiae, MESH: Dengue, Genome, MESH: Membrane Transport Proteins, Dengue, MESH : Membrane Transport Proteins, Aedes, Insect Vectors/ genetics/metabolism, MESH : Drosophila melanogaster, MESH : Female, Membrane Transport Proteins/genetics, Genetics, MESH : Insect Proteins, Sex Characteristics, Multidisciplinary, MESH: Synteny, MESH: Aedes, MESH : Genome, Insect, MESH : DNA Transposable Elements, Insect Proteins, Female, Orthologous Gene, MESH : Male, MESH : Dengue, Aedes aegypti, MESH: Insect Vectors, Biology, 010603 evolutionary biology, Synteny, MESH: Drosophila melanogaster, Protein Structure, Tertiary/genetics, MESH : Yellow Fever, parasitic diseases, medicine, MESH : Species Specificity, Animals, 030304 developmental biology, MESH : Aedes, Base Sequence, MESH: Genome, Insect, MESH: Transcription, Genetic, MESH : Synteny, MESH : Transcription, Genetic, Sequence Analysis, DNA, biology.organism_classification, MESH: Male, DNA Transposable Elements, MESH : Base Sequence, MESH : Animals, Arboviruses, Anopheles gambiae/genetics/metabolism
Abstract

We present a draft sequence of the genome of Aedes aegypti , the primary vector for yellow fever and dengue fever, which at ∼1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae . Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of ∼4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster . Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of ∼2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.

Published
2016
Full Text
View/download PDF

2. A genome-wide map of diversity in Plasmodium falciparum

Author

Danny A. Milner, David DeCaprio, Daniel E. Neafsey, Manoj T. Duraisingh, James E. Galagan, S. Mboup, Eric S. Lander, Nicole Stange-Thomann, Ousmane Sarr, Evan Mauceli, Amanda K. Lukens, Sante Gnerre, Stephen F. Schaffner, Alan Derr, David B. Jaffe, Roger C. Wiegand, Dyann F. Wirth, Daouda Ndiaye, Joanne Zainoun, Pardis C. Sabeti, Bruce W. Birren, Liuda Ziaugra, Daniel L. Hartl, Robert C. Onofrio, Sarah K. Volkman, Skye G. Waggoner, Omar Ndir, and Johanna P. Daily

Subjects
Genetics, Linkage disequilibrium, Genetic diversity, Genetic variation, Population genetics, Single-nucleotide polymorphism, Plasmodium falciparum, Biology, biology.organism_classification, Genotyping, Genome
Abstract

Genetic variation allows the malaria parasite Plasmodium falciparum to overcome chemotherapeutic agents, vaccines and vector control strategies and remain a leading cause of global morbidity and mortality. Here we describe an initial survey of genetic variation across the P. falciparum genome. We performed extensive sequencing of 16 geographically diverse parasites and identified 46,937 SNPs, demonstrating rich diversity among P. falciparum parasites (pi = 1.16 x 10(-3)) and strong correlation with gene function. We identified multiple regions with signatures of selective sweeps in drug-resistant parasites, including a previously unidentified 160-kb region with extremely low polymorphism in pyrimethamine-resistant parasites. We further characterized 54 worldwide isolates by genotyping SNPs across 20 genomic regions. These data begin to define population structure among African, Asian and American groups and illustrate the degree of linkage disequilibrium, which extends over relatively short distances in African parasites but over longer distances in Asian parasites. We provide an initial map of genetic diversity in P. falciparum and demonstrate its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite.

Published
2006
Full Text
View/download PDF

3. The Complete Genome and Proteome of Mycoplasma mobile

Author

Howard C. Berg, Nicole Stange-Thomann, Chinnappa D. Kodira, Robert Nicol, Jonathan Butler, John E. Major, George M. Church, Jacob D. Jaffe, Cherylyn Smith, Jane E. Wilkinson, Nabil Hafez, Sheila Fisher, Shunguang Wang, Sarah E. Calvo, Tim Elkins, Bruce W. Birren, Chad Nusbaum, David DeCaprio, and Michael Fitzgerald

Subjects
Genetics, Genome evolution, Proteome, Gliding motility, Molecular Sequence Data, Computational Biology, Articles, Mycoplasma, Genome project, Biology, Physical Chromosome Mapping, medicine.disease_cause, Genome, Phylogenetics, Horizontal gene transfer, medicine, Amino Acid Sequence, Genome, Bacterial, Phylogeny, Genetics (clinical)
Abstract

Although often considered “minimal” organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete genomic sequence and proteogenomic map for the piscine mycoplasma Mycoplasma mobile, noted for its robust gliding motility. For the first time, proteomic data are used in the primary annotation of a new genome, providing validation of expression for many of the predicted proteins. Several novel features were discovered including a long repeating unit of DNA of ∼2435 bp present in five complete copies that are shown to code for nearly identical yet uniquely expressed proteins. M. mobile has among the lowest DNA GC contents (24.9%) and most reduced set of tRNAs of any organism yet reported (28). Numerous instances of tandem duplication as well as lateral gene transfer are evident in the genome. The multiple available complete genome sequences for other motile and immotile mycoplasmas enabled us to use comparative genomic and phylogenetic methods to suggest several candidate genes that might be involved in motility. The results of these analyses leave open the possibility that gliding motility might have arisen independently more than once in the mycoplasma lineage.

Published
2004
Full Text
View/download PDF

4. The fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization

Author

David R. Nelson, Hans-Werner Mewes, H. Corby Kistler, Weihong Qi, Kerry O'Donnell, John C. Kennell, Scott E. Baker, Liane R. Gale, Igor V. Tetko, Jon K. Magnuson, Gary J. Muehlbauer, Martin Münsterkötter, Martijn Rep, Karen Hilburn, Jiqiang Yao, B. Gillian Turgeon, Thérèse Ouellet, Hadi Quesneville, Li-Jun Ma, Todd J. Ward, Linda J. Harris, Gerhard Adam, Kim E. Hammond-Kosack, Sarah E. Calvo, Scott Kroken, M. Isabel G. Roncero, Kye Yong Seong, Jin-Rong Xu, Gertrud Mannhaupt, Yueh-Long Chang, Antonio Di Pietro, Ulrich Güldener, Christina A. Cuomo, Evan Mauceli, Rudolf Mitterbauer, John F. Antoniw, Rubella S. Goswami, David DeCaprio, Martin Urban, Cees Waalwijk, Jonathan D. Walton, Sante Gnerre, Frances Trail, Thomas K. Baldwin, Bruce W. Birren, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Purdue University [West Lafayette], Michigan State University [East Lansing], Michigan State University System, Cornell University [New York], Universidad de Córdoba [Cordoba], Pacific Northwest National Laboratory (PNNL), University of Amsterdam [Amsterdam] (UvA), Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Rothamsted Research, University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Agriculture and Agri-Food [Ottawa] (AAFC), U.S. Department of Agriculture - Agricultural Research Service - Cereal Disease Laboratory (USDA), USDA-ARS : Agricultural Research Service, Saint Louis University (SLU), University of Arizona, University of Tennessee Memphis, The University of Tennessee Health Science Center [Memphis] (UTHSC), USDA ARS, National Center for Agricultural Utilization Research (USDA ARS,), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institute of Bioorganic Chemistry and Photochemistry, National Ukrainian Academy of Sciences, Institute Bioorganic Chemistry an Photochemistry, Plant Research International (PRI), Wageningen University and Research [Wageningen] (WUR), Molecular Plant Pathology (SILS, FNWI), Technische Universität München [München] (TUM), Cornell University, University of Minnesota [Twin Cities], and Wageningen University and Research Centre [Wageningen] (WUR)

Subjects
localized polymorphism, MESH: Sequence Analysis, DNA, neurospora, Sequence analysis, Molecular Sequence Data, Single-nucleotide polymorphism, Genomics, Gene mutation, Biology, dna, medicine.disease_cause, Genome, Polymorphism, Single Nucleotide, Evolution, Molecular, 03 medical and health sciences, MESH: Plant Diseases, Fusarium, MESH: Polymorphism, Genetic, medicine, Point Mutation, DNA, Fungal, Gene, MESH: Evolution, Molecular, 030304 developmental biology, Plant Diseases, MESH: Point Mutation, Genetics, 0303 health sciences, Mutation, MESH: Fusarium, Multidisciplinary, Polymorphism, Genetic, MESH: Molecular Sequence Data, Biointeracties and Plant Health, 030306 microbiology, Point mutation, MESH: Polymorphism, Single Nucleotide, food and beverages, Hordeum, Sequence Analysis, DNA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: DNA, Fungal, MESH: Hordeum, MESH: Genome, Fungal, Fusarium graminearum genome, PRI Biointeractions en Plantgezondheid, Genome, Fungal, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum , a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.

Published
2007
Full Text
View/download PDF

5. A High-Density Single Nucleotide Polymorphism Map for Neurospora crassa

Author

Jennifer J. Loros, David DeCaprio, Daniel J. Park, James E. Galagan, Matthew S. Sachs, Matthew R. Henn, Jay C. Dunlap, Mi Shi, William J. Belden, Randy Lambreghts, Bruce W. Birren, and Meray Baştürkmen

Subjects
Genetics, Expressed Sequence Tags, Genetic Markers, Recombination, Genetic, Expressed sequence tag, biology, Neurospora crassa, Genes, Fungal, Bulked segregant analysis, Chromosome Mapping, Single-nucleotide polymorphism, Investigations, biology.organism_classification, Genome, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Single Nucleotide Polymorphism Map, Species Specificity, Genetic marker, Cleaved amplified polymorphic sequence, Mutation, DNA, Fungal, Databases, Nucleic Acid
Abstract

We report the discovery and validation of a set of single nucleotide polymorphisms (SNPs) between the reference Neurospora crassa strain Oak Ridge and the Mauriceville strain (FGSC 2555), of sufficient density to allow fine mapping of most loci. Sequencing of Mauriceville cDNAs and alignment to the completed genomic sequence of the Oak Ridge strain identified 19,087 putative SNPs. Of these, a subset was validated by cleaved amplified polymorphic sequence (CAPS), a simple and robust PCR-based assay that reliably distinguishes between SNP alleles. Experimental confirmation resulted in the development of 250 CAPS markers distributed evenly over the genome. To demonstrate the applicability of this map, we used bulked segregant analysis followed by interval mapping to locate the csp-1 mutation to a narrow region on LGI. Subsequently, we refined mapping resolution to 74 kbp by developing additional markers, resequenced the candidate gene, NCU02713.3, in the mutant background, and phenocopied the mutation by gene replacement in the WT strain. Together, these techniques demonstrate a generally applicable and straightforward approach for the isolation of novel genes from existing mutants. Data on both putative and validated SNPs are deposited in a customized public database at the Broad Institute, which encourages augmentation by community users.

Published
2009

6. TB database: an integrated platform for tuberculosis research

Author

Maria Mao, Michael Nitzberg, Brian Weiner, Robert Riley, James E. Galagan, Marcel Gellesch, David DeCaprio, Reinhard Engels, Phillip Montgomery, Dennis Jen, Lisa Larson, Jeremy Hubble, Peter Sisk, Michael Koehrsen, Heng Jin, Jared White, T. B. K. Reddy, Catherine A. Ball, Farrell Wymore, Gary K. Schoolnik, Gavin Sherlock, Christian Stolte, and Zachariah K. Zachariah

Subjects
Tuberculosis, Biomedical Research, Gene Expression, Genomics, Biology, computer.software_genre, Genome, Mycobacterium tuberculosis, Tuberculosis diagnosis, Databases, Genetic, Genetics, medicine, Computer Graphics, Humans, Whole genome sequencing, Comparative genomics, Database, Genome project, Articles, medicine.disease, biology.organism_classification, Systems Integration, computer, Genome, Bacterial
Abstract

The effective control of tuberculosis (TB) has been thwarted by the need for prolonged, complex and potentially toxic drug regimens, by reliance on an inefficient vaccine and by the absence of biomarkers of clinical status. The promise of the genomics era for TB control is substantial, but has been hindered by the lack of a central repository that collects and integrates genomic and experimental data about this organism in a way that can be readily accessed and analyzed. The Tuberculosis Database (TBDB) is an integrated database providing access to TB genomic data and resources, relevant to the discovery and development of TB drugs, vaccines and biomarkers. The current release of TBDB houses genome sequence data and annotations for 28 different Mycobacterium tuberculosis strains and related bacteria. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives. TBDB currently hosts data for nearly 1500 public tuberculosis microarrays and 260 arrays for Streptomyces. In addition, TBDB provides access to a suite of comparative genomics and microarray analysis software. By bringing together M. tuberculosis genome annotation and gene-expression data with a suite of analysis tools, TBDB (http://www.tbdb.org/) provides a unique discovery platform for TB research.

Published
2008

7. Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project

Author

Mi Shi, Michael Plamann, Matthew D. Pearson, Michael Koerhsen, Jay C. Dunlap, Christopher M. Crew, James E. Galagan, Hildur V. Colot, Takao Kasuga, Jeffrey P. Townsend, Kevin McCluskey, Lisa Larson, Jennifer J. Loros, Richard L. Weiss, Randy Lambreghts, Susan Curilla, Junhuan Xu, Matthew Crawford, Liubov Litvinkova, Lorena Altamirano, David DeCaprio, Bruce W. Birren, Patrick D. Collopy, Gyungsoon Park, Chaoguang Tian, Meray Baştürkmen, Mary Anne Nelson, Carol S. Ringelberg, Phil Montgomery, Matthew S. Sachs, Matthew R. Henn, Heather M. Hood, Katherine A. Borkovich, Gloria E. Turner, and N. Louise Glass

Subjects
Positional cloning, Genomics, Computational biology, Biology, Genome, Neurospora, Polymorphism, Single Nucleotide, Article, Neurospora crassa, DNA, Fungal, Gene Library, Oligonucleotide Array Sequence Analysis, Genetics, Base Sequence, Gene Expression Profiling, fungi, Fungal genetics, Chromosome Mapping, biology.organism_classification, Phenotype, Genetic Techniques, Mutation, DNA microarray, Genome, Fungal, Functional genomics, Gene Deletion
Abstract

A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to acccomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of nonyeast fungi. Building from the completely sequenced 43-Mb Neurospora genome, Project 1 is pursuing the systematic disruption of genes through targeted gene replacements, phenotypic analysis of mutant strains, and their distribution to the scientific community at large. Project 2, through a primary focus in Annotation and Bioinformatics, has developed a platform for electronically capturing community feedback and data about the existing annotation, while building and maintaining a database to capture and display information about phenotypes. Oligonucleotide-based microarrays created in Project 3 are being used to collect baseline expression data for the nearly 11,000 distinguishable transcripts in Neurospora under various conditions of growth and development, and eventually to begin to analyze the global effects of loss of novel genes in strains created by Project 1. cDNA libraries generated in Project 4 document the overall complexity of expressed sequences in Neurospora, including alternative splicing alternative promoters and antisense transcripts. In addition, these studies have driven the assembly of an SNP map presently populated by nearly 300 markers that will greatly accelerate the positional cloning of genes.

Published
2007

8. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

Author

Claire M. Wade, Matt J. Cahill, Eric C.H. Ho, Plinio Guzmán, Bruce W. Birren, David DeCaprio, Li-Jun Ma, Gabi Friedrich, Jan Schirawski, Sarah Young, Gero Steinberg, Gertrud Mannhaupt, Heine J. Deelstra, Steven J. Klosterman, Patricia Sánchez-Alonso, Thomas Brefort, Karen M. Snetselaar, Candace Swimmer, Han A. B. Wösten, Christoph W. Basse, Jose Ruiz-Herrera, Dirk Haase, Jonathan Butler, Regine Kahmann, Michael P. McCann, Hans-Werner Mewes, Juan Manuel González-Prieto, Feng Chen, Martin Münsterkötter, Barry J. Saville, Chad Nusbaum, Evan Mauceli, Kylie J. Boyce, Jason E. Stajich, Miroslav Vranes, Scott E. Gold, Olaf Müller, Michael H. Perlin, John C. Kennell, Björn Sandrock, Volker Vincon, James W. Kronstad, Valentina Vysotskaia, Oliver Ladendorf, Michael Bölker, Andreas Gnirke, Peter Schreier, José Pérez-Martín, Matthias Oesterheld, Lazaro Molina, Isolde Häuser-Hahn, David B. Jaffe, Michael Feldbrügge, Shaowu Meng, Martin Vaupel, José I. Ibeas, Jörg Kämper, Darren Mark Platt, Cristina G. Reynaga-Peña, Jonathan Margolis, Jana Klose, Rafael Sentandreu, Karin Münch, Edda Koopmann, Ulrich Güldener, Mark L. Farman, Doris Greilinger, Uta Fuchs, Hartmut Voss, Flora Banuett, Lucila Ortiz-Castellanos, Thomas Schlüter, Artemio Mendoza-Mendoza, Mario Scherer, William K. Holloman, Weixi Li, Ronald P. de Vries, Sarah E. Calvo, Nicole Rössel, and James E. Galagan

Subjects
Corn smut, Genetics, Multidisciplinary, biology, Virulence, Ustilago, Gene Expression Profiling, Genes, Fungal, Fungal genetics, Genomics, biology.organism_classification, Genome, Zea mays, Fungal Proteins, Gene Expression Regulation, Fungal, Multigene Family, Gene family, Genome, Fungal, Gene, Pathogen
Abstract

Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence strategies to kill its host. U. maydis belongs to the group of biotrophic parasites (the smuts) that depend on living tissue for proliferation and development. Here we report the genome sequence for a member of this economically important group of biotrophic fungi. The 20.5-million-base U. maydis genome assembly contains 6,902 predicted protein-encoding genes and lacks pathogenicity signatures found in the genomes of aggressive pathogenic fungi, for example a battery of cell-wall-degrading enzymes. However, we detected unexpected genomic features responsible for the pathogenicity of this organism. Specifically, we found 12 clusters of genes encoding small secreted proteins with unknown function. A significant fraction of these genes exists in small gene families. Expression analysis showed that most of the genes contained in these clusters are regulated together and induced in infected tissue. Deletion of individual clusters altered the virulence of U. maydis in five cases, ranging from a complete lack of symptoms to hypervirulence. Despite years of research into the mechanism of pathogenicity in U. maydis, no 'true' virulence factors had been previously identified. Thus, the discovery of the secreted protein gene clusters and the functional demonstration of their decisive role in the infection process illuminate previously unknown mechanisms of pathogenicity operating in biotrophic fungi. Genomic analysis is, similarly, likely to open up new avenues for the discovery of virulence determinants in other pathogens.

Published
2006

9. Genome sequence, comparative analysis and haplotype structure of the domestic dog

Author

Tsering Wangchuk, Mayank Kumar, Sharon Stavropoulos, James Cuff, Mostafa Benamara, David DeCaprio, Birhane Hagos, Nathaniel Novod, Tashi Lokyitsang, Nyima Norbu, Jennifer Baldwin, Sabrina M. Stone, Catherine Stone, Geneva Young, Osebhajajeme Egbiremolen, Dawa Thoulutsang, Tanya Mihova, Lisa Kim, Julie Sahalie, Jan Macdonald, Amr Abouelleil, Toby Bloom, Yama Cheshatsang, Carolyne Bardeleben, Qing Yu, Berta Blitshteyn, Tuyen T. Nguyen, Tarjei S. Mikkelsen, Edward Grandbois, Claire M. Wade, John E. Major, Filip Rege, Cindy Nguyen, Andrew Barry, Tracey Honan, Pablo Alvarez, Andy Vo, Manuel Garber, Cristyn Kells, Rachel Mittelman, Lucien Oyono, Norbu Dhargay, Sean M. Sykes, Diallo Ferguson, Tyler Aldredge, Tenchoe Nyima, Todd Sparrow, Daniel S. Hagopian, Christophe Hitte, Andreas Heger, Jane E. Wilkinson, Verneda Ray, Peter Rogov, Ewen F. Kirkness, Jill Falk, Robert Nicol, Christopher Patti, Danielle Perrin, Ted Sharpe, Douglas Smith, Peter Olandt, Matthew Breen, Ali Aslam, Cherylyn Smith, Tara Biagi, Diane Gage, Jean L. Chang, Karen Hughes Miller, Valentine Mlenga, Andrea Horn, Jessie Sloan, Claire M. Healy, Adam Wilson, Ngawang Sherpa, Riza M. Daza, David B. Jaffe, Leonid Boguslavskiy, Jody Camarata, Peter Kisner, William H. Lee, Kunsang Dorjee, M. Husby, Sante Gnerre, Kunsang Gyaltsen, Asha Kamat, Jonathan Butler, Terrance Shea, Alicia Franke, Patrick Cooke, Rayale Rameau, Andrew Zimmer, Gary Gearin, Nabil Hafez, Kerri Topham, Kebede Maru, Chris P. Ponting, Jerome Naylor, Yama Thoulutsang, Keith O'Neill, Jinlei Liu, Manolis Kellis, Claude Bonnet, Claudel Antoine, Passang Dorje, Adal Abebe, Tsamla Tsamla, Michael Kleber, Michael Weiand, Audra Goyette, Rachael Thomas, Lisa Zembek, Atanas Mihalev, Daniel Bessette, Helen Vassiliev, Pasang Bachantsang, Adam Navidi, Kathleen Dooley, Caleb Webber, Pierre Tchuinga, Tashi Bayul, Michael Kamal, Heidi G. Parker, Ben Kanga, Kimberly Dooley, Nadia Calixte, Mostafa Ait-zahra, Niall J. Lennon, Ira Topping, Eric S. Lander, Pieter J. deJong, Nicole R. Allen, Peter An, Boris Boukhgalter, Richard Elong, Thomas E. Landers, Anthony Rachupka, Michael Fitzgerald, Lisa Leuper, William Brockman, Marcia Lara, Susan Faro, Elaine A. Ostrander, Joanne Zainoun, Leigh Anne Hunnicutt, Mark J. Daly, Leanne Hughes, April Cook, Patrick Cahill, Sujaa Raghuraman, Manfred Grabherr, Robert K. Wayne, Adam Brown, Xiaohong Liu, Charles Matthews, Scott Anderson, Margaret Priest, Shailendra Yadav, Evan Mauceli, Kerstin Lindblad-Toh, Patricia Ferreira, Yeshi Lokyitsang, Harindra Arachchi, Alexandre Melnikov, Christina Raymond, James Meldrim, Dmitry Khazanovich, Mieke Citroen, Aaron M. Berlin, Alix Chinh Kieu, John Stalker, Francis Galibert, Noah Duffey, Krista Lance, Louis Meneus, Jennifer Ruth Sadler Hall, Choe Norbu, Pema Tenzing, Richard Marabella, Chee-Wye Chin, Karen Foley, Xiaoping Yang, Nga Nguyen, Tenzin Dawoe, Ryan Hegarty, Julie Rogers, Joseph Graham, Chelsea D. Foley, Leonidas Mulrain, Tsering Wangdi, Karin Decktor, Sarah LeVine, Shuli Yang, Dennis C. Friedrich, Tina Goode, Cecil Rise, Teena Mehta, Laura Ayotte, Michele Clamp, Nicole Stange-Thomann, Annie Lui, Edward J. Kulbokas, Pema Phunkhang, Alan Dupes, Elinor K. Karlsson, Lynne Aftuck, Sahal Osman, Abderrahim Farina, Barry O'Neill, Diana M. Shih, Xiaohui Xie, Lester Dorris, Vijay Venkataraman, Benjamin Jester, Sampath Settipalli, Thu Nguyen, Alville Collymore, Klaus-Peter Koepfli, Senait Tesfaye, Nathan Houde, Susan McDonough, Leo Goodstadt, Glen Munson, Georgia Giannoukos, Jeffrey Chu, Nathan B. Sutter, Sheila A. Fisher, Charlien Jones, Michael C. Zody, Jianying Shi, John P. Pollinger, Mechele Sheehan, Stephen M. J. Searle, Fritz Pierre, Jason Blye, Jean-Pierre Leger, and Stuart DeGray

Subjects
Male, Genomics, Single-nucleotide polymorphism, Biology, Genome, Polymorphism, Single Nucleotide, Synteny, Conserved sequence, Evolution, Molecular, Mice, Dogs, Molecular evolution, Animals, Humans, Dog Diseases, Conserved Sequence, Short Interspersed Nucleotide Elements, Genetics, Whole genome sequencing, Multidisciplinary, Dog leukocyte antigen, Haplotype, Rats, Haplotypes, Mutagenesis, biology.protein, Hybridization, Genetic, Female
Abstract

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

Published
2005

10. Combo: a whole genome comparative browser

Author

Reinhard Engels, Jill P. Mesirov, Christopher B. Burge, James E. Galagan, David DeCaprio, and Tamara Yu

Subjects
Statistics and Probability, Java, Molecular Sequence Data, Information Storage and Retrieval, Genome browser, Biology, Biochemistry, Genome, World Wide Web, User-Computer Interface, Annotation, Databases, Genetic, Computer Graphics, Zoom, Molecular Biology, Dot plot (bioinformatics), computer.programming_language, Base Sequence, Chromosome Mapping, Sequence Analysis, DNA, File format, Computer Science Applications, Visualization, Computational Mathematics, Computational Theory and Mathematics, Database Management Systems, Sequence Alignment, computer, Algorithms, Software
Abstract

Summary: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization perspectives. The perpendicular (dot plot) view provides a dot plot of genome alignments synchronized with a display of genome annotations along each axis. The parallel view displays two genome annotations horizontally, synchronized through a panel displaying local alignments as trapezoids. Users can zoom to any resolution, from whole chromosomes to individual bases. They can select, highlight and view detailed information from specific alignments and annotations. Combo is an organism agnostic and can import data from a variety of file formats. Availability: Combo is integrated as part of the Argo Genome Browser which also provides single-genome browsing and editing capabilities. Argo is written in Java, runs on multiple platforms and is freely available for download at . Contact: reinhard@broad.mit.edu

Published
2006
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results