Christopher D Town

Summary

Affiliation: The Institute for Genomic Research
Country: USA

Publications

  1. ncbi request reprint Comparative sequence and genetic analyses of asparagus BACs reveal no microsynteny with onion or rice
    Jernej Jakse
    Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
    Theor Appl Genet 114:31-9. 2006
  2. ncbi request reprint Construction, characterization, and preliminary BAC-end sequencing analysis of a bacterial artificial chromosome library of white clover (Trifolium repens L.)
    Melanie Febrer
    Teagasc, Crops Research Centre, Oak Park, Carlow, Ireland
    Genome 50:412-21. 2007
  3. pmc Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana
    Joann Mudge
    Dept of Plant Pathology, University of Minnesota, St Paul, MN 55108, USA
    BMC Plant Biol 5:15. 2005
  4. pmc Spotted cotton oligonucleotide microarrays for gene expression analysis
    Joshua A Udall
    Department of Plant and Animal Sciences, Brigham Young University, Provo, UT 84062, USA
    BMC Genomics 8:81. 2007
  5. pmc The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms
    Seung Bum Lee
    Dept of Molecular Biology and Microbiology, University of Central Florida, Biomolecular Science, Building 20, Orlando, FL 32816 2364, USA
    BMC Genomics 7:61. 2006
  6. ncbi request reprint Annotating the genome of Medicago truncatula
    Christopher D Town
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Curr Opin Plant Biol 9:122-7. 2006
  7. pmc Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants
    Yong Li Xiao
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Plant Physiol 139:1323-37. 2005
  8. pmc Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy
    Christopher D Town
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Plant Cell 18:1348-59. 2006
  9. pmc Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology
    Foo Cheung
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    BMC Genomics 7:272. 2006
  10. pmc Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
    Brian J Haas
    The Institute for Genomic Research, 9172 Medical Center Drive, Rockville, Maryland 20850, USA
    BMC Biol 3:7. 2005

Collaborators

Detail Information

Publications42

  1. ncbi request reprint Comparative sequence and genetic analyses of asparagus BACs reveal no microsynteny with onion or rice
    Jernej Jakse
    Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
    Theor Appl Genet 114:31-9. 2006
    ....
  2. ncbi request reprint Construction, characterization, and preliminary BAC-end sequencing analysis of a bacterial artificial chromosome library of white clover (Trifolium repens L.)
    Melanie Febrer
    Teagasc, Crops Research Centre, Oak Park, Carlow, Ireland
    Genome 50:412-21. 2007
    ..The results suggest that a large-scale BAC-end sequencing strategy has the potential to anchor a significant proportion of the genome of white clover onto the gene-space sequence of M. truncatula...
  3. pmc Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana
    Joann Mudge
    Dept of Plant Pathology, University of Minnesota, St Paul, MN 55108, USA
    BMC Plant Biol 5:15. 2005
    ..Characterizing syntenic relationships in legumes is important in transferring knowledge from model legumes to crops that are important sources of protein, fixed nitrogen, and health-promoting compounds...
  4. pmc Spotted cotton oligonucleotide microarrays for gene expression analysis
    Joshua A Udall
    Department of Plant and Animal Sciences, Brigham Young University, Provo, UT 84062, USA
    BMC Genomics 8:81. 2007
    ..Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species...
  5. pmc The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms
    Seung Bum Lee
    Dept of Molecular Biology and Microbiology, University of Central Florida, Biomolecular Science, Building 20, Orlando, FL 32816 2364, USA
    BMC Genomics 7:61. 2006
    ..In addition, the sequence data were used to assess phylogenetic relationships among the major clades of rosids using cotton and 25 other completely sequenced angiosperm chloroplast genomes...
  6. ncbi request reprint Annotating the genome of Medicago truncatula
    Christopher D Town
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Curr Opin Plant Biol 9:122-7. 2006
    ....
  7. pmc Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants
    Yong Li Xiao
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Plant Physiol 139:1323-37. 2005
    ..Thus, by using this targeted approach, high-throughput RACE, we revealed numerous transcripts including many uncharacterized variants from these hypothetical genes...
  8. pmc Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy
    Christopher D Town
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Plant Cell 18:1348-59. 2006
    ..We found evidence for the frequent insertion of gene fragments of nuclear genomic origin and identified four apparently intact genes in noncollinear positions in the B. oleracea and A. thaliana genomes...
  9. pmc Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology
    Foo Cheung
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    BMC Genomics 7:272. 2006
    ....
  10. pmc Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
    Brian J Haas
    The Institute for Genomic Research, 9172 Medical Center Drive, Rockville, Maryland 20850, USA
    BMC Biol 3:7. 2005
    ..However, the initial genome annotation was submitted by multiple centers using inconsistent methods, making the data difficult to use for many applications...
  11. pmc Experimental validation of novel genes predicted in the un-annotated regions of the Arabidopsis genome
    William A Moskal
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    BMC Genomics 8:18. 2007
    ..A high throughput RACE pipeline was utilized in an attempt to verify the structure and expression of these novel genes...
  12. pmc Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis
    Mulu Ayele
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 15:487-95. 2005
    ..Collectively our results and these data sets suggest that several thousand new Arabidopsis genes remain to be identified and annotated...
  13. ncbi request reprint Development of Arabidopsis whole-genome microarrays and their application to the discovery of binding sites for the TGA2 transcription factor in salicylic acid-treated plants
    Francoise Thibaud-Nissen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Plant J 47:152-62. 2006
    ..The effect of the 2-h SA treatment on gene expression was measured using Affymetrix ATH1 arrays, and SA-induced genes were found to be significantly over-represented among genes neighboring putative TGA2-binding sites...
  14. pmc High throughput generation of promoter reporter (GFP) transgenic lines of low expressing genes in Arabidopsis and analysis of their expression patterns
    Yong Li Xiao
    J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Plant Methods 6:18. 2010
    ..Another way to understand the function of individual genes is to investigate their in vivo expression patterns by reporter constructs in transgenic plants which can provide basic information on the patterns of gene expression...
  15. pmc Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray
    Heenam Kim
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Genome Res 13:327-40. 2003
    ..Further, by examining the distribution of expression along the physical chromosome, we were able to identify a region of repressed transcription that may represent a previously undescribed heterochromatic region...
  16. pmc A BAC end view of the Musa acuminata genome
    Foo Cheung
    J Craig Venter Institute, Rockville, MD 20850, USA
    BMC Plant Biol 7:29. 2007
    ..Here, we report the analysis of 6,252 BAC end-sequences, in order to view the sequence composition of the Musa acuminata genome in a cost effective and efficient manner...
  17. ncbi request reprint Simultaneous high-throughput recombinational cloning of open reading frames in closed and open configurations
    Beverly A Underwood
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Plant Biotechnol J 4:317-24. 2006
    ..We illustrated its implementation for the isolation and validation of 346 Arabidopsis ORF entry clones...
  18. pmc Full-length messenger RNA sequences greatly improve genome annotation
    Brian J Haas
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 3:RESEARCH0029. 2002
    ..We have mapped these transcripts to their exact chromosomal locations and, using alignment programs, have created gene models that provide a reference set for this organism...
  19. pmc Cloning and sequencing of cDNAs for hypothetical genes from chromosome 2 of Arabidopsis
    Yong Li Xiao
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Plant Physiol 130:2118-28. 2002
    ..In addition, a total of six genes displayed more than one polyadenylation site. These data will be used to update gene models in The Institute for Genomic Research annotation database ATH1...
  20. ncbi request reprint Development and evaluation of an Arabidopsis whole genome Affymetrix probe array
    Julia C Redman
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Plant J 38:545-61. 2004
    ..Mapping of the oligonucleotides on the ATH1 array to the latest (version 4.0) annotation showed that over 95% of the probe sets (based on version 2.0 annotation) still fully represented their original target genes...
  21. pmc Annotation of the Arabidopsis genome
    Jennifer R Wortman
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Plant Physiol 132:461-8. 2003
  22. pmc Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
    Brian J Haas
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 31:5654-66. 2003
    ..The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations...
  23. pmc Sequencing and analysis of the gene-rich space of cowpea
    Michael P Timko
    Department of Biology, University of Virginia, Charlottesville, Virginia 22903, USA
    BMC Genomics 9:103. 2008
    ..With a nuclear genome size estimated at ~620 Mb, the cowpea genome is an ideal target for reduced representation sequencing...
  24. pmc Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages
    M A Rouf Mian
    Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73402, USA
    BMC Plant Biol 8:27. 2008
    ..The results of inter-library and library-specific in silico expression analyses of these ESTs are also reported...
  25. doi request reprint Gene expression profiling of M. truncatula transcription factors identifies putative regulators of grain legume seed filling
    Jérôme Verdier
    Unité Mixte de Recherche en Génétique et Ecophysiologie des Légumineuses à Graines UMR LEG, Institut National de la Recherche Agronomique INRA, Domaine d Epoisses, 21110, Bretenieres, France
    Plant Mol Biol 67:567-80. 2008
    ....
  26. ncbi request reprint Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants
    Kevin A T Silverstein
    Department of Plant Biology, University of Minnesota, St Paul, MN 55108, USA
    Plant J 51:262-80. 2007
    ..These findings highlight limitations in current annotation procedures for small divergent peptide classes...
  27. pmc Genome-wide identification of nodule-specific transcripts in the model legume Medicago truncatula
    Maria Fedorova
    Department of Agronomy and Plant Genetics, 1991 Upper Bedford Circle, University of Minnesota, St Paul, MN 55108, USA
    Plant Physiol 130:519-37. 2002
    ..Nodule-enhanced expression was confirmed experimentally for the TCs composed of five or more ESTs, whereas the results for those TCs containing fewer ESTs were variable...
  28. pmc A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R
    Jan Bartos
    Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Olomouc, Czech Republic
    BMC Plant Biol 8:95. 2008
    ..1RS translocation. A better knowledge of the rye genome could facilitate rye improvement and increase the efficiency of utilizing rye genes in wheat breeding...
  29. ncbi request reprint Arbuscular mycorrhizal symbiosis is accompanied by local and systemic alterations in gene expression and an increase in disease resistance in the shoots
    Jinyuan Liu
    Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, Ithaca, NY14853, USA
    Plant J 50:529-44. 2007
    ..Thus, the symbiosis is accompanied by a complex pattern of local and systemic changes in gene expression, including the induction of a functional defense response...
  30. pmc Insights into the Musa genome: syntenic relationships to rice and between Musa species
    Magali Lescot
    French Agricultural Research Center for International Development, UMR 1096, Avenue Agropolis, TA40 03, FR 34398, Montpellier, Cedex 5, France
    BMC Genomics 9:58. 2008
    ..Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome...
  31. ncbi request reprint Comparative analysis of 87,000 expressed sequence tags from the fumonisin-producing fungus Fusarium verticillioides
    Daren W Brown
    Mycotoxin Research Unit, U S Department of Agriculture ARS, Peoria, IL 61604, USA
    Fungal Genet Biol 42:848-61. 2005
    ..Finally, analysis of an EST that aligns to genomic sequence between FUM12 and FUM13 provided evidence for a previously unidentified gene (FUM20) in the FUM gene cluster...
  32. pmc A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales
    Joseph C Kuhl
    Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
    Plant Cell 16:114-25. 2004
    ..The Asparagales were more similar to eudicots than to the Poales for these genomic characteristics...
  33. ncbi request reprint Comparative genomic analyses in Asparagus
    Joseph C Kuhl
    Department of Horticulture, Michigan State University, East Lansing 48824, USA
    Genome 48:1052-60. 2005
    ..officinalis relative to A. plumosus. These results indicate that members of the genus Asparagus with smaller genomes may be useful genomic models for plants in the core Asparagales...
  34. ncbi request reprint Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity
    William J Martin
    Agricultural Research Service, USDA, Department of Horticulture, University of Wisconsin, Madison, 53706, USA
    Mol Genet Genomics 274:197-204. 2005
    ..Our results demonstrate that the grasses may not be appropriate genomic models for other major monocot groups such as the Asparagales; this will make it necessary to develop genomic resources for these important plants...
  35. pmc Transcript profiling coupled with spatial expression analyses reveals genes involved in distinct developmental stages of an arbuscular mycorrhizal symbiosis
    Jinyuan Liu
    Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
    Plant Cell 15:2106-23. 2003
    ....
  36. ncbi request reprint Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton
    S Samuel Yang
    Department of Soil and Crop Sciences, Texas A and M University, College Station, TX 77843, USA
    Plant J 47:761-75. 2006
    ..These results suggest general roles for genome-specific, phytohormonal and transcriptional gene regulation during the early stages of fiber cell development in cotton allopolyploids...
  37. pmc Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms
    Tracey Ruhlman
    Department of Molecular Biology and Microbiology, University of Central Florida, Biomolecular Science, Building 20, Room 336, Orlando, FL 32816 2364, USA
    BMC Genomics 7:222. 2006
    ..Additionally, the sequence data add to the rapidly growing database of plastid genomes for assessing phylogenetic relationships among angiosperms...
  38. pmc Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes
    Steven B Cannon
    Department of Plant Pathology, University of Minnesota, St Paul, MN 55108, USA
    Proc Natl Acad Sci U S A 103:14959-64. 2006
    ..Phylogenetic comparisons place this duplication within the Rosid I clade, clearly after the split between legumes and Salicaceae (poplar)...
  39. pmc The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max
    Jeffry L Shultz
    Genomics Core Facility, Southern Illinois University at Carbondale, Carbondale, IL 62901 4415, USA
    Nucleic Acids Res 34:D758-65. 2006
    ..The genome browser portal showed each data type as a separate track. Tetraploid, octoploid, diploid and homologous regions are shown clearly in relation to an integrated genetic and physical map...
  40. pmc Phosphorus stress in common bean: root transcript and metabolic responses
    Georgina Hernandez
    Centro de Ciencias Genómicas Universidad Nacional Autónoma de México, 66210 Cuernavaca, Mor, Mexico
    Plant Physiol 144:752-67. 2007
    ..Candidate genes have been identified that may contribute to root adaptation to P deficiency and be useful for improvement of common bean...
  41. pmc Toward sequencing cotton (Gossypium) genomes
    Z Jeffrey Chen
    Plant Physiol 145:1303-10. 2007
  42. ncbi request reprint Analysis of indole-3-butyric acid-induced adventitious root formation on Arabidopsis stem segments
    Jutta Ludwig-Müller
    Institut fur Botanik, Technische Universitat Dresden, Zellescher Weg 22, D 01062 Dresden, Germany
    J Exp Bot 56:2095-105. 2005
    ..In stem explants, residual endogenous IAA is transported to the basal end of each segment, thereby inducing root formation. In stem segments in which the polar auxin transport is inhibited by TIBA, root formation does not occur...