plant dna

Summary

Summary: Deoxyribonucleic acid that makes up the genetic material of plants.

Top Publications

  1. ncbi Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)
    T Thiel
    Institute of Plant Genetics and Crop Plant Research IPK, Corrensstrasse 3, D 06466 Gatersleben, Germany
    Theor Appl Genet 106:411-22. 2003
  2. ncbi Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis
    Xiaoyu Zhang
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Cell 126:1189-201. 2006
  3. ncbi Genome-wide insertional mutagenesis of Arabidopsis thaliana
    Jose M Alonso
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Science 301:653-7. 2003
  4. ncbi Gateway-compatible vectors for plant functional genomics and proteomics
    Keith W Earley
    Biology Department, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA
    Plant J 45:616-29. 2006
  5. pmc Physical and functional interactions between pathogen-induced Arabidopsis WRKY18, WRKY40, and WRKY60 transcription factors
    Xinping Xu
    Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907 2054, USA
    Plant Cell 18:1310-26. 2006
  6. ncbi Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages
    Y W Yang
    Institute of Botany, Academia Sinica, Taipei, Taiwan 11529
    J Mol Evol 48:597-604. 1999
  7. ncbi Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily
    B C Meyers
    Department of Vegetable Crops, University of California, Davis 95616, USA
    Plant J 20:317-32. 1999
  8. ncbi Arabidopsis WRKY33 transcription factor is required for resistance to necrotrophic fungal pathogens
    Zuyu Zheng
    Department of Botany and Plant Pathology, Purdue University, 915 W State Street, West Lafayette, IN 47907 2054, USA
    Plant J 48:592-605. 2006
  9. ncbi A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
    Stephen A Goff
    Torrey Mesa Research Institute, Syngenta, 3115 Merryfield Row, San Diego, CA 92121, USA
    Science 296:92-100. 2002
  10. ncbi ARF1, a transcription factor that binds to auxin response elements
    T Ulmasov
    Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA
    Science 276:1865-8. 1997

Detail Information

Publications300 found, 100 shown here

  1. ncbi Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)
    T Thiel
    Institute of Plant Genetics and Crop Plant Research IPK, Corrensstrasse 3, D 06466 Gatersleben, Germany
    Theor Appl Genet 106:411-22. 2003
    ....
  2. ncbi Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis
    Xiaoyu Zhang
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Cell 126:1189-201. 2006
    ....
  3. ncbi Genome-wide insertional mutagenesis of Arabidopsis thaliana
    Jose M Alonso
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Science 301:653-7. 2003
    ..Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene...
  4. ncbi Gateway-compatible vectors for plant functional genomics and proteomics
    Keith W Earley
    Biology Department, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA
    Plant J 45:616-29. 2006
    ..Antibodies detecting the FLAG, HA, cMyc and AcV5 tags show relatively little cross-reaction with endogenous proteins in a variety of monocotyledonous and dicotyledonous plants, suggesting broad utility for the tags and vectors...
  5. pmc Physical and functional interactions between pathogen-induced Arabidopsis WRKY18, WRKY40, and WRKY60 transcription factors
    Xinping Xu
    Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907 2054, USA
    Plant Cell 18:1310-26. 2006
    ..cinerea. These results indicate that the three WRKY proteins interact both physically and functionally in a complex pattern of overlapping, antagonistic, and distinct roles in plant responses to different types of microbial pathogens...
  6. ncbi Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages
    Y W Yang
    Institute of Botany, Academia Sinica, Taipei, Taiwan 11529
    J Mol Evol 48:597-604. 1999
    ..5-20.4 Myr for the Brassica-Arabidopsis split, and 14.5-20.4 Myr for the Arabidopsis-Arabideae split...
  7. ncbi Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily
    B C Meyers
    Department of Vegetable Crops, University of California, Davis 95616, USA
    Plant J 20:317-32. 1999
    ..Sequence inferences suggest that these genes encode a novel class of nucleotide-binding proteins...
  8. ncbi Arabidopsis WRKY33 transcription factor is required for resistance to necrotrophic fungal pathogens
    Zuyu Zheng
    Department of Botany and Plant Pathology, Purdue University, 915 W State Street, West Lafayette, IN 47907 2054, USA
    Plant J 48:592-605. 2006
    ..Together, these results indicate that pathogen-induced WRKY33 is an important transcription factor that regulates the antagonistic relationship between defense pathways mediating responses to P. syringae and necrotrophic pathogens...
  9. ncbi A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
    Stephen A Goff
    Torrey Mesa Research Institute, Syngenta, 3115 Merryfield Row, San Diego, CA 92121, USA
    Science 296:92-100. 2002
    ..Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops...
  10. ncbi ARF1, a transcription factor that binds to auxin response elements
    T Ulmasov
    Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA
    Science 276:1865-8. 1997
    ..The carboxyl terminus of ARF1 contains two motifs found in the Aux/IAA class of proteins and appears to mediate protein-protein interactions...
  11. ncbi RNA polymerase IV directs silencing of endogenous DNA
    A J Herr
    Sainsbury Laboratory, John Innes Centre, Norwich NR4 7UH, UK
    Science 308:118-20. 2005
    ..The existence of this distinct silencing polymerase may explain the paradoxical involvement of an RNA silencing pathway in maintenance of transcriptional silencing...
  12. ncbi Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis
    Hidetoshi Saze
    Friedrich Miescher Institute for Biomedical Research, P O Box 2543, CH 4002 Basel, Switzerland
    Nat Genet 34:65-9. 2003
    ....
  13. ncbi CyMATE: a new tool for methylation analysis of plant genomic DNA after bisulphite sequencing
    Jennifer Hetzl
    Institute for Computer Graphics and Algorithms, Vienna University of Technology, Favoritenstrasse 9 11, A 1040 Vienna, Austria
    Plant J 51:526-36. 2007
    ..Methylation Analysis Tool for Everyone) for in silico analysis of DNA sequences after bisulphite conversion of plant DNA, in which methylation is more divergent with respect to sequence context and biological relevance...
  14. pmc A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa
    Hong Kyu Choi
    Department of Plant Pathology, University of California, Davis, California 95616, USA
    Genetics 166:1463-502. 2004
    ..sativa. The resulting comparative map, which includes 68 bridging markers, indicates that the two Medicago genomes are highly similar and establishes the basis for a Medicago composite map...
  15. pmc Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype
    Robert T Gaeta
    Department of Agronomy, University of Wisconsin, Madison, Wisconsin, USA
    Plant Cell 19:3403-17. 2007
    ..Our data indicate that exchanges among homoeologous chromosomes are a major mechanism creating novel allele combinations and phenotypic variation in newly formed B. napus polyploids...
  16. ncbi Functional markers in plants
    Jeppe R Andersen
    Department of Plant Biology, Danish Institute of Agricultural Sciences, Research Center Flakkebjerg, 4200, Slagelse, Denmark
    Trends Plant Sci 8:554-60. 2003
    ..Functional markers are superior to random DNA markers such as RFLPs, SSRs and AFLPs owing to complete linkage with trait locus alleles. We outline the definition, development, application and prospects of functional markers...
  17. pmc Mechanisms of recent genome size variation in flowering plants
    Jeffrey L Bennetzen
    Department of Genetics, University of Georgia, Athens, GA 30602, USA
    Ann Bot 95:127-32. 2005
    ..This research focuses on characterizing DNA removal from the rice and Arabidopsis genomes, and discusses whether loss of DNA has effectively competed with amplification in these species...
  18. pmc Sequencing of natural strains of Arabidopsis thaliana with short reads
    Stephan Ossowski
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
    Genome Res 18:2024-33. 2008
    ..Our pipeline for aligning reads and predicting SNPs and indels, SHORE, is available for download at http://1001genomes.org...
  19. pmc A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome
    Marcio C Moretzsohn
    EMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF, Brazil
    BMC Plant Biol 9:40. 2009
    ..This can be overcome by the utilization of wild species of Arachis, which present the A- and B-genomes in the diploid state, and show high levels of genetic variability...
  20. ncbi Nested core collections maximizing genetic diversity in Arabidopsis thaliana
    Heather I McKhann
    Centre National de Genotypage, 2 rue Gaston Cremieux, 91057 Evry Cedex, France
    Plant J 38:193-202. 2004
    ....
  21. pmc DNA demethylation in the Arabidopsis genome
    Jon Penterman
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 104:6752-7. 2007
    ..Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation...
  22. pmc Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle
    Junli Zhou
    Peking Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing, 100871, People s Republic of China
    Plant Mol Biol 63:591-608. 2007
    ..Overall, our data supports a notion that organ-specific gene regulation in response to the two abiotic stresses may primarily be mediated by organ-specific transcription responses...
  23. pmc Evolution of genome size in Brassicaceae
    J Spencer Johnston
    Department of Entomology, Texas A and M University, College Station, TX 77843, USA
    Ann Bot 95:229-35. 2005
    ..The aim of this study was to erect a cytological and molecular phylogenetic framework for a selected subset of the Brassicacae, and use this as a template to examine genome size evolution in Brassicaceae...
  24. ncbi Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed
    Kazumi Nakabayashi
    Plant Science Center, RIKEN, Suehiro cho 1 7 22, Tsurumi, Yokohama, Kanagawa 230 0045, Japan
    Plant J 41:697-709. 2005
    ..Our analyses reveal that transcriptomes of Arabidopsis seed are characterized by multiple regulatory mechanisms: epigenetic chromatin structures, chromosomal locations (e.g. co-regulated gene clusters) and cis-acting elements...
  25. pmc Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution
    Keith L Adams
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 99:9905-12. 2002
    ..Most of these mitochondrial gene losses are probably the consequence of gene transfer to the nucleus; thus, rates of functional gene transfer also may vary dramatically in angiosperms...
  26. pmc Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce
    Nathalie Pavy
    Arborea and Canada Research Chair in Forest and Environmental Genomics, Centre d Etude de la Forêt, Pavillon Charles Eugène Marchand, Universite Laval, Quebec, Quebec G1V 0A6, Canada
    BMC Genomics 9:21. 2008
    ..b.s.p.)...
  27. pmc Epigenetic natural variation in Arabidopsis thaliana
    Matthew W Vaughn
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
    PLoS Biol 5:e174. 2007
    ..This may account for the instability of gene methylation, if occasional failure of maintenance methylation cannot be restored by other means...
  28. ncbi Mining and characterizing microsatellites from citrus ESTs
    Chunxian Chen
    Institute of Food and Agricultural Sciences, Citrus Research and Education Center, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
    Theor Appl Genet 112:1248-57. 2006
    ..These EST-derived SSRs can be a resource used for understanding of the citrus SSR distribution and frequency, and development of citrus EST-SSR genetic and physical maps. These SSR primer sequences are available upon request...
  29. pmc Conservation of Arabidopsis flowering genes in model legumes
    Valerie Hecht
    School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia
    Plant Physiol 137:1420-34. 2005
    ..These results demonstrate the potential benefit of parallel model systems for an understanding of flowering phenology in crop and model legume species...
  30. ncbi Direct targeting of light signals to a promoter element-bound transcription factor
    J F Martínez-García
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Science 288:859-63. 2000
    ....
  31. ncbi Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes
    Michele Morgante
    E I DuPont de Nemours and Co, DuPont Agriculture and Nutrition Molecular Genetics, Newark, Delaware, USA
    Nat Genet 30:194-200. 2002
    ..Contrary to previous reports suggesting a preferential mechanism for the origin of microsatellites from repetitive DNA in both animals and plants, our findings show a significant association with the low-copy fraction of plant genomes...
  32. pmc Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce
    Marie Claire Namroud
    Canada Research Chair in Forest and Environmental Genomics and Arborea, Forest Research Centre, Pavillon Charles Eugène Marchand, Universite Laval, Quebec, Quebec, CanadaP4
    Mol Ecol 17:3599-613. 2008
    ..The results suggest that an approach separating the locus and population effects is useful to identify genes potentially under selection. These candidates are worth exploring in more details at the physiological and ecological levels...
  33. pmc Microsatellites as DNA markers in cultivated peanut (Arachis hypogaea L.)
    Guohao He
    Tuskegee University, Tuskegee, AL 36088, USA
    BMC Plant Biol 3:3. 2003
    ..Genomic research of cultivated peanut has lagged behind other crop species because of the paucity of polymorphic DNA markers found in this crop. It is necessary to identify additional DNA markers for further genetic research in peanut...
  34. pmc DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads
    Chodon Sass
    Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California, United States of America
    PLoS ONE 2:e1154. 2007
    ..We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants...
  35. ncbi In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species
    Rajeev K Varshney
    Institute of Plant Genetics and Crop Plant Research IPK, Corrensstrasse 3, D 06466 Gatersleben, Germany
    Cell Mol Biol Lett 7:537-46. 2002
    ....
  36. pmc Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements
    U Lagercrantz
    Department of Plant Biology, Swedish University of Agricultural Sciences, S 750 07 Uppsala, Sweden
    Genetics 150:1217-28. 1998
    ..thaliana and Brassica crops is likely to result in the identification of a large number of genes that affect important traits in Brassica crops...
  37. pmc Plant DNA flow cytometry and estimation of nuclear genome size
    Jaroslav Dolezel
    Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovska 6, Olomouc, CZ 77200, Czech Republic
    Ann Bot 95:99-110. 2005
    ..While the former applications are relatively straightforward, estimation of absolute DNA amount requires special attention to possible errors in sample preparation and analysis...
  38. pmc Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea)
    Luu M Cuc
    International Crop Research Institute for Semi Arid Tropics, Patancheru 502 324, Greater Hyderabad, Andhra Pradesh, India
    BMC Plant Biol 8:55. 2008
    ..The low level of polymorphism in cultivated germplasm, however, warrants a need of larger number of polymorphic microsatellite markers for cultivated groundnut...
  39. ncbi Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B
    Etienne Paux
    UMR ASP 1095, INRA, Universite Blaise Pascal, 63100 Clermont Ferrand, France
    Plant J 48:463-74. 2006
    ..Our data demonstrate that BAC-end sequencing from flow-sorted chromosomes is a powerful tool for analysing the structure and evolution of polyploid and highly repetitive genomes...
  40. pmc A high quality draft consensus sequence of the genome of a heterozygous grapevine variety
    Riccardo Velasco
    IASMA Research Center, San Michele all Adige, Trento, Italy
    PLoS ONE 2:e1326. 2007
    ..In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented...
  41. pmc A microsatellite map of wheat
    M S Roder
    Institut für Pflanzengenetik und Kulturpflanzenforschung IPK, 06466 Gatersleben, Germany
    Genetics 149:2007-23. 1998
    ..Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions...
  42. pmc Antiquity of microRNAs and their targets in land plants
    Michael J Axtell
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Plant Cell 17:1658-73. 2005
    ..Therefore, several individual miRNA regulatory circuits have ancient origins and have remained intact throughout the evolution and diversification of plants...
  43. pmc Investigation of the bottleneck leading to the domestication of maize
    A Eyre-Walker
    Department of Plant Sciences and Center for Theoretical and Applied Genetics, Rutgers University, New Brunswick, NJ 08902, USA
    Proc Natl Acad Sci U S A 95:4441-6. 1998
    ..For example, the breadth of genetic diversity in maize is consistent with a founding population of only 20 individuals when the domestication event is 10 generations in length...
  44. pmc Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana
    Stephen I Wright
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, Scotland EH9 3JT, UK
    Genome Res 13:1897-903. 2003
    ..thaliana. High rates of self-fertilization may reduce the importance of recombination rate in genome structuring in inbreeding organisms such as A. thaliana and Caenorhabditis elegans...
  45. ncbi A C-terminal Myb extension domain defines a novel family of double-strand telomeric DNA-binding proteins in Arabidopsis
    Zemfira N Karamysheva
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas 77843 2128, USA
    J Biol Chem 279:47799-807. 2004
    ..Thus, Myb-ext is required for binding plant telomeric DNA and defines a novel class of proteins in Arabidopsis...
  46. pmc Two new nuclear isolation buffers for plant DNA flow cytometry: a test with 37 species
    João Loureiro
    Laboratory of Biotechnology and Cytomics, CESAM and Department of Biology, University of Aveiro, Campus Universitario de Santiago, 3810 193 Aveiro, Portugal
    Ann Bot 100:875-88. 2007
    ..In this work, recent data on the performance of nuclear isolation buffers are utilized in order to develop new buffers, general purpose buffer (GPB) and woody plant buffer (WPB), for plant DNA flow cytometry.
  47. ncbi Identification of Dendrobium species by a candidate DNA barcode sequence: the chloroplast psbA-trnH intergenic region
    Hui Yao
    Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, PR China
    Planta Med 75:667-9. 2009
    ..5 %. Our results support the notion that the psbA-trnH intergenic spacer region could be used as a barcode to distinguish various Dendrobium species and to differentiate Dendrobium species from other adulterating species...
  48. pmc Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome
    Marcio de Carvalho Moretzsohn
    EMBRAPA Recursos Geneticos e Biotecnologia, C P 02372, 70 770 900, Brasilia DF, Brazil
    BMC Plant Biol 4:11. 2004
    ..Here we report the use of a set of microsatellite markers, including newly developed ones, for phylogenetic inferences and the analysis of genetic variation of accessions of A. hypogea and its wild relatives...
  49. ncbi A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.)
    Daryl J Somers
    Agriculture and Agri Food Canada, Cereal Research Centre, 195 Dafoe Rd, Winnipeg, MB, Canada, R3T 2 M9
    Theor Appl Genet 109:1105-14. 2004
    ..This enables users to predict allele sizes in new breeding populations and develop molecular breeding and genomics strategies...
  50. pmc Identification of Amazonian trees with DNA barcodes
    Mailyn Adriana Gonzalez
    Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier and CNRS, UMR 5174, Toulouse, France
    PLoS ONE 4:e7483. 2009
    ..Large-scale plant diversity inventories are critical to develop informed conservation strategies. However, the workload required for classic taxonomic surveys remains high and is particularly problematic for megadiverse tropical forests...
  51. ncbi A high density barley microsatellite consensus map with 775 SSR loci
    R K Varshney
    Leibniz Institute of Plant Genetics and Crop Plant Research IPK, Corrensstrasse 3, 06466 Gatersleben, Germany
    Theor Appl Genet 114:1091-103. 2007
    ..This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley...
  52. ncbi Long-term genome diploidization in allopolyploid Nicotiana section Repandae (Solanaceae)
    James J Clarkson
    Jodrell Laboratory, Royal Botanic Gasrdens, Kew, Richmond, Surrey, TW9 3DS, UK
    New Phytol 168:241-52. 2005
    ..In Nicotiana, 4.5 Myr of allopolyploid evolution renders genomic in situ hybridization (GISH) unsuitable for the complete resolution of parental genomes...
  53. pmc Diversity arrays: a solid state technology for sequence information independent genotyping
    D Jaccoud
    Center for the Application of the Molecular Biology to International Agriculture (CAMBIA) Canberra, ACT, Australia
    Nucleic Acids Res 29:E25. 2001
    ..Diversity Arrays enable rapid and economical application of a highly parallel, solid-state genotyping technology to any genome or complex genomic mixtures...
  54. ncbi Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes
    Henry Daniell
    Department of Molecular Biology and Microbiology, Biomolecular Science, University of Central Florida, 4000 Central Florida Blvd, Bldg 20, Room 336, Orlando, FL 32816 2364, USA
    Theor Appl Genet 112:1503-18. 2006
    ..It is possible that there has been a loss of conserved editing sites in potato and tomato...
  55. ncbi Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes
    Rosemarie C Haberle
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    J Mol Evol 66:350-61. 2008
    ..Genes for tRNAs occur at many but not all inversion endpoints, so some combination of repeats and tRNA genes may have mediated these rearrangements...
  56. pmc Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well
    Aron J Fazekas
    Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
    PLoS ONE 3:e2802. 2008
    ..to the contentious debate on plant barcoding should therefore involve increased attention to practical issues related to the ease of sequence recovery, global alignability, and marker redundancy in multilocus plant DNA barcoding systems.
  57. pmc The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis
    Iain Searle
    Max Planck Institute for Plant Breeding, D 50829 Cologne, Germany
    Genes Dev 20:898-912. 2006
    ..Thus vernalization relieves transcriptional repression of key regulatory genes in both the leaf and meristem, allowing production of systemic signals in the leaves and conferring competence on the meristem to respond to these signals...
  58. ncbi Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems
    Kyonoshin Maruyama
    Biological Resources Division, Japan International Research Center for Agricultural Sciences, 1 1 Ohwashi, Tsukuba, Ibaraki 305 8686, Japan
    Plant J 38:982-93. 2004
    ..The recombinant DREB1A protein bound to A/GCCGACNT more efficiently than to A/GCCGACNA/G/C...
  59. ncbi Cytogenetics for the model system Arabidopsis thaliana
    P Fransz
    School of Biological Sciences, University of Birmingham, Edgbaston, UK
    Plant J 13:867-76. 1998
    ..Together with the presented karyotype this makes Arabidopsis a model system for detailed cytogenetic mapping...
  60. ncbi Bin mapping of genomic and EST-derived SSRs in melon (Cucumis melo L.)
    I Fernández-Silva
    IRTA, Centre de Recerca en Agrigenòmica CSIC IRTA UAB CRAG, Carretera de Cabrils, Km 2, 08348, Cabrils, Barcelona, Spain
    Theor Appl Genet 118:139-50. 2008
    ..A final bin-map was constructed including 80 RFLPs, 212 SSRs, 3 SNPs and the Nsv locus, distributed in 122 bins with an average bin length of 10.2 cM and a maximum bin length of 33 cM. Map density was 4.2 cM/marker or 5.9 cM/SSR...
  61. pmc Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques
    S M Aljanabi
    Cenargen Embrapa, SAIN Parque Rural, W5 Norte C P 02372, CEP 70849 970 Brasilia, DF, Brazil
    Nucleic Acids Res 25:4692-3. 1997
    ..The quantity and the quality of the DNA extracted by this method is high enough to perform hundreds of PCR-based reactions and also to be used in other DNA manipulation techniques such as restriction digestion, Southern blot and cloning...
  62. ncbi A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
    Jun Yu
    Beijing Genomics Institute Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China
    Science 296:79-92. 2002
    ..4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences...
  63. ncbi Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics
    Douglas E Soltis
    Department of Botany and the Genetics Institute, University of Florida, Gainesville, FL 32611, USA
    Trends Plant Sci 9:477-83. 2004
    ..We provide a conspicuous example that includes Amborella, the putative sister of all other extant angiosperms, highlighting the limits of phylogenetics when whole genomes are used but taxon sampling is poor...
  64. pmc Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane
    Andre L Vettore
    Centro de Biologia Molecular e Engenharia Genetica, Instituto da Computação, Universidade Estadual de Campinas, 13083 970 Campinas SP, Brazil
    Genome Res 13:2725-35. 2003
    ..This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged...
  65. pmc The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants
    Shu Ouyang
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 32:D360-3. 2004
    ..Collectively, these databases provide a resource for the identification, classification and analysis of repetitive sequences in plants...
  66. pmc Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing
    Keith L Adams
    Department of Botany, Iowa State University, Ames, IA 50011, USA
    Proc Natl Acad Sci U S A 100:4649-54. 2003
    ..Both long-term and immediate responses to polyploidization were implicated. Data suggest that some silencing events are epigenetically induced during the allopolyploidization process...
  67. pmc Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species
    Xuanqiang Liang
    Crops Research Institute, Guangdong Academy of Agricultural Sciences, Wushan 510640, Guangzhou, PR China
    BMC Plant Biol 9:35. 2009
    ..With the development of peanut EST projects, a vast amount of available EST sequence data has been generated. These data offered an opportunity to identify SSR in ESTs by data mining...
  68. pmc A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region
    W John Kress
    Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
    PLoS ONE 2:e508. 2007
    ..This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level...
  69. pmc Use of DNA barcodes to identify flowering plants
    W John Kress
    Department of Botany and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, P O Box 37012, Washington, DC 20013 7012
    Proc Natl Acad Sci U S A 102:8369-74. 2005
    ....
  70. pmc Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata
    Jeffrey Ross-Ibarra
    Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
    PLoS ONE 3:e2411. 2008
    ..Arabidopsis lyrata, a self-incompatible, perennial species with a circumpolar distribution, is an excellent model system in which to study the roles of demographic history and local adaptation in patterning genetic variation...
  71. pmc The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux
    Mitsuhiro Matsuo
    Center for Gene Research, Nagoya University, Nagoya 464 8602, Japan
    Plant Cell 17:665-75. 2005
    ....
  72. ncbi Phylogenetic relationships and evolutionary traits in Ranunculus s.l. (Ranunculaceae) inferred from ITS sequence analysis
    Elvira Hörandl
    Department of Systematic and Evolutionary Botany, Faculty of Life Sciences, University of Vienna, Rennweg 14, A 1030 Vienna, Austria
    Mol Phylogenet Evol 36:305-27. 2005
    ....
  73. ncbi Steady-state transposon mutagenesis in inbred maize
    Donald R McCarty
    Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
    Plant J 44:52-61. 2005
    ..org; http://endosperm.info) includes pedigree and phenotypic data for over 2000 independent seed mutants selected from a population of 31 548 F2 lines and integrated with analyses of 34 255 MuTAIL sequences...
  74. ncbi Dynamic and reversible changes in histone H3-Lys4 methylation and H3 acetylation occurring at submergence-inducible genes in rice
    Hiroyuki Tsuji
    Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo, 113 8657 Japan
    Plant Cell Physiol 47:995-1003. 2006
    ..Together, these results showed dynamic and reversible changes of histone H3-K4 methylation and H3 acetylation in stress-responsive genes in a higher plant in response to the appearance or disappearance of an environmental stress...
  75. pmc Transcriptional regulation of sorghum defense determinants against a phloem-feeding aphid
    Keyan Zhu-Salzman
    Department of Entomology, Texas A and M University, College Station, Texas 77843, USA
    Plant Physiol 134:420-31. 2004
    ....
  76. ncbi Interactions of putative telomere-binding proteins in Arabidopsis thaliana: identification of functional TRF2 homolog in plants
    Milan Kuchar
    Department of Functional Genomics and Proteomics, Masaryk University Brno, Kotlarska 2, CZ 611 37 Brno, Czech Republic
    FEBS Lett 578:311-5. 2004
    ..In humans, the TRF1-complex recruits hPot1 to telomeres by protein-protein interactions where it is involved in telomere length regulation. Possibly, AtTRB1 has a similar role in recruiting AtPot1...
  77. ncbi A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region
    Shu Miaw Chaw
    Institute of Botany, Academia Sinica, Taipei, Taiwan
    Mol Phylogenet Evol 37:214-34. 2005
    ..The matK gene and ITS/5.8S region contain more useful information than the trnK intron in addressing phylogeny. Redelimitations of Zamiaceae, Stangeriaceae, subfamily Encephalartoideae and subtribe Macrozamiineae are necessary...
  78. ncbi Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers
    M T Cervera
    Departamento de Biotecnologia, SGIT, INIA, Ctra de la Coruña Km 7, 28049 Madrid, Spain
    Mol Genet Genomics 268:543-52. 2002
    ....
  79. ncbi Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat
    Etienne Paux
    INRA UBP UMR 1095, Genetics, Diversity and Ecophysiology of Cereals, Clermont Ferrand, France
    Plant Biotechnol J 8:196-210. 2010
    ..All together, our results suggest that ISBP markers have the potential to lead to a breakthrough in wheat marker-assisted selection...
  80. pmc Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species
    Shilin Chen
    Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People s Republic of China
    PLoS ONE 5:e8613. 2010
    ..The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over...
  81. pmc Rice sHsp genes: genomic organization and expression profiling under stress and development
    Neelam K Sarkar
    Department of Plant Molecular Biology, University of Delhi South Campus, N Delhi 110021, India
    BMC Genomics 10:393. 2009
    ..Database search was performed to investigate the sHsp gene family across rice genome sequence followed by comprehensive expression analysis of these genes...
  82. pmc High potential of a transposon mPing as a marker system in japonica x japonica cross in rice
    Yuki Monden
    Plant Breeding Laboratory, Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
    DNA Res 16:131-40. 2009
    ..Moreover, we could easily map two novel loci involved in the culm length on the short arms of chromosomes 3 and 10...
  83. ncbi Engineering of gibberellin levels in citrus by sense and antisense overexpression of a GA 20-oxidase gene modifies plant architecture
    Carmen Fagoaga
    Centro de Proteccion Vegetal y Biotecnologia, Instituto Valenciano de Investigaciones Agrarias IVIA, Apdo Oficial, Moncada 46113, Valencia, Spain
    J Exp Bot 58:1407-20. 2007
    ..This suggests that roots contribute to the GA economy of aerial parts in citrus and opens the possibility of using the antisense plants as dwarfing rootstocks...
  84. pmc A genomewide analysis of the cinnamyl alcohol dehydrogenase family in sorghum [Sorghum bicolor (L.) Moench] identifies SbCAD2 as the brown midrib6 gene
    Ana Saballos
    School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
    Genetics 181:783-95. 2009
    ..The modeling revealed unique changes in structure consistent with the observed phenotypes of the mutants...
  85. ncbi Genome-wide transcript analysis of maize hybrids: allelic additive gene expression and yield heterosis
    Mei Guo
    Pioneer Hi Bred International, Inc, 7250 NW 62nd Avenue, Johnston, IA 50131, USA
    Theor Appl Genet 113:831-45. 2006
    ..Our findings suggest that differential allele regulation may play an important role in hybrid yield or heterosis, and provide a new insight to the molecular understanding of the underlying mechanisms of heterosis...
  86. ncbi Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): new insights from phylogenetic analyses of low-copy nuclear genes
    M Rousseau-Gueutin
    INRA, UR 419, Unité de Recherche sur les Espèces Fruitières, Domaine de la Grande Ferrade, Villenave D Ornon, France
    Mol Phylogenet Evol 51:515-30. 2009
    ..Additionally, sequence analyses also revealed relaxed constraints on homoeologous copies at high ploidy level, as demonstrated by deletion events within DHAR coding sequences of some allo-octoploid haplotypes...
  87. ncbi MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome
    Ning Bao
    Program in Plant Breeding and Plant Genetics, University of Wisconsin, Madison, WI 53706, USA
    Dev Cell 7:653-62. 2004
    ..These results suggest a model in which the microRNA interacts with nascent, newly processed PHB mRNA to alter chromatin of the corresponding PHB template DNA predominantly in differentiated cells...
  88. ncbi Identification of genes associated with flesh morphogenesis during grapevine fruit development
    Lucie Fernandez
    UMR BEPC, Campus Agro M INRA, 2 place Viala, 34060, Montpellier, Cedex 01, France
    Plant Mol Biol 63:307-23. 2007
    ..Expression of these genes appeared to be affected during young fruit development in the mutant, suggesting that they may play a role in grape berry morphogenesis...
  89. ncbi An accumulation of tandem DNA repeats on the Y chromosome in Silene latifolia during early stages of sex chromosome evolution
    Roman Hobza
    Laboratory of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of Czech Republic, Kralovopolska Street 135, Brno 612 65, Czech Republic
    Chromosoma 115:376-82. 2006
    ..TRAYC accumulation is most prominent near the centromere of the Y chromosome. We propose a role for the centromere as a starting point for the cessation of recombination between the X and Y chromosomes...
  90. pmc Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine
    Tuncay Baubec
    Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr Bohr Gasse 3, 1030 Vienna, Austria
    Plant J 57:542-54. 2009
    ..Zebularine represents a promising new and versatile tool for investigating the role of DNA methylation in plants with regard to transcriptional control, maintenance and formation of (hetero-) chromatin...
  91. pmc Rolling-circle transposons in eukaryotes
    V V Kapitonov
    Genetic Information Research Institute, 2081 Landings Drive, Mountain View, CA 94043, USA
    Proc Natl Acad Sci U S A 98:8714-9. 2001
    ..Sequence conservation suggests that Helitrons continue to be transposed...
  92. ncbi Expression profiling identifies genes expressed early during lint fibre initiation in cotton
    Yingru Wu
    CSIRO Plant Industry, Canberra, ACT, Australia
    Plant Cell Physiol 47:107-27. 2006
    ..Cotton fibre initiation therefore has some parallels with leaf trichome development, although the detailed molecular mechanisms are clearly different...
  93. pmc Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae
    Christopher L Parkinson
    Department of Biology, Indiana University, Bloomington, IN 47405 3700, USA
    BMC Evol Biol 5:73. 2005
    ..Only a single case of extensive, mitochondrial-specific rate changes has been described, in the angiosperm genus Plantago...
  94. ncbi A reference integrated map for cultivated grapevine (Vitis vinifera L.) from three crosses, based on 283 SSR and 501 SNP-based markers
    Silvia Vezzulli
    IASMA Research Centre, San Michele a Adige, Italy
    Theor Appl Genet 117:499-511. 2008
    ..This integrated map can serve as a fundamental tool for molecular breeding in V. vinifera and related species and provide a basis for studies of genome organization and evolution in grapevines...
  95. ncbi Bipartite determinants of DNA-binding specificity of plant basic leucine zipper proteins
    X Niu
    Pioneer Hi Bred International, Inc, Johnston, IA 50131, USA
    Plant Mol Biol 41:1-13. 1999
    ..These results suggest that factorial contributions of the amino acid residues in the basic domain combine to determine DNA-binding specificity of bZIP proteins...
  96. ncbi Molecular analysis of plant migration and refugia in the Arctic
    R J Abbott
    Division of Environmental and Evolutionary Biology, Harold Mitchell Building, School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, UK
    Science 289:1343-6. 2000
    ..The geographical distribution of chloroplast DNA variation in the species supports the hypothesis that, during Pleistocene glaciations, some plant refugia were located in the Arctic as well as at more southern latitudes...
  97. pmc Challenges of detecting directional selection after a bottleneck: lessons from Sorghum bicolor
    Martha T Hamblin
    Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
    Genetics 173:953-64. 2006
    ..Despite a known history of recent selection, we find little evidence for directional selection, likely due to low statistical power and lack of an appropriate null model...
  98. ncbi Evolution by reticulation: European dogroses originated by multiple hybridization across the genus rosa
    C M Ritz
    Institute of Systematic Botany, University of Jena, Philosophenweg 16, D 07743 Jena, Germany
    J Hered 96:4-14. 2005
    ..Secondary structure predictions do not point to the existence of pseudogenes within these ITS-1 types. Our data suggest that the pentaploid Caninae genome originated from different members of nondogroses and the now extinct Protocaninae...
  99. pmc A rice Tc1/mariner-like element transposes in yeast
    Guojun Yang
    Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
    Plant Cell 18:2469-78. 2006
    ..This report of an active plant Tc1/mariner in yeast will provide a foundation for future comparative analyses of animal and plant elements in addition to making a new wide host range transposable element available for plant gene tagging...
  100. ncbi Genome-wide transcriptome profiling of the early cadmium response of Arabidopsis roots and shoots
    S Herbette
    CEA Cadarache, DSV DEVM Laboratoire des Echanges Membranaires et Signalisation, UMR 6191 CNRS CEA Aix Marseille II, 13108 Saint Paul les Durance cedex, France
    Biochimie 88:1751-65. 2006
    ..Finally, our results provide new insights to understand the molecular mechanisms involved in transcriptional regulation in response to cadmium exposure in plants...
  101. ncbi Evidence of a secondary grapevine domestication centre detected by SSR analysis
    F Grassi
    Department of Biology, University of Milan, Via Celoria 26, 20133 Milan, Italy
    Theor Appl Genet 107:1315-20. 2003
    ..Six Lambrusco varieties were also included in this analysis as ancient putative ancestors of the cultivated grapevines. The molecular analysis excluded this hypothesis and suggest Lambrusco as an independent Vitis taxon...

Research Grants17

  1. Analysis of Crr1, a regulator of copper homeostasis
    DIANA AZURDIA; Fiscal Year: 2007
    ..Sequence analysis suggests that one domain of Crr1 is related to a conserved but novel domain in a family of plant DNA binding proteins. It is therefore likely that Crr1 is a DNA binding protein...
  2. Rapid, Universal, Low Cost Automated Genomic DNA Purification from Micro Samples
    WILLIAM MACCONNELL; Fiscal Year: 2007
    ..I is to demonstrate that the method can be universally applied to the purification of bacterial, mammalian, and plant DNA from a wide range of sample sizes...
  3. T-DNA INTEGRATION DURING CROWN GALL TUMORIGENESIS
    LLOYD REAM; Fiscal Year: 1991
    ..To examine the molecular mechanism by which T-DNA integrates into plant DNA, we will characterize changes that occur in host DNA during T-DNA integration...
  4. Rapid, Universal, Low Cost Automated Genomic DNA Purification from Micro Samples
    WILLIAM MACCONNELL; Fiscal Year: 2009
    ..process can be universally and reproducibility applied to the purification of bacterial, mammalian, and plant DNA from a wide range of sample sizes...
  5. DEVELOPMENT OF LARGE DNA METHODS FOR ARABIDOPSIS
    Joseph Ecker; Fiscal Year: 1991
    ..to this problem is to develop methods for the cloning and introduction into plant cells of large segments of plant DNA. These studies will involve the development of "large DNA" methods for chromosome walking, gene isolation and ..
  6. ANALYSIS OF A LIGHT-REGULATED DEVELOPMENT SWITCH
    Xing Wang Deng; Fiscal Year: 2003
    ..abstract_text> ..
  7. Expression of Human Therapeutic Proteins in Transgenic Tobacco Chloroplasts
    Henry Daniell; Fiscal Year: 2010
    ..Successful completion of these studies would make transgenic chloroplasts ideal bioreactors for the production of safe and less expensive therapeutic proteins and open the door for in depth studies of membrane proteins. ..
  8. Molecular Mechanisms of Genome Duplication
    ZENGJIAN CHEN; Fiscal Year: 2009
    ..abstract_text> ..
  9. First International Biocurator Meeting
    Seung Rhee; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable]..
  10. Functional Genomics of Nuclei
    David Galbraith; Fiscal Year: 2005
    ..Moreover, the constructs will be used to develop mouse lines from which investigators can perform the cell specific gene array studies, as well a studies of cell function within sections of living tissue. ..
  11. A Literature Curation Tool for Organism Databases
    Seung Rhee; Fiscal Year: 2003
    ..The system will be central to the curation efforts of the collaborating databases and will be useable as a whole or in parts by other existing or emerging MODs. ..
  12. Mathematical and Statistical Models for Nucleosome
    Ji Ping Wang; Fiscal Year: 2010
    ..5) Automate the developed tools and algorithms. ..
  13. The molecular basis of reproductive isolation
    STUART MCDANIEL; Fiscal Year: 2007
    ..The identification of molecular variants underlying complex traits, like reproductive isolation, opens several new avenues of research into the specific mechanisms of adaptation and speciation. [unreadable] [unreadable]..
  14. Plant Transposases and their MITEs
    Susan Wessler; Fiscal Year: 2007
    ..As such, knowledge of TE-mediated mechanisms of diversification are intimately involved in improving human health and understanding how plant and animal genomes evolve. ..
  15. Self recognition and signaling in plant reproduction
    JUNE NASRALLAH; Fiscal Year: 2005
    ..abstract_text> ..
  16. Comparative Genomics in the Enterobateriaceae
    Sandra Clifton; Fiscal Year: 2009
    ....
  17. Identification of Hypericum using Microscopy and DNA
    MATTHEW CIMINO; Fiscal Year: 2006
    ..Phase II aims are to expand the Phase I dataset for Hypericum and develop a working prototype assay for the detection, identification, and quantification for Hypericum species. [unreadable] [unreadable] [unreadable]..