Blake C Meyers

Summary

Affiliation: University of Delaware
Country: USA

Publications

  1. pmc Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant
    Kan Nobuta
    Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Proc Natl Acad Sci U S A 105:14958-63. 2008
  2. pmc Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing
    Venu Kalavacharla
    College of Agriculture and Related Sciences, Delaware State University, Dover, DE 19901, USA
    BMC Plant Biol 11:135. 2011
  3. pmc Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana
    Wanhui You
    Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
    BMC Plant Biol 12:51. 2012
  4. pmc Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses
    Kankshita Swaminathan
    Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Genome Biol 11:R12. 2010
  5. pmc Characterization of paralogous protein families in rice
    Haining Lin
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    BMC Plant Biol 8:18. 2008
  6. pmc Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis
    Xiaoping Tan
    The Genome Center, University of California, Davis, California 95616, USA
    BMC Plant Biol 7:56. 2007
  7. pmc Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures
    Alberto Iandolino
    Department of Plant Pathology and College of Agricultural and Environmental Sciences Genomics Facility, University of California, One Shields Avenue, Davis, CA 95616, USA
    BMC Plant Biol 8:53. 2008
  8. pmc Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods
    Malali Gowda
    Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA
    BMC Genomics 7:310. 2006
  9. pmc A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis
    Junfeng Chen
    School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    BMC Genomics 8:414. 2007
  10. pmc Prediction of novel miRNAs and associated target genes in Glycine max
    Trupti Joshi
    Digital Biology Laboratory, Computer Science Department and Christopher S, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
    BMC Bioinformatics 11:S14. 2010

Detail Information

Publications68

  1. pmc Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant
    Kan Nobuta
    Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Proc Natl Acad Sci U S A 105:14958-63. 2008
    ..The enrichment of miRNAs and loss of 24-nt heterochromatic siRNAs in mop1-1 should be advantageous for miRNA discovery as the maize genome becomes more fully sequenced...
  2. pmc Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing
    Venu Kalavacharla
    College of Agriculture and Related Sciences, Delaware State University, Dover, DE 19901, USA
    BMC Plant Biol 11:135. 2011
    ..However, the number and description of common bean sequences are very limited, which greatly inhibits genome and transcriptome research. Here we used 454 pyrosequencing to obtain a substantial transcriptome dataset for common bean...
  3. pmc Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana
    Wanhui You
    Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
    BMC Plant Biol 12:51. 2012
    ..Here we report on a group of atypical genes that display in their coding region a transposon-like methylation pattern, which is associated with gene silencing in sporophytic tissues...
  4. pmc Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses
    Kankshita Swaminathan
    Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Genome Biol 11:R12. 2010
    ..The essentially uncharacterized triploid genome (3n = 57, x = 19) of Mxg is likely critical for the rapid growth of this vegetatively propagated interspecific hybrid...
  5. pmc Characterization of paralogous protein families in rice
    Haining Lin
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    BMC Plant Biol 8:18. 2008
    ..This, coupled with other genetic events such as tandem duplications, has resulted in a substantial number of its genes, and resulting proteins, occurring in paralogous families...
  6. pmc Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis
    Xiaoping Tan
    The Genome Center, University of California, Davis, California 95616, USA
    BMC Plant Biol 7:56. 2007
    ..8% of all ORFs so far annotated in Arabidopsis ecotype Col-0. Despite their prevalence in the genome and functional importance, there was little information regarding expression of these genes...
  7. pmc Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures
    Alberto Iandolino
    Department of Plant Pathology and College of Agricultural and Environmental Sciences Genomics Facility, University of California, One Shields Avenue, Davis, CA 95616, USA
    BMC Plant Biol 8:53. 2008
    ..The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry...
  8. pmc Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods
    Malali Gowda
    Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA
    BMC Genomics 7:310. 2006
    ....
  9. pmc A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis
    Junfeng Chen
    School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    BMC Genomics 8:414. 2007
    ....
  10. pmc Prediction of novel miRNAs and associated target genes in Glycine max
    Trupti Joshi
    Digital Biology Laboratory, Computer Science Department and Christopher S, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
    BMC Bioinformatics 11:S14. 2010
    ..Many plant miRNAs play critical roles in nutrient homeostasis, developmental processes, abiotic stress and pathogen responses. Currently, only 70 miRNA have been identified in soybean...
  11. ncbi request reprint Evolving disease resistance genes
    Blake C Meyers
    Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19714, USA
    Curr Opin Plant Biol 8:129-34. 2005
    ..Diversity within populations is maintained by balancing selection. Analyses of whole-genome sequences have and will continue to provide new insight into the dynamics of resistance gene evolution...
  12. ncbi request reprint Sweating the small stuff: microRNA discovery in plants
    Blake C Meyers
    Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19714, USA
    Curr Opin Biotechnol 17:139-46. 2006
    ....
  13. pmc The use of MPSS for whole-genome transcriptional analysis in Arabidopsis
    Blake C Meyers
    Department of Plant and Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19714, USA
    Genome Res 14:1641-53. 2004
    ..More than 89% of the sum of the expressed signature abundances matched the Arabidopsis genome, and many of the unmatched signatures found in high abundances were predicted to match to previously uncharacterized transcripts...
  14. pmc Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments
    Kevin P McCormick
    Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Silence 2:2. 2011
    ..While our focus is on sRNA sequencing experiments, many of the principles discussed are applicable to the sequencing of other RNA populations...
  15. pmc Arabidopsis MPSS. An online resource for quantitative expression analysis
    Blake C Meyers
    Department of Plant and Soil Sciences, University of Delaware, Newark, USA
    Plant Physiol 135:801-13. 2004
  16. ncbi request reprint Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing
    Blake C Meyers
    Delaware Biotechnology Institute, 15 Innovation Way, University of Delaware, Newark, Delaware 19714, USA
    Nat Biotechnol 22:1006-11. 2004
    ..thaliana genes transcribed in these libraries. The MPSS expression data suggest that the A. thaliana transcriptome is complex and contains many as-yet uncharacterized variants of normal coding transcripts...
  17. pmc Methods for transcriptional profiling in plants. Be fruitful and replicate
    Blake C Meyers
    Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Plant Physiol 135:637-52. 2004
  18. pmc Criteria for annotation of plant MicroRNAs
    Blake C Meyers
    Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Plant Cell 20:3186-90. 2008
    ..Herein, we update the specific criteria required for the annotation of plant miRNAs, including experimental and computational data, as well as refinements to standard nomenclature...
  19. pmc Deep sequencing of chicken microRNAs
    Joan Burnside
    Department of Animal and Food Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    BMC Genomics 9:185. 2008
    ..We have applied this approach to the identification of chicken microRNAs and to the comparison of microRNAs in chicken embryo fibroblasts (CEF) infected with Marek's disease virus (MDV) to those present in uninfected CEF...
  20. pmc A spatial dissection of the Arabidopsis floral transcriptome by MPSS
    Jason A Peiffer
    Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
    BMC Plant Biol 8:43. 2008
    ....
  21. ncbi request reprint An expression atlas of rice mRNAs and small RNAs
    Kan Nobuta
    Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Nat Biotechnol 25:473-7. 2007
    ..Among these, numerous clusters of highly regulated small RNAs were readily observed. We developed a genome browser (http://mpss.udel.edu/rice) for public access to the transcriptional profiling data for this important crop...
  22. pmc Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage
    Dong Hoon Jeong
    Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711, USA
    Plant Cell 23:4185-207. 2011
    ..This high-resolution analysis of rice miRNAs should be relevant to plant miRNAs in general, particularly in the Poaceae...
  23. ncbi request reprint Elucidation of the small RNA component of the transcriptome
    Cheng Lu
    Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Science 309:1567-9. 2005
    ..Targets of antisense RNA or miRNA did not appear to be preferentially associated with siRNAs. Many genomic regions previously considered featureless were found to be sites of numerous small RNAs...
  24. pmc Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA
    Mayumi Nakano
    Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19714, USA
    Nucleic Acids Res 34:D731-5. 2006
    ..Interpretation of the small RNA MPSS data is facilitated by the inclusion of extensive repeat data in our genome viewer. All the data and the tools introduced in this article are available at http://mpss.udel.edu...
  25. doi request reprint Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends
    Marcelo A German
    Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Nat Biotechnol 26:941-6. 2008
    ..This versatile approach will affect the study of other aspects of RNA processing beyond miRNA-target RNA pairs...
  26. doi request reprint A microRNA of infectious laryngotracheitis virus can downregulate and direct cleavage of ICP4 mRNA
    Lisa A Waidner
    Elcriton, Inc 15 Innovation Way, Suite 288, Newark, DE 19711, USA
    Virology 411:25-31. 2011
    ..Thus, in this system, iltv-miR-I5 decreased ILTV ICP4 mRNA levels via transcript cleavage and degradation. Downregulation of ICP4 could impact the balance between the lytic and latent states of the virus in vivo...
  27. pmc Sequence conservation and differential expression of Marek's disease virus microRNAs
    Robin Morgan
    Department of Animal and Food Sciences, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
    J Virol 82:12213-20. 2008
    ..These data suggest that the meq cluster microRNAs play an important role in the pathogenicity of MDV...
  28. pmc Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus, Magnaporthe oryzae
    Vidhyavathi Raman
    Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
    BMC Genomics 14:326. 2013
    ..oryzae, and the degree to which these elements regulate fungal stress responses. To this end, we have characterized sRNAs under different physiological stress conditions, which had not yet been examined in this fungus...
  29. doi request reprint An integrated workflow for DNA methylation analysis
    Pingchuan Li
    Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    J Genet Genomics 40:249-60. 2013
    ..Our laboratory provides public access to plant DNA methylation data via visualization tools available at our "Next-Gen Sequence" websites (http://mpss.udel.edu), along with small RNA, RNA-seq and other data types...
  30. pmc RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats
    Tzuu Fen Lee
    Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
    Epigenetics 7:781-95. 2012
    ..RNAP V, along with RNAP IV and DRM1/2, may target and silence a set of small, intergenic transposable elements located in dispersed genomic regions for silencing. Silencing at these loci may be actively reinforced by RdDM...
  31. ncbi request reprint Construction of small RNA cDNA libraries for deep sequencing
    Cheng Lu
    Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Methods 43:110-7. 2007
    ..Here, we describe the methods used in our laboratory to construct small RNA cDNA libraries for high-throughput sequencing using technologies such as MPSS, 454 or SBS...
  32. ncbi request reprint Use of massively parallel signature sequencing to study genes expressed during the plant defense response
    Blake C Meyers
    Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, USA
    Methods Mol Biol 354:105-19. 2007
    ....
  33. ncbi request reprint Methods for analysis of gene expression in plants using MPSS
    Kan Nobuta
    Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
    Methods Mol Biol 406:387-408. 2007
    ..Here, we focus on a subset of these tools (e.g., Gene Analysis [GA], Chromosome Viewer [CV], and Library Analysis [LIBAN]) and describe how the users can analyze and interpret our MPSS expression data...
  34. pmc Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)
    Cheng Lu
    Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Proc Natl Acad Sci U S A 105:4951-6. 2008
    ..These findings suggest that other natural cis-antisense loci with similar exon-intron arrangements could be another source of miRNA genes...
  35. doi request reprint MicroRNAs of Gallid and Meleagrid herpesviruses show generally conserved genomic locations and are virus-specific
    Lisa A Waidner
    Department of Animal and Food Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Virology 388:128-36. 2009
    ..The prevalence of microRNAs in the genomic repeat regions as well as in local repeats suggests the importance of genetic plasticity in herpesviruses for microRNA evolution and preservation of function...
  36. pmc MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant
    Cheng Lu
    Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Genome Res 16:1276-88. 2006
    ..Deep sequencing of mutants provides a genetic approach for the dissection and characterization of diverse small RNA populations and the identification of low abundance miRNAs...
  37. pmc Comprehensive investigation of microRNAs enhanced by analysis of sequence variants, expression patterns, ARGONAUTE loading, and target cleavage
    Dong Hoon Jeong
    Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Plant Physiol 162:1225-45. 2013
    ....
  38. doi request reprint Bioinformatics analysis of small RNAs in plants using next generation sequencing technologies
    Kan Nobuta
    Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
    Methods Mol Biol 592:89-106. 2010
    ..Here, we describe the challenges and our strategies to handle the very large quantity of small RNA data generated by these next-generation sequencing technologies...
  39. doi request reprint Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome
    Marcelo A German
    Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Nat Protoc 4:356-62. 2009
    ..The data are then matched to cDNAs and analyzed through bioinformatics filters. We describe the high-throughput protocol in detail and indicate alternative uses for PARE. The procedure presented here can be accomplished in 6-7 d...
  40. pmc MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs
    Jixian Zhai
    Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19717, USA
    Genes Dev 25:2540-53. 2011
    ....
  41. doi request reprint Short-read sequencing technologies for transcriptional analyses
    Stacey A Simon
    Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Annu Rev Plant Biol 60:305-33. 2009
    ....
  42. pmc Plant microRNAs display differential 3' truncation and tailing modifications that are ARGONAUTE1 dependent and conserved across species
    Jixian Zhai
    Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Plant Cell 25:2417-28. 2013
    ..Our results showed AGO1-bound miRNAs are actively 3' truncated and tailed, possibly reflecting the activity of cofactors acting in conserved patterns in miRNA degradation. ..
  43. doi request reprint Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes
    Jia Xing Yue
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
    New Phytol 193:1049-63. 2012
    ....
  44. doi request reprint Computational methods for comparative analysis of plant small RNAs
    Gayathri Mahalingam
    Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
    Methods Mol Biol 592:163-81. 2010
    ..Here, we focus on these tools, and we describe how the users can implement these tools to analyze and interpret the small RNA data and how the users could use similar approaches for other sets of plant small RNAs from diverse species...
  45. doi request reprint MicroRNA processing: battle of the bulge
    Blake C Meyers
    Department of Plant and Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Curr Biol 20:R68-70. 2010
    ..Several recent analyses of plant microRNA precursors define the contributions of secondary structure to the precise positions at which processing of these precursors occurs...
  46. pmc Marek's disease virus encodes MicroRNAs that map to meq and the latency-associated transcript
    Joan Burnside
    Department of Animal and Food Sciences, University of Delaware, Newark, 19711, USA
    J Virol 80:8778-86. 2006
    ..We propose that the MDV miRNAs function to enable MDV pathogenesis and contribute to MDV-induced transformation of chicken T cells...
  47. doi request reprint Biogenesis and function of rice small RNAs from non-coding RNA precursors
    Siwaret Arikit
    Department of Plant and Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Curr Opin Plant Biol 16:170-9. 2013
    ..Although many small RNAs have been identified by deep sequencing in rice, their precise regulatory functions and cell-type specificity are in many cases still unknown...
  48. pmc The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum
    Keerthi P Venkataramanan
    Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
    BMC Genomics 14:849. 2013
    ....
  49. doi request reprint Small RNA-mediated epigenetic modifications in plants
    Stacey A Simon
    Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Curr Opin Plant Biol 14:148-55. 2011
    ..As the multiple layers of epigenetic regulation in plants are dissected, a more comprehensive understanding of the biological importance of epigenetic marks and states has been developed...
  50. pmc The role of TIR-NBS and TIR-X proteins in plant basal defense responses
    Raja Sekhar Nandety
    Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711, USA
    Plant Physiol 162:1459-72. 2013
    ....
  51. doi request reprint RNA-Seq reveals infection-related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew
    Sridhara G Kunjeti
    Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
    Mol Plant Pathol 13:454-66. 2012
    ..These results are discussed with respect to the differences and similarities in the pathogenicity mechanisms of P. phaseoli and P. infestans...
  52. ncbi request reprint Mapping and sequencing complex genomes: let's get physical!
    Blake C Meyers
    Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Nat Rev Genet 5:578-88. 2004
  53. pmc Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis
    Georg Haberer
    Munich Information Center for Protein Sequences, Institute for Bioinformatics, GSF Research Center for Environment and Health, 85758 Neuherberg, Germany
    Plant Physiol 136:3009-22. 2004
    ..Our work lays a foundation for future comparative studies to elucidate the molecular manifestation of regulatory similarities and dissimilarities of duplicated genes...
  54. doi request reprint Genome-wide identification of NBS resistance genes in Populus trichocarpa
    Annegret Kohler
    Unité Mixte de Recherche INRA UHP 1136 Interactions Arbres Microorganismes, Institut National de la Recherche Agronomique, Centre de Recherches de Nancy, 54280 Champenoux, France
    Plant Mol Biol 66:619-36. 2008
    ..The transcripts of only 34 NBS-LRR genes were detected in rust-infected and non-infected leaves using a whole-genome oligoarray. None showed an altered expression two days post inoculation...
  55. doi request reprint Discovery of ADP-ribosylation and other plant defense pathway elements through expression profiling of four different Arabidopsis-Pseudomonas R-avr interactions
    Lori Adams-Phillips
    Department of Plant Pathology, University of Wisconsin Madison, Madison, WI 53706, USA
    Mol Plant Microbe Interact 21:646-57. 2008
    ....
  56. doi request reprint Frequent sequence exchanges between homologs of RPP8 in Arabidopsis are not necessarily associated with genomic proximity
    Hanhui Kuang
    The Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Plant J 54:69-80. 2008
    ..Therefore, the differentiation of type I and type II RPP8 homologs seems to have occurred before speciation of A. thaliana, A. arenosa and A. lyrata...
  57. pmc The Rice Annotation Project Database (RAP-DB): 2008 update
    Tsuyoshi Tanaka
    National Institute of Agrobiological Sciences, Ibaraki 305 8602, Japan
    Nucleic Acids Res 36:D1028-33. 2008
    ..We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/...
  58. ncbi request reprint Divergence in expression between duplicated genes in Arabidopsis
    Eric W Ganko
    Department of Biology, University of North Carolina at Chapel Hill, USA
    Mol Biol Evol 24:2298-309. 2007
    ....
  59. pmc Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere
    Huihuang Yan
    Department of Horticulture, University of Wisconsin, Madison, 53706, USA
    Plant Cell 18:2123-33. 2006
    ..These results support the hypothesis that centromeres can evolve from gene-containing genomic regions...
  60. pmc Small RNA-directed epigenetic natural variation in Arabidopsis thaliana
    Jixian Zhai
    State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
    PLoS Genet 4:e1000056. 2008
    ..Methylation analysis revealed that 88% of the examined loci (37 out of 42) were specifically methylated in Ler but not Col, suggesting that small RNA can direct epigenetic differences between two closely related Arabidopsis ecotypes...
  61. pmc Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana
    Mariana Mondragon-Palomino
    Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92612, USA
    Genome Res 12:1305-15. 2002
    ..LRRs also contain substantial indel variation, suggesting elasticity in LRR length could also influence resistance specificity...
  62. pmc Multiple genetic processes result in heterogeneous rates of evolution within the major cluster disease resistance genes in lettuce
    Hanhui Kuang
    Department of Vegetable Crops, University of California, Davis, California 95616, USA
    Plant Cell 16:2870-94. 2004
    ..Unequal crossover, insertion/deletion, and point mutation events were distributed unequally through the gene. Different evolutionary forces have impacted different parts of the LRR...
  63. ncbi request reprint TIR-X and TIR-NBS proteins: two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomes
    Blake C Meyers
    Department of Vegetable Crops, University of California, Davis, CA 95616, USA
    Plant J 32:77-92. 2002
    ..These TX and TN proteins could be plant analogues of small TIR-adapter proteins that function in mammalian innate immune responses such as MyD88 and Mal...
  64. pmc Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis
    Blake C Meyers
    Department of Vegetable Crops, University of California, Davis, California 95616, USA
    Plant Cell 15:809-34. 2003
    ..The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges...
  65. ncbi request reprint Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata
    Stephen I Wright
    ICAPB, University of Edinburgh Ashworth Labs, Edinburgh, UK
    Mol Biol Evol 21:1719-26. 2004
    ....
  66. pmc Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression
    Stephen Rudd
    Munich Information Center for Protein Sequences Institute for Bioinformatics, GSF National Research Center for Environment and Health, 85764 Neuherberg, Germany
    Plant Physiol 135:715-22. 2004
    ..On the basis of a genome-wide in silico S/MAR analysis, we found a significant correlation between the presence of intragenic S/MARs and transcriptional down-regulation...
  67. ncbi request reprint hATpin, a family of MITE-like hAT mobile elements conserved in diverse plant species that forms highly stable secondary structures
    Santiago Moreno-Vázquez
    Departamento de Biologia Vegetal, E T S Ingenieros Agronomos, Universidad Politecnica de Madrid, Ciudad Universitaria, 28040, Madrid, Spain
    Plant Mol Biol 58:869-86. 2005
    ..This family of class II mobile elements is found primarily in monocot species, but is also present in dicot species...
  68. ncbi request reprint Dm3 is one member of a large constitutively expressed family of nucleotide binding site-leucine-rich repeat encoding genes
    Katherine A Shen
    Department of Vegetable Crops, University of California, Davis 95616, USA
    Mol Plant Microbe Interact 15:251-61. 2002
    ..In a wildtype Dm3-expressing genotype, many of the RGC2 family members are expressed at low levels throughout the plant...