Rod A Wing

Summary

Affiliation: University of Arizona
Country: USA

Publications

  1. pmc A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome
    Thais Rezende E Silva Figueira
    Centro de Biologia Molecular e Engenharia Genetica, Universidade Estadual de Campinas UNICAMP, Campinas, SP, 13083 875, Brazil
    BMC Res Notes 5:185. 2012
  2. pmc Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series
    Matthew W Blair
    CIAT International Center for Tropical Agriculture, Biotechnology Unit and Bean Project, AA6713, Cali, Valle, Colombia
    BMC Plant Biol 11:50. 2011
  3. pmc Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis
    Zhixi Tian
    Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
    BMC Genomics 12:142. 2011
  4. 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
  5. pmc A draft physical map of a D-genome cotton species (Gossypium raimondii)
    Lifeng Lin
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA
    BMC Genomics 11:395. 2010
  6. pmc Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum
    Barbara L Hass-Jacobus
    Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
    BMC Genomics 7:199. 2006
  7. ncbi request reprint The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species
    Rod A Wing
    Arizona Genomics Institute, The University of Arizona, Tucson, AZ, USA
    Plant Mol Biol 59:53-62. 2005
  8. pmc Physical and genetic structure of the maize genome reflects its complex evolutionary history
    Fusheng Wei
    Arizona Genomics Institute, University of Arizona, Tucson, Arizona, United States of America
    PLoS Genet 3:e123. 2007
  9. pmc Detailed analysis of a contiguous 22-Mb region of the maize genome
    Fusheng Wei
    Arizona Genomics Institute, School of Plant Sciences and Department of Ecology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
    PLoS Genet 5:e1000728. 2009
  10. pmc The physical and genetic framework of the maize B73 genome
    Fusheng Wei
    Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
    PLoS Genet 5:e1000715. 2009

Research Grants

Detail Information

Publications82

  1. pmc A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome
    Thais Rezende E Silva Figueira
    Centro de Biologia Molecular e Engenharia Genetica, Universidade Estadual de Campinas UNICAMP, Campinas, SP, 13083 875, Brazil
    BMC Res Notes 5:185. 2012
    ..The construction and sequencing of a bacterial artificial chromosome (BAC) library of an elite commercial variety of sugarcane could help assembly the sugarcane genome...
  2. pmc Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series
    Matthew W Blair
    CIAT International Center for Tropical Agriculture, Biotechnology Unit and Bean Project, AA6713, Cali, Valle, Colombia
    BMC Plant Biol 11:50. 2011
    ..The root libraries were made from high and low phosphorus treated plants...
  3. pmc Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis
    Zhixi Tian
    Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
    BMC Genomics 12:142. 2011
    ..However, the nature, timing, lineages and adaptation of local genomic rearrangement in closely related species (e.g., within a genus) and haplotype variation of genomic rearrangement within populations have not been well documented...
  4. 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
    ....
  5. pmc A draft physical map of a D-genome cotton species (Gossypium raimondii)
    Lifeng Lin
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA
    BMC Genomics 11:395. 2010
    ..Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor Gossypium raimondii for complete sequencing...
  6. pmc Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum
    Barbara L Hass-Jacobus
    Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
    BMC Genomics 7:199. 2006
    ..Similar studies were undertaken in Sorghum bicolor, a species which diverged from cultivated rice 40-50 million years ago...
  7. ncbi request reprint The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species
    Rod A Wing
    Arizona Genomics Institute, The University of Arizona, Tucson, AZ, USA
    Plant Mol Biol 59:53-62. 2005
    ..In this paper we describe our strategy to construct robust physical maps of all 12 rice species with an emphasis on the AA diploid O. nivara--thought to be the progenitor of modern cultivated rice...
  8. pmc Physical and genetic structure of the maize genome reflects its complex evolutionary history
    Fusheng Wei
    Arizona Genomics Institute, University of Arizona, Tucson, Arizona, United States of America
    PLoS Genet 3:e123. 2007
    ..Reconstructing the paleoethnobotany of the maize genome indicates that the progenitors of modern maize contained ten chromosomes...
  9. pmc Detailed analysis of a contiguous 22-Mb region of the maize genome
    Fusheng Wei
    Arizona Genomics Institute, School of Plant Sciences and Department of Ecology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
    PLoS Genet 5:e1000728. 2009
    ..Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses...
  10. pmc The physical and genetic framework of the maize B73 genome
    Fusheng Wei
    Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
    PLoS Genet 5:e1000715. 2009
    ..Finally we used all available physical, sequence, genetic, and optical data to generate a golden path (AGP) of chromosome-based pseudomolecules, herein referred to as the B73 Reference Genome Sequence version 1 (B73 RefGen_v1)...
  11. pmc Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains
    William Nelson
    Arizona Genomics Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
    BMC Genomics 9:621. 2008
    ..These libraries differ from other gene-rich datasets in having larger insert sizes, and the MSLL clones are designed to provide reads localized to "epigenetic boundaries" where methylation begins or ends...
  12. doi request reprint Comparative sequence analysis of the SALT OVERLY SENSITIVE1 orthologous region in Thellungiella halophila and Arabidopsis thaliana
    Gyoungju Nah
    Department of Plant Sciences, University of Arizona, Tucson, 85721 0036, USA
    Genomics 94:196-203. 2009
    ..thaliana SOS1 including 11 predicted transmembrane domains and a cyclic nucleotide-binding domain; however, different patterns of Simple Sequence Repeats were found within a 540-bp region upstream of SOS1 in the two species...
  13. ncbi request reprint Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza
    Jetty S S Ammiraju
    Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
    Plant J 52:342-51. 2007
    ..Finally we describe the recent evolutionary origin of Dasheng, a large retrotransposon derivative of the RWG family, specifically found in the A, B and C genome lineages of Oryza...
  14. pmc The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza
    Jetty S S Ammiraju
    Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721 USA
    Genome Res 16:140-7. 2006
    ....
  15. pmc A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure
    Andrea Zuccolo
    Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA
    Genome Biol 12:R48. 2011
    ..A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome...
  16. pmc Transposable element distribution, abundance and role in genome size variation in the genus Oryza
    Andrea Zuccolo
    Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
    BMC Evol Biol 7:152. 2007
    ....
  17. pmc Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave
    Marianyoly Ortiz
    Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, USA
    ISME J 8:478-91. 2014
    ..These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts. ..
  18. doi request reprint Species trees from highly incongruent gene trees in rice
    Karen A Cranston
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    Syst Biol 58:489-500. 2009
    ..Finally, we discuss the challenges of scaling these analyses for data sets with thousands of gene trees and extensive levels of missing data...
  19. pmc The 19 genomes of Drosophila: a BAC library resource for genus-wide and genome-scale comparative evolutionary research
    Xiang Song
    Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
    Genetics 187:1023-30. 2011
    ..1-42.9×). Further, we demonstrated the utility of this BAC resource for generating physical maps of targeted loci, refining draft sequence assemblies and identifying potential genomic rearrangements across the phylogeny...
  20. pmc Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set
    Jetty S S Ammiraju
    Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
    Plant Cell 20:3191-209. 2008
    ..Three cases of long-range structural variation (inversions/deletions) spanning several hundred kilobases were identified that contributed significantly to genome diversification...
  21. doi request reprint Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza
    Jetty S S Ammiraju
    Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USABiodiversity Synthesis Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USADepartment of Genetics, University of Georgia, Athens, GA 30602 7223, USAState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, ChinaDepartment of Agronomy, Purdue University, West Lafayette, IN 47907 2054, USADepartment of Horticulture, Michigan State University, East Lansing, MI 48823, USA
    Plant J 63:430-42. 2010
    ....
  22. pmc Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey
    Meizhong Luo
    Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
    BMC Genomics 7:106. 2006
    ....
  23. pmc The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice
    Chuanzhu Fan
    Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
    Mol Plant 1:839-50. 2008
    ....
  24. ncbi request reprint Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome
    Jetty S S Ammiraju
    Department of Plant Sciences and BIO5 Institute, Arizona Genomics Institute, The University of Arizona, Tucson, AZ 85721, USA
    Theor Appl Genet 111:1596-607. 2005
    ..Further sequencing of 12 of the gap-specific fosmid clones uncovered unique rice genome sequence that was not previously reported in the finished IRGSP sequence and emphasizes the need to complete finishing of the rice genome...
  25. doi request reprint Profiling bacterial diversity and taxonomic composition on speleothem surfaces in Kartchner Caverns, AZ
    Marianyoly Ortiz
    Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721 0038, USA
    Microb Ecol 65:371-83. 2013
    ....
  26. pmc Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza
    Hyeran Kim
    Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
    Genome Biol 9:R45. 2008
    ..sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date...
  27. pmc Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences
    Jianwei Zhang
    National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
    Bioinformatics 32:3058-3064. 2016
    ....
  28. ncbi request reprint Efficacy of clone fingerprinting methodologies
    William M Nelson
    Arizona Genomics Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
    Genomics 89:160-5. 2007
    ..Our data indicate that the five-enzyme method known as SNaPshot is the most effective and that the assembly can in fact be significantly improved with greater than 10x coverage...
  29. pmc Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type)
    Hyeran Kim
    Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USA
    Genetics 176:379-90. 2007
    ....
  30. doi request reprint Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza
    Bonnie L Hurwitz
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    Plant J 63:990-1003. 2010
    ..This catalog of confirmed SV in reference to O. sativa provides an entry point for future research in genome evolution, speciation, domestication and novel gene discovery...
  31. ncbi request reprint Utilization of a zebra finch BAC library to determine the structure of an avian androgen receptor genomic region
    Meizhong Luo
    Department of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721, USA
    Genomics 87:181-90. 2006
    ..Comparison of BAC end sequences and the whole BAC sequence with the chicken genome draft sequence showed a high degree of conserved synteny between the zebra finch and the chicken genome...
  32. ncbi request reprint Efficient insertional mutagenesis in rice using the maize En/Spm elements
    Chellian Santhosh Kumar
    Department of Plant Sciences, Life Sciences Addition 1002, University of California, Davis, 95616, USA
    Plant J 44:879-92. 2005
    ..Further, the efficacy of the non-invasive fluorescence-based selection system is promising for its application to other crops...
  33. pmc Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics
    Wenming Wang
    Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
    BMC Plant Biol 5:10. 2005
    ..Although the lycophytes occupy an important phylogenetic position for understanding the evolution of plants and their genomes, no genomic resources exist for this group of plants...
  34. ncbi request reprint An improved method for plant BAC library construction
    Meizhong Luo
    Department of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, AZ, USA
    Methods Mol Biol 236:3-20. 2003
    ..Here, we present the protocol used in our laboratory to construct BAC libraries...
  35. pmc Conservation and purifying selection of transcribed genes located in a rice centromere
    Chuanzhu Fan
    Arizona Genomics Institute, School of Plant Sciences, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    Plant Cell 23:2821-30. 2011
    ..This suggests that Oryza has a mechanism to maintain the fidelity and functionality of Cen8 genes, even when embedded in a sea of repetitive sequences and transposable elements...
  36. pmc Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors
    Patrick H Degnan
    Department of Ecology and Evolutionary Biology, Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721 USA
    Proc Natl Acad Sci U S A 106:9063-8. 2009
    ..The genome is also littered with mobile DNA, including phage-derived genes, plasmids, and insertion-sequence elements, highlighting its dynamic nature and the continued role horizontal gene transfer plays in shaping it...
  37. pmc A fruitful outcome to the papaya genome project
    Fusheng Wei
    Department of Plant Sciences and the Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721, USA
    Genome Biol 9:227. 2008
    ..The draft genome sequence of a transgenic virus-resistant papaya marks the first genome sequence of a commercially important transgenic crop plant...
  38. doi request reprint Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion
    Julie Jacquemin
    Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
    Mol Plant 7:642-56. 2014
    ..Hence, the lineage-specific expansions observed between Oryza species were partly driven by directional selection. ..
  39. pmc Construction, characterization, and preliminary BAC-end sequence analysis of a bacterial artificial chromosome library of the tea plant (Camellia sinensis)
    Jinke Lin
    School of Plant Sciences, Arizona Genomics Institute, The University of Arizona, Tucson AZ 85721, USA
    J Biomed Biotechnol 2011:476723. 2011
    ..93%-87.24%), followed by DNA retrotransposons (11.16%-11.69%). Additionally, we found 25 simple sequence repeats (SSRs) that could potentially be used as genetic markers...
  40. doi request reprint The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question
    Julie Jacquemin
    Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
    Curr Opin Plant Biol 16:147-56. 2013
    ..As wild Oryza populations are threatened by human activity and climate change, we also discuss the urgent need for sustainable in situ conservation of the genus...
  41. pmc Whole-genome validation of high-information-content fingerprinting
    William M Nelson
    Arizona Genomics Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, 85721, USA
    Plant Physiol 139:27-38. 2005
    ..Finally, repetitive bands are isolated, and their effect on the assembly is studied...
  42. ncbi request reprint Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing
    Tae Jin Yang
    Arizona Genomics Institute, Department of Plant Sciences, 303 Forbes Building, University of Arizona, Tucson, AZ 85721, USA
    Theor Appl Genet 107:652-60. 2003
    ..This method represents a useful way to close clone gaps and thus to complete the entire rice genome...
  43. doi request reprint Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3
    Derrick J Zwickl
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA, and Robert W Holley Center for Agriculture and Health, United States Department of Agriculture Agricultural Research Service, Ithaca, NY 14853, USA
    Syst Biol 63:645-59. 2014
    ..We discuss our findings in the context of well-established relationships in Oryza and continuing controversies regarding the domestication history of O. sativa...
  44. pmc Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids
    Hyun Jo Koo
    School of Plant Sciences and BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA
    BMC Plant Biol 13:27. 2013
    ..Despite their importance, relatively little is known regarding gene expression in the rhizomes of ginger and turmeric...
  45. pmc Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63
    Jianwei Zhang
    National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721 BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721
    Proc Natl Acad Sci U S A 113:E5163-71. 2016
    ..The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement. ..
  46. doi request reprint Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile
    Julia W Neilson
    Department of Soil, Water and Environmental Science, University of Arizona, Shantz Bldg Room 429, P O Box 210038, Tucson, AZ 85721 0038, USA
    Extremophiles 16:553-66. 2012
    ....
  47. ncbi request reprint Toward closing rice telomere gaps: mapping and sequence characterization of rice subtelomere regions
    Tae Jin Yang
    Brassica Genomics Team, National Institute of Agricultural Biotechnology, RDA, Suwon, 441 707, Korea
    Theor Appl Genet 111:467-78. 2005
    ....
  48. pmc Incongruent patterns of local and global genome size evolution in cotton
    Corrinne E Grover
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
    Genome Res 14:1474-82. 2004
    ....
  49. pmc Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana
    Takeshi Itoh
    Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305 8602, Japan
    Genome Res 17:175-83. 2007
    ..Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene...
  50. ncbi request reprint Comparison of peach and Arabidopsis genomic sequences: fragmentary conservation of gene neighborhoods
    Laura L Georgi
    Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, U S A
    Genome 46:268-76. 2003
    ..thaliana...
  51. pmc Genome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley
    Fusheng Wei
    Interdepartmental Genetics Program and Department of Plant Pathology, Iowa State University, Ames, IA 50011 1020, USA
    Plant Cell 14:1903-17. 2002
    ..We present a model for the evolution of the Mla region that encompasses several emerging features of large cereal genomes...
  52. pmc Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice
    Ning Jiang
    Departments of Plant Biology and Genetics, University of Georgia, Athens, GA 30602, USA
    Genetics 161:1293-305. 2002
    ..Taken together, Dasheng is one of the highest-copy-number LTR elements and one of the most recent elements to amplify in the rice genome...
  53. pmc MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea
    Stanton L Martin
    Fungal Genomics Laboratory, North Carolina State University, 840 Main Campus Drive, Suite 1200, Raleigh, NC 27606, USA
    Nucleic Acids Res 30:121-4. 2002
    ..grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm...
  54. pmc A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium)
    Junkang Rong
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genetics 166:389-417. 2004
    ..These data provide new insights into polyploid evolution and represent a foundation for assembly of a finished sequence of the cotton genome...
  55. doi request reprint A phylogenetic analysis of indel dynamics in the cotton genus
    Corrinne E Grover
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Iowa, USA
    Mol Biol Evol 25:1415-28. 2008
    ..Illegitimate recombination, although not demonstrated to be a dominant mechanism of genome size change, was biased in the polyploid toward deletions, which may provide a partial explanation of polyploid genomic downsizing...
  56. pmc Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium
    Jennifer S Hawkins
    Iowa State University, Department of Ecology, Evolution and Organismal Biology, Ames, Iowa 50011, USA
    Genome Res 16:1252-61. 2006
    ..Like maize, Gossypium has undergone a threefold increase in genome size due to the accumulation of LTR retrotransposons over the 5-10 Myr since its origin...
  57. pmc Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice
    Benoit Piegu
    Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS IRD, Universite de Perpignan, Perpignan 66860, France
    Genome Res 16:1262-9. 2006
    ..This provides direct evidence of retrotransposon-mediated variation of genome size within a plant genus...
  58. 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...
  59. ncbi request reprint Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium)
    Corrinne E Grover
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    Plant J 50:995-1006. 2007
    ..In conjunction with previous work, the data here confirm the conclusion that genome size evolution reflects many forces that collectively operate heterogeneously among genomic regions...
  60. pmc Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses
    John E Bowers
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 102:13206-11. 2005
    ..Bridging of 35 physical gaps in the rice sequence by sorghum BAC contigs illustrates reciprocal benefits of comparative approaches that extend at least across the cereals and perhaps beyond...
  61. pmc Evolutionary history and positional shift of a rice centromere
    Jianxin Ma
    Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
    Genetics 177:1217-20. 2007
    ..Our comparative genomics analysis indicates that Cen8 was formed at its current location at least 7-9 million years ago and was physically shifted by a more recent inversion of a segment spanning centromeric and pericentromeric regions...
  62. pmc Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species
    C Robin Buell
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 15:1284-91. 2005
    ....
  63. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  64. pmc Uneven chromosome contraction and expansion in the maize genome
    Remy Bruggmann
    Munich Information Center for Protein Sequences MIPS, Institute for Bioinformatics, GSF Research Center for Environment and Health, D 85764 Neuherberg, Germany
    Genome Res 16:1241-51. 2006
    ..In addition, no differences in methylation of single genes and tandemly repeated gene copies have been detected. These results, therefore, provide new insights into the diploidization of polyploid species...
  65. ncbi request reprint Plant centromere organization: a dynamic structure with conserved functions
    Jianxin Ma
    Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
    Trends Genet 23:134-9. 2007
    ..This review article focuses on the structural and evolutionary dynamics of plant centromere organization and the potential molecular mechanisms responsible for the rapid changes of centromeric components...
  66. ncbi request reprint Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza
    Anne Roulin
    Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS IRD Université de Perpignan, 52, Avenue Paul Alduy, 66860 Perpignan, France
    Plant J 53:950-9. 2008
    ..australiensis and seven other reproductively isolated Oryza species. This constitutes a new case of horizontal transfer in plants...
  67. pmc The Amborella genome: an evolutionary reference for plant biology
    Douglas E Soltis
    Department of Botany and the Genetics Institute, University of Florida, Gainesville, FL 32611, USA
    Genome Biol 9:402. 2008
    ..The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics...
  68. ncbi request reprint New resources for marine genomics: bacterial artificial chromosome libraries for the Eastern and Pacific oysters (Crassostrea virginica and C. gigas)
    Charles Cunningham
    Marine Biomedicine and Environmental Sciences Center and Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Hollings Marine Laboratory, Charleston, SC 29412, USA
    Mar Biotechnol (NY) 8:521-33. 2006
    ..Classical inheritance studies are needed to confirm the nature of these polymorphisms. The oyster BAC libraries are publicly available to the research community on a cost-recovery basis at (www.genome.clemson.edu)...
  69. pmc An integrated physical and genetic map of the rice genome
    Mingsheng Chen
    Clemson University Genomics Institute, 100 Jordan Hall, Clemson, South Carolina 29634 5727, USA
    Plant Cell 14:537-45. 2002
    ..Furthermore, the physical map will aid map-based cloning of agronomically important genes and will provide an important tool for the comparative analysis of grass genomes...
  70. pmc Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction
    Chatchawan Jantasuriyarat
    Department of Plant Pathology, The Ohio State University, Columbus, Ohio 43210, USA
    Plant Physiol 138:105-15. 2005
    ..The large cataloged collection of rice ESTs in this study provides a solid foundation for further characterization of the rice defense response and is a useful public genomic resource for rice functional genomics studies...
  71. ncbi request reprint Functional genomics of cell elongation in developing cotton fibers
    A Bulak Arpat
    Department of Agronomy and Range Science, University of California, One Shields Ave, CA, USA
    Plant Mol Biol 54:911-29. 2004
    ....
  72. pmc Structure and architecture of the maize genome
    Georg Haberer
    Munich Information Center for Protein Sequences, Institute for Bioinformatics, Gesellschaft für Strahlenforschung Research Center for Environment and Health, D 85764 Neuherberg, Germany
    Plant Physiol 139:1612-24. 2005
    ..Our results indicate that much of the increase in genome size of maize relative to rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) is attributable to an increase in number of both repetitive elements and genes...
  73. 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/...
  74. pmc Sequence composition and genome organization of maize
    Joachim Messing
    Plant Genome Initiative at Rutgers, Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
    Proc Natl Acad Sci U S A 101:14349-54. 2004
    ..Although the ancestor of maize arose by tetraploidization, fewer than half of the genes appear to be present in two orthologous copies, indicating that the maize genome has undergone significant gene loss since the duplication event...
  75. ncbi request reprint BAC end sequences and a physical map reveal transposable element content and clustering patterns in the genome of Magnaporthe grisea
    Michael R Thon
    Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh 27695 7251, USA
    Fungal Genet Biol 41:657-66. 2004
    ..This study illustrates the general utility of a physical map and BAC end sequences for the study of genome-wide repetitive DNA content and organization...
  76. ncbi request reprint Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers
    Zhukuan Cheng
    Department of Horticulture, University of Wisconsin Madison, 53706, USA
    Chromosome Res 10:379-87. 2002
    ..21 kb/microm among the seven BAC clones. Fiber-FISH results derived from a BAC contig that spanned 1 Mb DNA matched remarkably to the sequencing data, demonstrating the high resolution of this technique in cytological mapping...
  77. ncbi request reprint Rate variation among nuclear genes and the age of polyploidy in Gossypium
    David S Senchina
    Department of Botany, Iowa State University, USA
    Mol Biol Evol 20:633-43. 2003
    ..Using the mean synonymous substitution rate calculated across the 48 genes, allopolyploid cotton is estimated to have formed circa 1.5 million years ago (MYA), after divergence of the diploid progenitors about 6.7 MYA...
  78. ncbi request reprint In-depth sequence analysis of the tomato chromosome 12 centromeric region: identification of a large CAA block and characterization of pericentromere retrotranposons
    Tae Jin Yang
    Brassica Genomics Team, National Institute of Agricultural Biotechnology, RDA, Suwon 441 707, South Korea
    Chromosoma 114:103-17. 2005
    ..Five putative genes in the remaining 14% of the centromere region were identified, of which one is similar to a transcription regulator (ToCPL1) and a candidate jointless-2 gene...
  79. pmc Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor
    Martha T Hamblin
    Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
    Genetics 167:471-83. 2004
    ..Comparisons of polymorphism and divergence suggest that both directional and diversifying selection have played important roles in shaping variation in the sorghum genome...
  80. ncbi request reprint The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome
    Fred S Dietrich
    Biozentrum der Universitat Basel, Klingelbergstrasse 50, CH 4056 Basel, Switzerland
    Science 304:304-7. 2004
    ..cerevisiae included a whole genome duplication or fusion of two related species and showed, through inferred ancient gene orders, which of the duplicated genes lost one copy and which retained both copies...
  81. pmc A new resource for cereal genomics: 22K barley GeneChip comes of age
    Timothy J Close
    Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
    Plant Physiol 134:960-8. 2004
    ..We expect that this first generation array will accelerate hypothesis generation and gene discovery in disease defense pathways, responses to abiotic stresses, development, and evolutionary diversity in monocot plants...
  82. pmc Structural features of the rice chromosome 4 centromere
    Yu Zhang
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    Nucleic Acids Res 32:2023-30. 2004
    ..The presence of three intact retrotransposons in the centromere suggests that they may be responsible for functional centromere initiation through a transcription-mediated mechanism...

Research Grants1

  1. BAC Library Production /Distribuion for 'Healthy people
    Rod Wing; Fiscal Year: 2006
    ..abstract_text> ..