J F Wendel

Summary

Affiliation: Iowa State University
Country: USA

Publications

  1. pmc Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome
    Mi Jeong Yoo
    Department of Biology, University of Florida, Gainesville, Florida, United States of America
    PLoS Genet 10:e1004073. 2014
  2. pmc Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species
    Lei Gong
    Department of Ecology, Evolution and Organismal Biology, Iowa State University
    Genome Biol Evol 5:2449-59. 2013
  3. pmc Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence
    Simon Renny-Byfield
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
    Genome Biol Evol 6:559-71. 2014
  4. pmc Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton
    Armel Salmon
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    G3 (Bethesda) 2:921-30. 2012
  5. pmc Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton
    Lex E Flagel
    Department of Biology, Duke University, Durham, NC 27708, USA
    BMC Genomics 13:302. 2012
  6. pmc Spotted cotton oligonucleotide microarrays for gene expression analysis
    Joshua A Udall
    Department of Plant and Animal Sciences, Brigham Young University, Provo, UT 84062, USA
    BMC Genomics 8:81. 2007
  7. 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
  8. pmc Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium)
    Bhupendra Chaudhary
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
    BMC Genomics 10:378. 2009
  9. pmc Genomic expression dominance in allopolyploids
    Ryan A Rapp
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50010, USA
    BMC Biol 7:18. 2009
  10. pmc Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution
    Lex Flagel
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    BMC Biol 6:16. 2008

Collaborators

Detail Information

Publications58

  1. pmc Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome
    Mi Jeong Yoo
    Department of Biology, University of Florida, Gainesville, Florida, United States of America
    PLoS Genet 10:e1004073. 2014
    ....
  2. pmc Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species
    Lei Gong
    Department of Ecology, Evolution and Organismal Biology, Iowa State University
    Genome Biol Evol 5:2449-59. 2013
    ..A complex correlated expression pattern of microRNA target genes with their controlling microRNAs indicates that possible functional divergence of conserved microRNA families can also exist even within a single plant genus...
  3. pmc Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence
    Simon Renny-Byfield
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
    Genome Biol Evol 6:559-71. 2014
    ..These data indicate massive, near-complete expression level neo- and/or subfunctionalization among ancient gene duplicates, suggesting these processes are essential in their maintenance over ∼ 60 Ma...
  4. pmc Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton
    Armel Salmon
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    G3 (Bethesda) 2:921-30. 2012
    ..The approach used here is general, scalable, and may be adapted for many different research inquiries involving polyploid plant genomes...
  5. pmc Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton
    Lex E Flagel
    Department of Biology, Duke University, Durham, NC 27708, USA
    BMC Genomics 13:302. 2012
    ..In this paper we present a comprehensive EST assembly derived from diploid and model allotetraploid cottons and demonstrate several evolutionary inferences regarding genic evolution that can be drawn from these data...
  6. pmc Spotted cotton oligonucleotide microarrays for gene expression analysis
    Joshua A Udall
    Department of Plant and Animal Sciences, Brigham Young University, Provo, UT 84062, USA
    BMC Genomics 8:81. 2007
    ..Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species...
  7. 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...
  8. pmc Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium)
    Bhupendra Chaudhary
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
    BMC Genomics 10:378. 2009
    ..To study the evolution of oxidative stress related genes in a single plant cell, we conducted comparative expression profiling analyses of the elongated seed trichomes ("fibers") of cotton (Gossypium), using a phylogenetic approach...
  9. pmc Genomic expression dominance in allopolyploids
    Ryan A Rapp
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50010, USA
    BMC Biol 7:18. 2009
    ..Here we describe global patterns of gene expression accompanying genomic merger and doubling in inter-specific crosses in the cotton genus (Gossypium L.)...
  10. pmc Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution
    Lex Flagel
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    BMC Biol 6:16. 2008
    ..Owing to this redundancy, these genomes can play host to an array of evolutionary processes that act on duplicate genes...
  11. pmc Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication
    Ryan A Rapp
    Department of Ecology, 251 Bessey Hall, Iowa State University, Ames, IA 50011, USA
    BMC Biol 8:139. 2010
    ....
  12. ncbi request reprint Genome evolution in polyploids
    J F Wendel
    Department of Botany, Iowa State University, Ames 50011, USA
    Plant Mol Biol 42:225-49. 2000
    ....
  13. ncbi request reprint Feast and famine in plant genomes
    Jonathan F Wendel
    Department of Botany, Iowa State University, Ames 50011, USA
    Genetica 115:37-47. 2002
    ..Moreover, the research sets the stage for fine-scale analysis of the evolutionary dynamics and directionality of change for the full spectrum of genomic constituents...
  14. pmc Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium)
    R L Small
    Department of Botany, University of Tennessee, Knoxville, Tennessee 37996, USA
    Genetics 155:1913-26. 2000
    ..We suggest that dynamic fluctuation in copy number will prove common for nuclear genes, and we discuss the implications of this perspective for inferences of orthology and functional evolution...
  15. ncbi request reprint Phylogeny, duplication, and intraspecific variation of Adh sequences in New World diploid cottons (Gossypium l., malvaceae)
    R L Small
    Department of Botany, Iowa State University, Iowa, Ames, 50011, USA
    Mol Phylogenet Evol 16:73-84. 2000
    ..Potential explanations for this latter phenomenon, including gene duplication, gene flow, and lineage sorting, are discussed...
  16. ncbi request reprint Polyploid formation in cotton is not accompanied by rapid genomic changes
    B Liu
    Department of Botany, Iowa State University, Ames 50011, USA
    Genome 44:321-30. 2001
    ..These contrasts indicate polyploid speciation in plants is accompanied by a diverse array of molecular evolutionary phenomena, which will vary among both genomic constituents and taxa...
  17. doi request reprint Homoeologous nonreciprocal recombination in polyploid cotton
    Armel Salmon
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    New Phytol 186:123-34. 2010
    ..In addition, some genomic regions show multiple patterns of homoeologous recombination among species...
  18. doi request reprint Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation
    Lex E Flagel
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    New Phytol 186:184-93. 2010
    ....
  19. ncbi request reprint Evolution and expression of MYB genes in diploid and polyploid cotton
    M L Cedroni
    Departament of Botany, Iowa State University, Ames, IA 50011, USA
    Plant Mol Biol 51:313-25. 2003
    ..However, the duplicated copies of MYB1 in the tetraploid are not expressed at equal levels or equivalently in all organs, suggesting possible functional differentiation...
  20. pmc Homoeolog expression bias and expression level dominance in allopolyploid cotton
    M J Yoo
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    Heredity (Edinb) 110:171-80. 2013
    ..These observations suggest that natural selection reconciles the regulatory mismatches caused by initial genomic merger, while new gene expression conditions are generated for evaluation by selection...
  21. ncbi request reprint Ribosomal ITS sequences and plant phylogenetic inference
    I Alvarez
    Department of Botany, Iowa State University, Ames, IA 50011, USA
    Mol Phylogenet Evol 29:417-34. 2003
    ..It is suggested that more robust insights are likely to emerge from the use of single-copy or low-copy nuclear genes...
  22. doi request reprint Coordinated and fine-scale control of homoeologous gene expression in allotetraploid cotton
    Lex E Flagel
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    J Hered 100:487-90. 2009
    ..Furthermore, these results suggest that both large- and small-scale regulatory mechanisms may control homoeolog expression patterns...
  23. 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...
  24. pmc Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton
    Ran Hovav
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
    Genetics 179:1725-33. 2008
    ..hirsutum and G. barbadense, leading to convergent rather than parallel genetic alterations and resulting morphology...
  25. pmc Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant
    Ran Hovav
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    Proc Natl Acad Sci U S A 105:6191-5. 2008
    ..Evidence suggests, however, that domestication may increase expression bias in fibers toward the D genome, potentially implicating D-genome recruitment under human selection during domestication...
  26. ncbi request reprint A majority of cotton genes are expressed in single-celled fiber
    Ran Hovav
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    Planta 227:319-29. 2008
    ..Genes implicated in vesicle coating and trafficking were found to be overexpressed throughout all stages of fiber development studied, indicating their important role in maintaining rapid growth of this unique plant cell...
  27. pmc A novel approach for characterizing expression levels of genes duplicated by polyploidy
    Joshua A Udall
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Iowa 50011, USA
    Genetics 173:1823-7. 2006
    ..These results demonstrate that relative expression levels of homeologous genes may be measured by microarrays and that deviation from equal expression levels of homeologous loci may be common in the allotetraploid nucleus of Gossypium...
  28. pmc A global assembly of cotton ESTs
    Joshua A Udall
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
    Genome Res 16:441-50. 2006
    ..The assembly and associated information provide a framework for future investigation of cotton functional and evolutionary genomics...
  29. ncbi request reprint Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium)
    Randall L Small
    Department of Botany, 437 Hesler Biology, The University of Tennessee, Knoxville, TN 37996 1100, USA
    Mol Biol Evol 19:597-607. 2002
    ..These observations indicate that for these two pairs of Adh loci, the null hypothesis of equivalent evolutionary dynamics for duplicated genes in allotetraploid cotton is rejected...
  30. 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...
  31. 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
    ....
  32. 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...
  33. doi request reprint The history and disposition of transposable elements in polyploid Gossypium
    Guanjing Hu
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    Genome 53:599-607. 2010
    ..Further, we provide evidence for present-day transcription of LINEs, a relatively minor component of Gossypium genomes, whereas the more abundant LTR retrotransposons display limited expression and only under stressed conditions...
  34. ncbi request reprint Comparative development of fiber in wild and cultivated cotton
    W L Applequist
    Botany Department, Iowa State University, Ames 50011-1020, USA
    Evol Dev 3:3-17. 2001
    ....
  35. pmc Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants
    Jennifer S Hawkins
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    Proc Natl Acad Sci U S A 106:17811-6. 2009
    ..These data indicate that rates of DNA loss can be highly variable even within a single plant genus, and that the known mechanisms of DNA loss can indeed reverse the march toward genomic obesity...
  36. ncbi 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...
  37. 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...
  38. doi request reprint Phylogenetic determination of the pace of transposable element proliferation in plants: copia and LINE-like elements in Gossypium
    Jennifer S Hawkins
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    Genome 51:11-8. 2008
    ..Interestingly, the magnitude of transpositional bursts in each lineage corresponds directly with extant estimated copy number...
  39. doi request reprint Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense
    Bhupendra Chaudhary
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    Evol Dev 10:567-82. 2008
    ....
  40. pmc Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid
    Keith L Adams
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
    Genetics 168:2217-26. 2004
    ..These results provide a detailed portrayal of gene silencing events that can occur following allopolyploidization and suggest epigenetic causal factors...
  41. ncbi request reprint Tobacco genomes quickly go up in smoke
    Corrinne E Grover
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    New Phytol 175:599-602. 2007
  42. doi request reprint Gene duplication and evolutionary novelty in plants
    Lex E Flagel
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    New Phytol 183:557-64. 2009
    ..We also highlight several recent and pertinent examples from the literature. These examples demonstrate the importance of the functional characteristics of genes and the source of duplication in influencing evolutionary outcome...
  43. ncbi request reprint Epigenetics and plant evolution
    Ryan A Rapp
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
    New Phytol 168:81-91. 2005
    ....
  44. ncbi request reprint Novel patterns of gene expression in polyploid plants
    Keith L Adams
    UBC Botanical Garden and Centre for Plant Research, 2357 Main Mall, MacMillan Building, University of British Columbia, Vancouver, British Colombia, Canada, V6T 1Z4
    Trends Genet 21:539-43. 2005
    ..Three recent reports have provided intriguing new insights into the patterns, timing and mechanisms of gene expression changes that accompany polyploidy in plants...
  45. 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...
  46. ncbi request reprint Polyploidy and genome evolution in plants
    Keith L Adams
    UBC Botanical Garden and Centre for Plant Research, MacMillan Building, 2357 Main Mall, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
    Curr Opin Plant Biol 8:135-41. 2005
    ..Polyploidy has extensive effects on gene expression, with gene silencing accompanying polyploid formation and continuing over evolutionary time...
  47. pmc Allele-specific, bidirectional silencing of an alcohol dehydrogenase gene in different organs of interspecific diploid cotton hybrids
    Keith L Adams
    UBC Botanical Garden, Centre for Plant Research and Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    Genetics 171:2139-42. 2005
    ..These results show that developmental regulation of gene expression is changed immediately upon hybridization between diploid species, possibly due to epigenetic factors or regulatory mismatch...
  48. pmc Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development
    Junkang Rong
    Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA
    Genetics 176:2577-88. 2007
    ..Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks...
  49. pmc The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism
    Ran Hovav
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, United States of America
    PLoS Genet 4:e25. 2008
    ..Our data suggest a model for the evolutionary origin of a novel morphology through differential gene regulation causing prolongation of an ancestral developmental program...
  50. ncbi request reprint Cryptic interspecific introgression and genetic differentiation within Gossypium aridum (Malvaceae) and its relatives
    Ines Alvarez
    Real Jardín Botánico de Madrid, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
    Evolution 60:505-17. 2006
    ..We suggest that cryptic and seemingly improbable interspecific introgression and molecular differentiation may be more common than appreciated in angiosperm evolution...
  51. ncbi request reprint Cryptic repeated genomic recombination during speciation in Gossypium gossypioides
    Richard Cronn
    Pacific Northwest Research Station, USDA Forest Service, 3200 SW Jefferson Way, Corvallis, Oregon 97331, USA
    Evolution 57:2475-89. 2003
    ..Gossypium gossypioides provides a striking example of the previously unsuspected chimeric nature of some plant genomes and the resulting phylogenetic complexity produced by multiple historical reticulation events...
  52. ncbi request reprint Intron size and genome size in plants
    Jonathan F Wendel
    Mol Biol Evol 19:2346-52. 2002
  53. pmc Toward sequencing cotton (Gossypium) genomes
    Z Jeffrey Chen
    Plant Physiol 145:1303-10. 2007
  54. ncbi request reprint Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae)
    Armel Salmon
    UMR 118 INRA Agrocampus Rennes, Amelioration des Plantes et Biotechnologies Vegetales, Station de Génétique et Amélioration des Plantes, F 35653 Le Rheu, France
    Mol Ecol 14:1163-75. 2005
    ..Hybridization rather than genome doubling seems to have triggered most of the methylation changes observed in Spartina anglica...
  55. ncbi request reprint Genetic mapping of a cross between Gossypium hirsutum (cotton) and the Hawaiian endemic, Gossypium tomentosum
    Vijay N Waghmare
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Theor Appl Genet 111:665-76. 2005
    ....
  56. ncbi request reprint Genetic mapping and comparative analysis of seven mutants related to seed fiber development in cotton
    Junkang Rong
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Theor Appl Genet 111:1137-46. 2005
    ..Increasing knowledge of the correspondence of the cotton and Arabidopsis genomes provides several avenues by which genetic dissection of cotton fiber development may be accelerated...
  57. ncbi request reprint Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.)
    Anna L Keyte
    Department of Biology, Duke University, Durham, NC 27710, USA
    J Hered 97:444-50. 2006
    ..We speculate that biased correlation of methylation-polymorphic sites and genes in cotton may be a consequence of polyploidy and the attendant doubling of all genes...
  58. ncbi request reprint Epigenetic phenomena and the evolution of plant allopolyploids
    Bao Liu
    Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
    Mol Phylogenet Evol 29:365-79. 2003
    ..It is likely that the evolutionary success of allopolyploidy is in part attributable to epigenetic phenomena that we are only just beginning to understand...