John E Carlson

Summary

Affiliation: Pennsylvania State University
Country: USA

Publications

  1. 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
  2. pmc Floral gene resources from basal angiosperms for comparative genomics research
    Victor A Albert
    Natural History Museum, University of Oslo, NO 0318 Oslo, Norway
    BMC Plant Biol 5:5. 2005
  3. 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
  4. pmc Conservation and divergence of microRNAs in Populus
    Abdelali Barakat
    Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, 403 Life Sciences Building, The Pennsylvania State University, University Park, PA 16802, USA
    BMC Genomics 8:481. 2007
  5. pmc Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids
    Zhengqiu Cai
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX 78712, USA
    BMC Evol Biol 6:77. 2006
  6. ncbi request reprint EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot
    John E Carlson
    The School of Forest Resources and Huck Institutes for Life Sciences, Pennsylvania State University, 323 Forest Resources Building, University Park, 16802, USA
    Plant Mol Biol 62:351-69. 2006
  7. pmc Phylogeny and expression profiling of CAD and CAD-like genes in hybrid Populus (P. deltoides x P. nigra): evidence from herbivore damage for subfunctionalization and functional divergence
    Abdelali Barakat
    The School of Forest Resources, and The Huck Institutes of the Life Sciences, Pennsylvania State University, 324 Forest Resources Building, University Park, PA 16802, USA
    BMC Plant Biol 10:100. 2010
  8. pmc Chestnut resistance to the blight disease: insights from transcriptome analysis
    Abdelali Barakat
    The School of Forest Resources, and The Huck Institutes of the Life Sciences, Pennsylvania State University, 326 Forest Resources Building, University Park, PA 16802, USA
    BMC Plant Biol 12:38. 2012
  9. pmc Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection
    Abdelali Barakat
    The School of Forest Resources, Department of Horticulture, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
    BMC Plant Biol 9:51. 2009
  10. pmc The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression
    Abdelali Barakat
    The School of Forest Resources, The Huck Institutes of the Life Sciences, Pennsylvania State University, 324 Forest Resources Building, University Park, PA 16802, USA
    BMC Plant Biol 9:26. 2009

Collaborators

Detail Information

Publications23

  1. 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...
  2. pmc Floral gene resources from basal angiosperms for comparative genomics research
    Victor A Albert
    Natural History Museum, University of Oslo, NO 0318 Oslo, Norway
    BMC Plant Biol 5:5. 2005
    ....
  3. 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...
  4. pmc Conservation and divergence of microRNAs in Populus
    Abdelali Barakat
    Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, 403 Life Sciences Building, The Pennsylvania State University, University Park, PA 16802, USA
    BMC Genomics 8:481. 2007
    ..In this study, we analyzed expressed small RNAs from leaves and vegetative buds of Populus using high throughput pyrosequencing...
  5. pmc Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids
    Zhengqiu Cai
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX 78712, USA
    BMC Evol Biol 6:77. 2006
    ....
  6. ncbi request reprint EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot
    John E Carlson
    The School of Forest Resources and Huck Institutes for Life Sciences, Pennsylvania State University, 323 Forest Resources Building, University Park, 16802, USA
    Plant Mol Biol 62:351-69. 2006
    ....
  7. pmc Phylogeny and expression profiling of CAD and CAD-like genes in hybrid Populus (P. deltoides x P. nigra): evidence from herbivore damage for subfunctionalization and functional divergence
    Abdelali Barakat
    The School of Forest Resources, and The Huck Institutes of the Life Sciences, Pennsylvania State University, 324 Forest Resources Building, University Park, PA 16802, USA
    BMC Plant Biol 10:100. 2010
    ..Expression of CAD/CAD-like genes in Populus tissues (xylem, leaves, and barks) was analyzed in herbivore-treated and non-treated plants by real time quantitative RT-PCR...
  8. pmc Chestnut resistance to the blight disease: insights from transcriptome analysis
    Abdelali Barakat
    The School of Forest Resources, and The Huck Institutes of the Life Sciences, Pennsylvania State University, 326 Forest Resources Building, University Park, PA 16802, USA
    BMC Plant Biol 12:38. 2012
    ....
  9. pmc Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection
    Abdelali Barakat
    The School of Forest Resources, Department of Horticulture, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
    BMC Plant Biol 9:51. 2009
    ....
  10. pmc The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression
    Abdelali Barakat
    The School of Forest Resources, The Huck Institutes of the Life Sciences, Pennsylvania State University, 324 Forest Resources Building, University Park, PA 16802, USA
    BMC Plant Biol 9:26. 2009
    ..This is the first comprehensive study on the CAD gene family in woody plants including genome organization, gene structure, phylogeny across land plant lineages, and expression profiling in Populus...
  11. doi request reprint Comparison of gene order of GIGANTEA loci in yellow-poplar, monocots, and eudicots
    Haiying Liang
    School of Forest Resources and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
    Genome 53:533-44. 2010
    ..In addition, evidence for transposition and large insertions and duplications was found, suggesting multiple and complex mechanisms of basal angiosperm genome evolution...
  12. doi request reprint Comparative genomics and evolutionary analyses of the O-methyltransferase gene family in Populus
    Abdelali Barakat
    The School of Forest Resources and The Huck Institutes of the Life Sciences, The Pennsylvania State University, 326 Forest Resources Building, University Park, PA 16802, USA
    Gene 479:37-46. 2011
    ..The divergence of protein sequences, the phylogenetic distribution, and the expression of COMT and COMT-like genes suggest that they have evolved different functions or tissue specificities following duplications...
  13. ncbi request reprint Within-plant signalling via volatiles overcomes vascular constraints on systemic signalling and primes responses against herbivores
    Christopher J Frost
    Center for Chemical Ecology, Pennsylvania State University, University Park, PA 16802, USA
    Ecol Lett 10:490-8. 2007
    ....
  14. ncbi request reprint Isolation of ESTs from cacao (Theobroma cacao L.) leaves treated with inducers of the defense response
    Joseph A Verica
    Department of Horticulture, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA 16802, USA
    Plant Cell Rep 23:404-13. 2004
    ..Additionally, we investigated gene activation by a phytotoxic elicitor-like protein, Nep1. We have identified a unigene set of 1,256 members, including 330 members representing genes induced during the defense response...
  15. ncbi request reprint Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants
    Abdelali Barakat
    Department of Biology, Institute of Molecular Evolutionary Genetics, 403 Life Sciences Building, The Pennsylvania State University, University Park, PA 16802, USA
    Plant J 51:991-1003. 2007
    ....
  16. pmc Plant defense priming against herbivores: getting ready for a different battle
    Christopher J Frost
    Center for Chemical Ecology, Pennsylvania State University, University Park, PA 16802, USA
    Plant Physiol 146:818-24. 2008
  17. pmc Comparison of next generation sequencing technologies for transcriptome characterization
    P Kerr Wall
    Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
    BMC Genomics 10:347. 2009
    ..19). We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica) and the magnoliid avocado (Persea americana) using a variety of methods for cDNA synthesis...
  18. doi request reprint Priming defense genes and metabolites in hybrid poplar by the green leaf volatile cis-3-hexenyl acetate
    Christopher J Frost
    Center for Chemical Ecology, Pennsylvania State University, University Park, PA 16802, USA
    New Phytol 180:722-34. 2008
    ..Thus, woody plants can detect and use z3HAC as a signal to prime defenses before actually experiencing damage. GLVs may therefore have important ecological functions in arboreal ecosystems...
  19. doi request reprint Microbial community profiling to investigate transmission of bacteria between life stages of the wood-boring beetle, Anoplophora glabripennis
    Scott M Geib
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Microb Ecol 58:199-211. 2009
    ....
  20. pmc Lignin degradation in wood-feeding insects
    Scott M Geib
    Department of Entomology and Center for Chemical Ecology, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 105:12932-7. 2008
    ..This is a soft-rot fungus that may be contributing to wood degradation. These results transform our understanding of lignin degradation by wood-feeding insects...
  21. ncbi request reprint Evidence for oxidative stress in sugar maple stands growing on acidic, nutrient imbalanced forest soils
    Samuel B St Clair
    Intercollegiate Graduate Program in Ecological and Molecular Plant Physiology, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
    Oecologia 145:258-69. 2005
    ....
  22. pmc Widespread genome duplications throughout the history of flowering plants
    Liying Cui
    Department of Biology, The Pennsylvania State University, University Park 16802, USA
    Genome Res 16:738-49. 2006
    ..We hypothesize that evidence of an ancient duplication observed in the Nuphar data may represent a genome duplication in the common ancestor of all or most extant angiosperms, except Amborella...
  23. 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...