John E. Carlson, Ph.D.

Academic Interests:

Research, education and technology transfer in forest genetics, genomics and plant biotechnology.

Courses Taught:

FOR/WFS430 "Conservation Biology"
FOR496 "Honors/Independent Research"
FOR530 "Conservation Genetics"
IBIOS597G "Plant Genomics"
PLBIO513 "Plant Communication and Growth Regulation"

Recent Research/Educational Projects:

Genomics  We study the organization of genes and genomes in trees through genetic linkage mapping, genome sequencing and molecular cytogenetics.  In collaboration with tree breeders, we are identifying genes, DNA markers and quantitative trait loci that govern growth, stress resistance, and wood quality in important forest trees  such as chestnuts, oaks and other hardwood species.

Molecular analysis of genetic diversity in forests Genetic diversity among natural populations forms the foundation for biodiversity.  We use DNA markers in the nuclear, mitochondrial and chloroplast genomes to study genetic variability within and among populations of forest trees and associated wildlife.  We wish to better understand and conserve the various genetic mechanisms that species have evolved to adapt to their natural surroundings.

Environmental tree biotechnology Research is being conducted on the molecular basis of lignin synthesis and the response of trees to environmental stresses such as pollutants.  This may lead to improved genotypes of trees for environmentally friendly pulp and paper production and for use in remediation of contaminated soils.

Selected Publications:

Barakat A, Yassin NBM, Park J, Choi A, Herr J, Carlson JE. 2011. Comparative and phylogenomic analyses of cinnamoyl-CoA reductase and cinnamoyl-CoA-reductase-like gene family in land plants. Plant Science, 181: 249-257.

Hsu C-Y, Adams JP, Kim H, No K, Ma C, Strauss SH, Drnevich J, Vandervelde L, Ellis JD, Rice BM, Wickett N, Gunter LE, Tuskan GA, Brunner AM, Page GP, Barakat A, Carlson JE, dePamphilis CW, Luthe DS, Yuceer C. 2011. FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar, PNAS 108(26): 10756–10761. 

Barakat A, Choi A, Yassin NBM, Sun Z, Carlson JE. 2011. Comparative genomics and evolutionary analyses of the O-methyltransferase gene family in Populus. Gene 479(1-2): 37-46.

Liang H, Barakat A, Schlarbaum SE, Carlson JE. 2011. Organization of the chromosome region harboring a FLORICAULA/LEAFY gene in Liriodendron. Tree Genetics & Genomes 7(2): 373-384.

Argout, et al.  2011.  The genome of Theobroma cacao L.  Nature Genetics 43: 101–109.

Barakat A, Bagniewska-Zadworna A, Frost CJ, Carlson JE. 2010. 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.  BMC Plant Biology 10:100

Liang H, Barakat A, Schlarbaum SE, Mandoli DF, Carlson J. 2010. Comparison of gene order of GIGANTEA loci in yellow-poplar, monocots and eudicots. GENOME 53: 533 – 544.

Tiburcio RA, Costa GGL, Carazzolle MF, Mondego GMC, Schuster SC; Carlson JE, Guiltinan MJ, Bailey BA, Mieckowski P, Meinhardt LW, Pereira, GAG. 2010. Genes acquired by horizontal transfer are potentially involved in the evolution of phytopathogenicity in Moniliophthora perniciosa and Moniliophthora roreri, two of the major pathogens of cacao.  Journal of Molecular Evolution, 70:85–97.

Wall PK, LeebensMack J, Chanderbali A, Barakat A, Liang H, Landherr L, Tomsho LP, Hu Y, Carlson JE, Ma H, Schuster S, Soltis DE, Soltis PS, Altman N, dePamphilis CW. 2009.  Comparison of next generation sequencing technologies for transcriptome characterization.  BMC Genomics, 10:347. 19 pages.

Barakat A, DiLoreto DS, Zhang Y, Smith C, Baier K, Powell W, Wheeler N, Sederoff R, Carlson. JE  2009. Comparison of transcriptome from cankers and healthy stems in American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima). BMC Plant Biology, 9:51.  11 pages.  

Geib SM, del Mar Jimenez-Gasco M, Carlson JE, Tien M, Hoover K. 2009. Effect of host tree species on cellulase activity and bacterial community composition in the gut of larval Anoplophora glabripennis. Environmental Entomology 38: 686-699.

Barakat A, Bagniewska-Zadworna A, Plakkat U, Choi A, DiLoreto DS, Carlson JE. 2009. The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression. BMC Plant Biology, 9:26. 15 pp.

Geib SM, del Mar Jimenez-Gasco M, Carlson JE, Tien M, Jabbour R, Hoover K. 2009. Microbial community profiling to investigate transmission of bacteria between life stages of the wood-boring beetle, Anoplophora glabripennis.  Microbial Ecology 58: 199-211.

Morse AM, Peterson dg, M. Islam-Faridi n, Smith KE, Garcia SA, Kubisiak TL, Amerson HV, Carlson JE, Nelson CD, Davis JM, 2009. Evolution of Genome Size and Complexity in Pinus. PLoS ONE 4(2): e4332.

Swanson J-D, Carlson JE, Guiltinan MJ. 2008. Flower development and floral gene expression in Theobroma cacao. International Journal of Plant Sciences, 169(9):1187–1199.

Frost CJ, Mescher MC, Dervinis C, Davis JM, Carlson JE, De Moraes CM. 2008. Priming defense genes and metabolites in hybrid poplar by the green leaf volatile cis-3-hexenyl acetate. New Phytologist, 180(3): 722-734.

Geib SM, Filley T, Hatcher P, Hoover K, Carlson J, del Mar Jimenez-Gasco M, Nakagawa-Izumi A, Sleighter R, Tien M. 2008. Lignin degradation in wood-feeding insects. Proc Natl Acad Sci USA 105(35): 12932 – 12937.

Liang H, Frost CJ, Wei X, Brown NR, Carlson JE, Tien M. 2008. A novel approach toward lignin modification to facilitate cellulosic ethanol production: introducing a tyrosine-rich cell wall peptide gene in poplar. Clean 36(8): 662-668.

Liang H, Carlson JE, Leebens-Mack JH, Wall PK, Mueller LA, BuzgoM, Landherr LL, Hu Y, DiLoreto DS, Ilut DC, Field D, Tanksley SD, Ma H, dePamphilis CW. 2008. An EST Database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron. Tree Genetics & Genomes 4(3): 419-433.

Soltis DE, Albert VA, Leebens-Mack J, Palmer J, Wing R, dePamphilis C, Ma H, Carlson JE, Altman N, Kim S, Wall PK, Zuccolo A, Soltis P. 2008. The Amborella Genome: An Evolutionary Reference for Plant Biology. Genome Biology 9:402, 6 pages.

Frost CJ, Mescher MC, Carlson JE, De Moraes CM. 2008. Plant defense priming against herbivores: getting ready for a different battle. Plant Physiology 146: 818–824.

Barakat A, Wall PK, DiLoreto S, dePamphilis CW, Carlson JE. 2007. Conservation and divergence of microRNAs in Populus. BMC Genomics 8:481.

Frost CJ, Appel HM, Carlson JE, DeMoraes C, Mescher MC, Schultz JC. 2007. Within-plant signaling via volatiles overcomes vascular constraints on systemic signaling and primes responses against herbivores. Ecology Letters 10(6): 490-498.

Gilbert MTP, Binladen J, Miller W, Wiuf C, Willerslev E, Poinar H, Carlson JE, Leebens-Mack JH, Schuster S. 2007. Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Research 35:1-10.

Liang H, Fang EG, Tomkins JP, Luo M, Kudrna D, Arumuganathan K, Zhao S, Schlarbaum SE, Banks JA, dePamphilis CW, Mandoli DF, Wing RA, Carlson JE. 2007. Development of a BAC library resource for yellow poplar (Liriodendron tulipifera) and the identification of genomic regions associated with flower development and lignin biosynthesis. Tree Genetics & Genomes 3(3): 215 - 225.

Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson J, dePamphilis CW, Boore JL, Jansen RK. 2006. Complete chloroplast genome sequences of Drimys, Liriodendron, and Piper: Implications for the phylogeny of magnoliids and the evolution of GC content. BMC Evolutionary Biology 6:77, 20 pp.

Tuskan GA, et al. 2006. The Genome of Western Black Cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw). Science 313: 1596-1604. (Sept 15, 2006).

Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis D, Doyle JJ, Soltis P, Carlson JE, Arumuganathan K, Barakat A, Albert V, Ma H, dePamphilis CW. 2006. Widespread genome duplications throughout the history of flowering plants. Genome Research 16: 738 - 749.