John E. Carlson Ph.D.

Responsibilities and 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:

Dr. Carlson's group conducts research in the areas of Genomics, Conservation Genetics, and Biotechnology. Current projects in The Schatz Center cover a wide range of topics from sequencing the chestnut genome to field trials of short rotation woody biomass crops.

Genomics  The organization of genes and genomes are studied through transcriptiomics, genome sequencing, genetic linkage mapping, and metagenomics. This research identifies genes, DNA markers and quantitative trait loci governing growth, stress resistance, and plant-microbe interactions in hardwood tree species.

Conservation genetics.  Genetic diversity is the foundation for biodiversity.  DNA markers in the nuclear, mitochondrial and chloroplast genomes are used to study genetic diversity in forest trees and associated organisms.

Environmental tree biotechnology. Research is being conducted on the molecular basis of lignin synthesis and the response of trees to environmental stresses such as introduced pests and diseases, climate change, and pollutants.  The goal for this research is environmentally friendly bioenergy production and ecosystem restoration.

Selected Publications:

Petit RJ, Carlson J, Curtu AL, Loustau ML, Plomion C, González-Rodríguez A, Sork V, Ducousso A. 2012. Fagaceae trees as models to integrate ecology, evolution and genomics. New Phytologist, 197: 369 – 371.

Hsu C-Y, Adams JP, No K, Liang H, Meilan R, Pechanova O, Barakat A, Carlson JE, Page GP, Yuceer C. 2012. Overexpression of Constans Homologs CO1 and CO2 Fails to Alter Normal Reproductive Onset and Fall Bud Set in Woody Perennial Poplar. PLoS ONE 7(9): e45448, 14 pp. PubReader

Costa GGL, et al.  2012. The mitochondrial genome of Moniliophthora roreri, the frosty pod rot pathogen of cacao.  Fungal Biology, 116 (5): 551-562. PubMed

Kremer K, Abbott AG, Carlson JS, Manos PS, Plomion C, Sisco P, Staton ME, Ueno S, Vendramin GG. 2012. Genomics of Fagaceae (Review). Tree Genetics & Genomes, 8(3): 583-610. 

Frost CJ, Dean JM, Smyers EC, Mescher MC, Carlson JE, De Moraes CM, Tooker JF. 2012. A petiole-galling insect herbivore decelerates leaf lamina litter decomposition rates. Functional Ecology 26: 628–636.

Barakat A, Staton M, Cheng C-H, Park J, Buang N, Yassin M, Ficklin S, Yeh C-C, Hebard F, Baier K, Powell W, Schuster S, Wheeler N, Abbott A, Carlson J, Sederoff R.  2012. Chestnut resistance to the blight disease: insights from transcriptome analysis. BMC Plant Biology, 12:38, 14 pp.  PubMed

Scully ED, Hoover K, Carlson J, Tien M, Geib SM 2012. Proteomic analysis of Fusarium solani isolated from the Asian longhorned beetle, Anoplophora glabripennis.  PLoS ONE 7(4): e32990. doi:10.1371.  15 pp.  PubMed

Geib SM, Scully ED, Jimenez-Gasco MDM, Carlson JE, Tien M, Hoover K. 2012.  Phylogenetic analysis of Fusarium solani associated with the Asian longhorned beetle, Anoplophora glabripennis, Insects 3(1), 141-160. 

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.  PubMed.

Hsu C-Y, et al. 2011. FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar, Proc Natl Acad Sci USA 108(26): 10756–10761. PubMed

Zuccolo A, et al. 2011. A Physical Map for the Amborella Genome Sheds Light on the Evolution of Angiosperm Genome Structure.  Genome Biology, 12:R48, 14 pp.PubMed

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.  PubMed

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.  PubMed

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.  11 pp.  PubMed

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.  PubMed.

Tiburcio RA, et al. 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.  PubMed

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 pp.  PubMed

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.

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.

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.

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