John E. Carlson, Ph.D.

  • Professor of Molecular Genetics
  • Director of The Schatz Center for Tree Molecular Genetics
John E. Carlson, Ph.D.
323 Forest Resources Building
University Park, PA 16802
Work Phone: 814-863-9164
Fax: 814-863-3725

Areas of Expertise

  • Genomics
  • Conservation Genetics
  • Renewable Energy
  • Biotechnology


  1. B.S., University of Pittsburgh (1974)
  2. M.Sc., University of Illinois (1978)
  3. Ph.D., University of Illinois (1983)

Responsibilities and Interests

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

Courses Taught

  • FOR430 "Conservation Biology"
  • FOR496 "Honors/Independent Research"
  • FOR530 "Conservation Genetics"
  • FOR880 "Bioenergy Feedstocks"
  • 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 soil metagenomics of short rotation biomass crops.


The organization of genes and genomes are studied through transcriptomics, 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.

Recent Publications:

Herr JR, Scully ED, Geib SM, Hoover K, Carlson JE, Geiser DM. 2016. Genome sequence of Fusarium isolate MYA-4552 from the midgut of Anoplophora glabripennis, an invasive, wood-boring beetle. Genome Announcements 4(4):e00544-16, 2 pages. (doi:10.1128/genomeA.00544-16).

Carroll RA, Jones C, Best T, Shumaker K, Carlson J. 2016. Gene expression in hardwood trees species exposed to ozone. Journal of Undergraduate Research and Scholarly Excellence, Volume VII: 32-35.

Odom T, Williams KN, Best T, Zembower N, Shumaker K, Carlson J. 2016. An analysis of gene expression induced by elevated atmospheric ozone in hardwood trees native to Eastern North America. Journal of Undergraduate Research and Scholarly Excellence, Volume VII: 36-40.

Owusu S, Schlarbaum S, Carlson J, Gailing O. 2016. Pollen gene flow and molecular identification of full-sib families in small and isolated population fragments of Gleditsia triacanthos L. Botany, 10.1139/cjb-2015-0244.

Staton ME, Best TO, Khodwekar SD, Owusu SA, Xu T, Yu Y, Jennings TN, Knaus BJ, Cronn RC, Arumuganathan AK, Coggeshall MV, Gailing O, Liang H, Romero-Severson J, Schlarbaum SE, Carlson JE. 2015. Preliminary genomic characterization of ten hardwood tree species from multiplexed low coverage whole genome sequencing. PLoS ONE, 10(12): e0145031 doi:10.1371/journal.pone.0145031.

Staton M, Zhebentyayeva T, Olukolu B, Fang GC, Nelson D, Carlson JE, Abbott AG. 2015. Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes. BMC Genomics, 16:744, DOI: 10.1186/s12864-015-1942-1.

Pang T, Guo L, Shim D, Cannon N, Tang S, Chen J,  Carlson JE, Xia X, Yin W. 2015. Characterization of the transcriptome of the xerophyte Ammopiptanthus mongolicus under drought stress by 454 pyrosequencing. PLoS ONE 10(8): e0136495, 25 pages. doi: 10.1371/journal.pone.0136495. Chen C-C, Xu Y, Xu T, Staton M, Stott G, Bukles O, Schlarbaum SE, Carlson JE, Liang H. 2015. Diversity level of genomic microsatellites in redbay (Persea borbonia L.) generated by Illumina sequencing. Journal of Plant Science and Molecular Breeding, 4:2  DOI:10.7243/2050-2389-4-2, 5 pp.

Khodwekar S, Staton M, Coggeshall MV, Carlson JE, Gailing O. 2015. Nuclear microsatellite markers for population genetic studies in sugar maple (Acer saccharum Marsh.). Annals of Forest Research, 58(2) DOI:10.15287/afr.2015.360, 12 pp.

Zhang X, Carlson A, Tian Z, Staton M, Schlarbaum SE, Carlson JE, Liang H. 2015. Genetic characterization of Liriodendron seed orchards with EST-SSR markers. Journal of Plant Science and Molecular Breeding, 4:1 DOI:10.7243/2050-2389-4-1, 9 pp.

Chen CC, Bates R, Carlson J. 2015. Effect of environmental and cultural conditions in medium pH and plant growth performance of Douglas-fir (Pseudotsuga menziesii) shoot culture, F1000 Research, 3:298 DOI: 10.12688/f1000research.5919.1, 14 pp.

Diningrat DS, Widiyanto SM, Pancoro1 A, Iriawati, Shim D, Panchangam B, Zembower N, Carlson JE. 2014. Transcriptomes of Teak (Tectona grandis, L.f) in Vegetative to Generative Transition Stage Development. International Journal of Innovation and Applied Studies, 9(3): 1416-1427, ISSN 2028-9324. 

Scully E; Geib SM; Carlson JE; Tien M; Hoover K. 2014. Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles. BMC Genomics, 15:1096 DOI: 10.1186/1471-2164-15-1096, 21 pp.  

Jang H-Y, Rhee J-Y, Carlson JE, Ahn S-J. 2014. The Camelina aquaporin CsPIP2;1 is regulated by phosphorylation at Ser273, but not at Ser277, of the C-terminus and is involved in salt- and drought-stress responses . Journal of Plant Physiology, 171(15): 1401-1412.

Meinhardt LW, Thomazella DPT, Teixeira PJPL, Costa GGL, Carazzolle MF, Schuster SC, Carlson JE, Guiltinan MJ, Mieczkowski P, Farmer A, Ramaraj T, Crozier J, Davis RE, Shao J, Melnick RL, Pereira GAG, Bailey BA.  2014.  Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: Mechanisms of the biotrophic and necrotrophic phases. BMC Genomics, 15(1): 164, 25 pp.

Sha T, Liang H, Yan D, Zhao Y, Han X, Carlson JE, Xia X, Yin W. 2013. Populus euphratica: the transcriptomic response to drought stress. Plant Molecular Biology 83(6): 539-557.

Owusu SA, Staton M, Jennings TN, Schlarbaum S, Coggeshall MV, Romero-Severson J, Carlson JE, Gailing O.  2013.  Development of Genomic Microsatellites in Gleditsia triacanthos (Fabaceae) Using Illumina Sequencing. Applications in Plant Sciences, 1(12): 1300050.

Scully ED, Hoover K, Carlson JE, Tien M, Geib SM. 2013. Midgut transcriptome profiling of Anoplophora glabripennis, a lignocellulose degrading cerambycid beetle. BMC Genomics, 14:850.

Xu Y, Chen C-F, Thomas TP, Azadi P, Diehl B, Tsai C-J, Brown N, Carlson JE, Tien M, Liang H.  2013.  Wood chemistry analysis and expression profiling of a poplar clone expressing a tyrosine-rich peptide. Plant Cell Reports, 32 (12), 1827-1841.

Scully ED, Geib SM, Hoover K, Tien M, Tringe SG, Barry KW, Glavina del Rio T, Chovitia M, Herr JR, Carlson JE. 2013. Metagenomic Profiling Reveals Lignocellulose Degrading System in a Microbial Community Associated with a Wood-Feeding Beetle. PLoS ONE 8(9): e73827.

Jang H-Y, Rhee J-Y, Carlson JE, Ahn S-J. 2014. The Camelina aquaporin CsPIP2;1 is regulated by phosphorylation at Ser273, but not at Ser277, of the C-terminus and is involved in salt- and drought-stress responses . Journal of Plant Physiology, 171(15): 1401-1412.

Kim H-S, Oh J-M, Luan S, Carlson JE, Ahn S-J. 2013. Cold stress causes rapid but differential changes in properties of plasma membrane H+-ATPase of camelina and rapeseed. Journal of Plant Physiology 170(9): 828–837.

Fang GC, Blackmon BP, Staton ME, Nelson CD, Kubisiak TL, Olukolu BA, Henry D, Zhebentyayeva Y, Saski CA, Cheng CH, Monsanto M, Ficklin S, Atkins M, Georgi LL, Barakat A, Wheeler N, Carlson JE, Sederoff R, Abbott AG. 2013. A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map. Tree Genetics & Genomes, 9(2): 525-537.

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. 

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

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. 

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. 

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. 

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. 

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.

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.