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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. http://dx.doi.org/10.7243/2050-2389-4-2.

Khodwekar S, Staton M, Coggeshall MV, Carlson JE, Gailing O. 2015. Nuclear microsatellite markers for population genetic studies in sugar maple (Acer saccharum Marsh.). Ann. For. Res. 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. (http://dx.doi.org/10.7243/2050-2389-4-1)

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, F1000Research, 3:298 (doi: 10.12688/f1000research.5919.1)

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 pages. 

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, doi:10.3732/apps.1300050, 4 pp.

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. 2013. 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, Cabrera OG, Tiburcio RA, Medrano FM, Carazzolle MF, Thomazella DPT, Schuster SC, Carlson JE, Guiltinan MJ, Bailey BA, Mieckowski P, Pereira CAG, Meinhardt LW.  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 JE, 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. 

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.

Bagniewska-Zadworna A, Zenkteler M, Zenkteler E, Wojciechowicz MK, Barakat A, Carlson JE. 2011. A successful application of the embryo rescue technique as a model for studying crosses between Salix viminalis and Populus species. Australian Journal of Botany 59: 382–392.

Zuccolo A, Bowers JE, Estill JC, Xiong Z, Luo M, Sebastian A, Goicoechea JL, Collura K, Yu Y, Jiao Y, Duarte J, Tang H, Rounsley S, Kudrna D, Paterson AH, Pires JC, Soltis DE, Chamala S, Barbazuk B, Soltis PS, Albert VA, Ma H, Mandoli D, Banks J, Carlson J, Tomkins J, dePamphilis C, Wing RA, Leebens-Mack J. 2011.  A Physical Map for the Amborella Genome Sheds Light on the Evolution of Angiosperm Genome Structure.  Genome Biology, 12:R48, 14 pp. doi: 10.1186/gb-2011-12-5-r48.

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.

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 pages.

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.

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 the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biology, 9:51.  11 pages.   doi:10.1186/1471-2229-9-51

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

Morse AM, Peterson DG, M. Islam-Faridi, 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. 11 pp.

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.

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.

Barakat A, Wall PK, DiLoreto S, dePamphilis CW, Carlson JE. 2007. Conservation and divergence of microRNAs in Populus.  BMC Genomics 8:481, 16 pp.

Barakat A, Wall K, Leebens-Mack J, Wang YJ, Carlson JE, dePamphilis CW. 2007. Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. The Plant Journal 51(6):991-1003.

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. 

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

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. 

St. Clair S, Carlson JE, Lynch J. 2005. Evidence for Oxidative Stress in Sugar Maple Stands Growing on Acidic, Nutrient Imbalanced Forest Soils.  Oecologia 145: 258 – 269.

Traore A, Xing Z, Bonser A, Carlson JE. 2005. Optimization of a Protocol for Sterilization and In Vitro Establishment of Vegetative Buds from Mature Douglas-Fir Trees. Hortscience 40: 1464 - 1468.

Albert VA, Soltis DE, Carlson JE, Farmerie WG, Wall PK, Ilut DC, Mueller LA, Landherr LL, Hu Y, Buzgo M, Kim S, Yoo M-J, Frohlich MW, Perl-Treves R, Schlarbaum S, Bliss B, Tanksley S, Oppenheimer DG, Soltis PS, Ma H, dePamphilis CW, Leebens-Mack JH. 2005. Floral Gene Resources from Basal Angiosperms for Comparative Genomics Research. BMC Plant Biology 5:5, 15 pp.