populus trichocarpa in green house aspen on bank of grand lake colorado aspen tree

The Plant Systems Biology Group seeks to explore and understand the network of genes, proteins, metabolites, and environmental signals that lead to complex phenotypes in DOE-relevant plant species. The group applies its expertise in plant physiology, development and evolution along with application of transcriptomics, proteomics, metabolomics, molecular genetics, spectroscopy, imaging and bioinformatics approaches to studying plant models ranging from perennial dicots and monocots, (Populus, Switchgrass, Brachypodium and Agave) to annuals (Arabidopsis) to mosses. Our current research portfolio includes projects centering on topics of bioenergy research, carbon fixation, allocation and cycling, responses to climate change, plant-microbe interaction and neutron and radiochemistry-based chemical in vivo imaging. The group collaborates with several DOE-funded (i.e. Pacific Northwest National Lab, Brookhaven National Lab and National Renewable Energy Laboratory) and other academic institutes.

Group Updates:

New Publications - January-March 2014

Yin H, Chen CJ, Yang J, Weston DJ, Chen JG, Muchero W, Ye N, Tschaplinski TJ, Wullschleger SD, Cheng ZM, Tuskan GA, Yang X. 2014. Functional Genomics of Drought Tolerance in Bioenergy Crops. Critical Reviews in Plant Sciences 33:205–224 doi: 10.1080/07352689.2014.870417.

Li Z, Czarnecki O, Chourey K, Yang J, Tuskan GA, Hurst GB, Pan C, Chen JG. Strigolactone-Regulated Proteins Revealed by iTRAQ-Based Quantitative Proteomics in Arabidopsis.J Proteome Res. 2014 Mar 7;13 (3):1359-72. doi: 10.1021/pr400925t. Epub 2014 Feb 24.

De Paoli HC, Borland AM, Tuskan GA, Cushman JC, Yang X. 2014. Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities. J Exp Bot. 2014 Feb 24. doi: 10.1093/jxb/eru038.

Borland AM, Hartwell J, Weston DJ, Schlauch KA, Tschaplinski TJ, Tuskan GA, Yang X, Cushman JC. Engineering crassulacean acid metabolism to improve water-use efficiency.2014. Trends Plant Sci. 2014 Feb 19. pii: S1360-1385(14)00021-1. doi: 10.1016/j.tplants.2014.01.006. [Epub ahead of print] Review.

Deveau A, Gross H, Morin E, Karpinets T, Utturkar S, Mehnaz S, Martin F, Frey-Klett P, Labbé J. 2014. Genome Sequence of the Mycorrhizal Helper Bacterium Pseudomonas fluorescens BBc6R8.Genome Announc. 2014 Jan 9;2(1). pii: e01152-13. doi: 10.1128/genomeA.01152-13.

Muchero W, Labbé J, Ranjan P, DiFazio SP, Tuskan GA. 2014. Genome Resequencing in Populus: Revealing Large-Scale Genome Variation and Implications on Specialized-Trait Genomics. In Challenges and Opportunities for the World's Forests in the 21st Century (pp. 587-595). Springer Netherlands. ISBN 978-94-007-7076-8.

Publications - 2013

Borland AM,Yang X. 2013. Informing the improvement and biodesign of crassulacean acid metabolism via system dynamics modelling. New Phytol. 2013 Dec;200(4):946-9. doi: 10.1111/nph.12529.

Tisserant E, et al. 2013. Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20117-22. doi: 10.1073/pnas.1313452110. Epub 2013 Nov 25.

Ma T, et al. 2013. Genomic insights into salt adaptation in a desert poplar. Nat Commun. 2013;4:2797. doi: 10.1038/ncomms3797.

Shakya M, Gottel N, Castro Het al. 2013. A multifactor analysis of fungal and bacterial community structure of the root microbiome of mature Populus deltoides trees. 2013. PLoS ONE 8 (10): e76382.doi:10.1371/journal.pone.0076382.

Weston DJ, Wullschleger SD, Tuskan GA. 2013. Extending the Arabidopsis flowering paradigm to a mass flowering phenomenon in the tropics. Mol Ecol. 2013 Sep;22(18):4603-5.doi: 10.1111/mec.12473.

Porth I, Klapšte J, Skyba O, Hannemann J, McKown AD, Guy RD, DiFazio SP, Muchero W, Ranjan P, Tuskan GA, Friedmann MC, Ehlting J, Cronk QC, El-Kassaby YA, Douglas CJ, Mansfield SD. 2013. Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms.New Phytol. Nov;200(3):710-26. doi: 10.1111/nph.12422. Epub 2013 Jul 26.

Abraham P, Adams RM, Tuskan GA, Hettich RL. 2013. Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus. J Proteome Res. 2013 Aug 2;12(8):3642-51. doi: 10.1021/pr400192r. Epub 2013 Jul 23..

Muchero W, Roberts PA, Diop NN, Drabo I, Cisse N, Close TJ, Muranaka S, Boukar O, Ehlers JD. 2013. Genetic architecture of delayed senescence, biomass, and grain yield under drought stress in cowpea. PLoS One. 2013 Jul 30;8(7):e70041. doi: 10.1371/journal.pone.0070041 .

Warren JM, Iversen CM, Garten CT Jr, Norby RJ, Childs J, Brice D, Evans RM, Gu L, Thornton P, Weston DJ. 2013.Timing and magnitude of C partitioning through a young loblolly pine (Pinus taeda L.) stand using 13C labeling and shade treatments. Tree Physiol. 2012 Jun;32(6):799-813. doi: 10.1093/treephys/tpr129. Epub 2011 Dec 30.

Wullschleger SD, Weston DJ. 2013. Modeling the molecular and climatic controls on flowering. New Phytol. 2012 May;194(3):599-601. doi: 10.1111/j.1469-8137.2012.04142.x.

Jin Z, Muchero W, Chen JG. 2013. Analysis of cell division and cell elongation in the hypocotyls of Arabidopsis heterotrimeric G protein mutants. Methods Mol Biol. 2013;1043:37-43. doi: 10.1007/978-1-62703-532-3_4.

Czarnecki O, Yang J, Weston DJ, Tuskan GA, Chen JG.2013. A dual role of strigolactones in phosphate acquisition and utilization in plants. Int J Mol Sci. 2013 Apr 9;14(4):7681-701. doi: 10.3390/ijms14047681.

Muchero W, Sewell MM, Ranjan P, Gunter LE, Tschaplinski TJ, Yin, T, Tuskan GA. Genome anchored QTLs for biomass productivity in hybrid Populus grown under contrasting environments.PLoS One. 2013;8(1):e54468. doi: 10.1371/journal.pone.0054468. Epub 2013 Jan 29.

Geraldes A, et al. 2013. A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species. Mol Ecol Resour. 2013 Mar;13(2):306-23. doi: 10.1111/1755-0998.12056.

Porth I, Klápště J, Skyba O, Lai BSK, Geraldes A, Muchero W, Tuskan GA, Douglas CJ, El-Kassaby YA, Mansfield SD. 2012. Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations. New Phytologist

Ye CY, Li T, Yin H, Weston DJ, Tuskan GA, Tschaplinski TJ, Yang X. 2013. Evolutionary analyses of non-family genes in plants. Plant J. 2013 Mar;73(5):788-97. doi: 10.1111/tpj.12073. Epub 2013 Jan 22.

Sukumar P, Legué V, Vayssières A, Martin F, Tuskan GA, Kalluri UC. Involvement of auxin pathways in modulating root architecture during beneficial plant-microorganism interactions.Plant Cell Environ. 2013 May;36(5):909-19. doi: 10.1111/pce.12036. Epub 2012 Dec 11. Review.

Publications - 2012

O. Czarnecki, & B. Grimm. 2012. New insights in the topology of the biosynthesis of 5-aminolevulinic acid. Plant Signal. Behav. 8: e23124.

Jung, S., Foston, M., Kalluri, U. C., Tuskan, G. A., and A. J. Ragauskas. 2012. 3D chemical image using TOF-SIMS revealing biopolymer component spatial and lateral distributions in biomass. Angew. Chem. Int. Edit. DOI: 10.1002/anie.201205243

Abraham, P., Giannone, R., Adams, R., Kalluri, U., Tuskan, G., and R. Hettich. 2012. Putting the pieces together: High-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus. Mol. Cell. Proteom. DOI: 10.1074/mcp.M112.022996

Stan D. Wullschleger, D.J. Weston, S.P. DiFazio, and G.A. Tuskan. 2012. Revisiting the sequencing of the first tree genome: Populus trichocarpa. Tree Physiology

Karve AA, Jawdy SS, Gunter LE, Allen SM, Yang X, Tuskan GA, Wullschleger SD, Weston DJ Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genes. New Phytol. 2012 Nov;196(3):726-37. doi: 10.1111/j.1469-8137.2012.04288.x. Epub 2012 Sep 3.

Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-­‐Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El Kassaby YA, Mansfield SD, Cronk QCB, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA. 2012. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytologist DOI: 10.1111/j.1469-­‐8137.2012.04258.x

Guo, J., Morrell-Falvey, J., Labbé JL, Muchero, W., Kalluri, U., Tuskan, G., and J.-G. Chen. 2012. Highly efficient isolation of Populus mesophyll protoplasts and its application in transient expression assays. PLoS ONE 7: e44908.

Weston DJ, Pelletier DA, Morrell-Falvey JL, Tschaplinski TJ, Jawdy SA, Lu TY, Allen SM, Karve A, Melton SJ, Martin MZ, Schadt CW, Chen JG, Yang X, Doktycz MJ, Tuskan G. 2012. Pseudomonas fluorescens induces strain-dependent and strain-independent host plant responses in defense networks, primary metabolism, photosynthesis and fitness. Molecular Plant-Microbe Interactions, 25: 765-778.

Bennetzen, JL, Schmutz, J, Wang, H, Percifield, R, Hawkins, J, Pontaroli, AC, Estep, M, Feng, L, Vaughn, JN, Grimwood, J, Jenkins, J, Barry, K, Lindquist, E, Hellsten, U, Deshpande, S, Wang, X, Wu, X, Mitros, T, Triplett, J, Yang, X, Ye, CY, Mauro-­‐Herrara, M, Wang, L, Li, P, Sharma, M, Sharma, R, Ronald, PC, Panaud, O, Kellogg, EA, Brutnell, T, Doust, A, Tuskan, GA, Rokhsar, D, Devos KM. 2012. Full genome sequence analysis of the model plant Setaria. Nat. Biotech. 30(6):555-­‐561.

Induri, BR, Ellis, DR, Slavov, GT, Yin, T, Zhang, X, Muchero, W, Tuskan, GA, DiFazio, SP. 2012. Identification of quantitative trait loci and candidate genes for cadmium tolerance in Populus. Tree Physiol 32(5): 626-­‐638.

GA Tuskan, S DiFazio, P Faivre-Rampant, M Gaudet, A Harfouche, V Jorge, JL Labbé, P Ranjan, M Sabatti, G Slavov, N Street, TJ Tschaplinski, T Yin. The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis (2012) Tree Genome and Genetics: DOI 10.1007/s11295-012-0495-6

Ye, X, S Yuan, H Guo, F Chen, GA Tuskan, Z-­‐M Cheng. 2012. Evolution and divergence of the poplar gene family encoding xyloglucan endotransglycosylase/hydrolases in the coding and promoter regions. Tree Genet Genom 8(1):177-­‐194.

Weston DJ, Hanson PJ, Norby RJ, Tuskan GA, Wullschleger SD. 2012. From systems biology to photosynthesis and whole-plant physiology: a conceptual model for integrating multi-scale networks. Plant Signal Behav. 2012 Feb;7(2):260-2. doi: 10.4161/psb.18802. Epub 2012 Feb 1.

Tisserant, E, Kohler A, Dozolme-­‐Seddas P, Balestrini R, Benabdellah K, Colard A, Croll D, Da Silva C, Gomez SK, Koul R, Ferrol N, Fiorilli V, Formey D, Franken P, Helber N, Hijri M, Lanfranco L, Lindquist E, Liu Y, Malbreil M, Morin E, Poulain J, Shapiro H, van Tuinen D, Waschke A, Azcón-­‐Aguilar C, Bécard G, Bonfante P, Harrison MJ, Küster H, Lammers P, Paszkowski U, Requena N, Rensing SA, Roux C, Sanders IR, Shachar-­‐Hill Y, Tuskan G, Young JP, Gianinazzi-­‐Pearson V, Martin F. 2012. The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional trade offs in an obligate symbiont. New Phyto. 193(3):755-­‐ 769.

L Vincenot, K Nara, C Sthultz, J Labbé, MP Dubois, L Tedersoo, F Martin and MA Selosse. Extensive gene flow over Europe and possible speciation over Eurasia in the ectomycorrhizal basidiomycete Laccaria amethystina complex (2012) Molecular Ecology 21(2): 281-299

Abraham, P, Adams, R, Giannone, R, Kalluri, U, Ranjan, P, Erickson, B, Shah, M, Tuskan, G, Hettich, R. 2012. Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics. J Proteome Res 11(1):449-­‐460.

Gerald A. Tuskan named Forest Biotechnologist of the Year

Cary, N.C., February 8, 2012 — Jerry Tuskan, Oak Ridge National Laboratory Distinguished Scientist in the BioSciences Division, has been named 2012 Forest Biotechnologist of the Year by the Institute of Forest Biotechnology (IFB).

His peers within the Forest Biotechnology Partnership, an international group of forestry and biotechnology professionals, selected Tuskan as the fourth scientist to win this award, which recognizes the forest biotechnologist who best exemplifies responsible uses of forest biotechnology and actively promotes science, dialogue and stewardship through their work. Read more...