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, Eucalyptus, Agave, Switchgrass, and Brachypodium), to annuals (Arabidopsis) and Sphagnum 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. the Joint Genome Institute, Pacific Northwest National Lab, Brookhaven National Lab and National Renewable Energy Laboratory) and other academic institutions.
Group News & Updates:
Publications - 2016
Mitigating climate change through managing constructed-microbial communities in agriculture. CE Hamilton, JD Bever, J Labbé, X Yang, H Yin. 2016. Agriculture, Ecosystems & Environment, Volume 216, 15 January 2016, pp 304–308. doi:10.1016/j.agee.2015.10.006.
An innovative platform for quick and flexible joining of assorted DNA fragments. HC De Paoli, GA Tuskan, X Yang. Scientific reports 6, 2016. Article number:19278. doi:10.1038/srep19278.
A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers. VG Vandavasi, DK Putnam, Q Zhang, L Petridis et al. Plant Physiology January 2016 vol. 170 no. 1 pp 123-135. doi:10.1104/pp.15.01356.
Publications - 2015
The pineapple genome and the evolution of CAM photosynthesis.R Ming, R VanBuren, CM Wai, H Tang, MC Schatz et al., Nature genetics 47, pp 1435-1442, 2015.doi:10.1038/ng.3435.
Integrating mRNA and Protein Sequencing Enables the Detection and Quantitative Profiling of Natural Protein Sequence Variants of Populus trichocarpa. PE Abraham, X Wang, P Ranjan, I Nookaew, B Zhang et al. J. Proteome Res., 2015, 14 (12), pp 5318–5326. doi: 10.1021/acs.jproteome.5b00823.
Climate-resilient agroforestry: physiological responses to climate change and engineering of crassulacean acid metabolism (CAM) as a mitigation strategy. AM Borland, SD Wullschleger, DJ Weston, J Hartwell et al. Plant, Cell & Environment, Volume 38, Issue 9 September 2015, pp 1833–1849. doi:10.1111/pce.12458.
Substrate-Assisted Catalysis in the Reaction Catalyzed by Salicylic Acid Binding Protein 2 (SABP2), a Potential Mechanism of Substrate Discrimination for Some Promiscuous Enzymes. J Yao, H Guo, M Chaiprasongsuk, N Zhao, F Chen et al. 2015. Biochemistry 54 (34), pp 5366–5375. doi:10.1021/acs.biochem.5b00638.
A host plant genome (Zizania latifolia) after a century-long endophyte infection. L Guo, J Qiu, Z Han, Z Ye, C Chen, C Liu, X Xin, CY Ye et al. The Plant Journal, Volume 83, Issue 4, August 2015, pp 600–609. doi:10.1111/nph.13393.
Scaling nitrogen and carbon interactions: what are the consequences of biological buffering? DJ Weston, A Rogers, TJ Tschaplinski, LE Gunter et al. Ecology and evolution, Volume 5, Issue 14, July 2015, pp 2839–2850. doi:10.1002/ece3.1565.
High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus. W Muchero, J Guo, SP DiFazio, JG Chen, P Ranjan et al. BMC Genomics 2015 16:24. doi:10.1186/s12864-015-1215-z.
Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment CM Timm, AG Campbell, SM Utturkar, SR Jun et al. Front Microbiol. 2015 Oct 14, 6: p 1118. Published online 2015 Oct 14. doi:10.3389/fmicb.2015.01118.
Genomics in a changing arctic: critical questions await the molecular ecologist. SD Wullschleger, AL Breen, CM Iversen, MS Olson et al. Molecular Ecology, Volume 24, Issue 10, May 2015, pp 2301–2309. doi:10.1111/mec.13166.
The impact of biotechnological advances on the future of US bioenergy. BH Davison, CC Brandt, AM Guss, UC Kalluri, AV Palumbo, RL Stouder, EG Webb. Biofuels, Bioproducts and Biorefining. 14 MAY 2015. doi:10.1002/bbb.1549.
High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus.
Publications - 2014
Physiological responses to climate change and engineering of crassulacean acid metabolism (CAM) as a mitigation strategy. Plant, Cell & Environment. doi: 10.1111/pce.12479.
Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance. Plant Biotechnol J. 2014 Dec;12(9):1207-16.doi: 10.1111/pbi.12283.
Metabolic profiling reveals altered sugar and secondary metabolism in response to UGPase overexpression in Populus. BMC Plant Biology 2014. 14:265.doi:10.1186/s12870-014-0265-8..
Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus. Frontiers Plant Sci 5 doi: 10.3389/fpls.2014.00579.
Population genomics of the model tree Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nature Genetics August 25, 2014. doi.org/10.1038/ng.3075.
Characterization of MORE AXILLARY GROWTH Genes in Populus. PLoS One. 2014 Jul 18;9(7):e102757. doi: 10.1371/journal.pone.0102757.
The willow genome and divergent evolution from poplar after the common genome duplication. Cell Res. 2014 Jul 1. doi: 10.1038/cr.2014.83.
The Genome of Eucalyptus grandis. Nature 2014 11 June. doi:10.1038/nature13308.
Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Mol Ecol. 2014 Jul;23(13):3356-70. doi: 10.1111/mec.12821.
Lignin Valorization: Improving Lignin Processing in the Biorefinery. Science 16 May 2014: 1246843 doi:10.1126/science.1246843.
Efficient Purging of Deleterious Mutations in Plants with Haploid Selfing Genome Biol Evol 2014 Vol. 6 1238-1252, first published online May 14, 2014. doi:10.1093/gbe/evu099.
Regulation of secondary cell wall biosynthesis by poplar R2R3 MYB transcription factor PtrMYB152 in Arabidopsis. Scientific Reports 4 doi: 10.1038/srep05054 Published: MAY 23 2014.
Regulation of cell fate determination by single-repeat R3 MYB transcription factors in Arabidopsis. Frontiers Plant Sci 5 doi: 10.3389/fpls.2014.00133.
Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa. New Phytologist, 203: 535–553. doi: 10.1111/nph.12815.
< Functional Genomics of Drought Tolerance in Bioenergy Crops. Critical Reviews in Plant Sciences 33:205–224 doi: 10.1080/07352689.2014.870417.
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.
Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities. J Exp Bot. 2014 Feb 24. doi: 10.1093/jxb/eru038.
Populus trichocarpa and Populus deltoides exhibit different metabolomic responses to colonization by the symbiotic fungus Laccaria bicolor. Mol Plant Microbe Interact. 2014 Jun;27(6):546-56. doi: 10.1094/MPMI-09-13-0286-R.
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.
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.
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
- Increasing advanced biofuels production from terpenes in Eucalyptus leaves
- BioEnergy Science Center Biomass Formation
- Engineering CAM Photosynthetic Machinery into Bioenergy Crops for Biofuels Production in Marginal Environments
- A genome-enabled approach for predicting plant functional traits in dynamic vegetation models
- GTL-Foundational Science Plant-Microbe Interfaces Scientific Focus Area
- Strigolactones in the Woody Bioenergy Crop Populus