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Plant Science at the JGI and KBase

The Department of Energy currently funds both a large scale user facility for plant genomics at the DOE Joint Genome Institute and a large scale computational resource for comparative functional genomics and systems biology of microbes, plants and their communities called the DOE Systems Biology Knowledgebase (KBase). The core mission of both of these endeavors is to help scientists carry out experiments and analyses in areas such as improving biofuel development, understanding plant model systems, advancing plant comparative science and investigating global carbon cycling. In this workshop, we will present current and ongoing developments from both the Plant Program at JGI and KBase toward integrative biology. We will also hear from researchers who are applying genomic sequence information from JGI to elucidate functions of plant systems and from users who are working to apply KBase computational infrastructure to plant biological inquiries. We will describe how to apply for a project with the JGI Community Science Program and how you can use the KBase system to accelerate your plant genomics research.
Date: Tuesday, January 17, 2017
Time: 4:00 PM-6:10 PM
Room: San Diego
Organizers:
Doreen Ware and Jeremy Schmutz
4:00 PM
Introduction and JGI Plant Science Update
Jeremy Schmutz, HudsonAlpha Institute for Biotechnology; Kerrie W. Barry, DOE Joint Genome Institute; David M. Goodstein, DOE Joint Genome Institute; Jane Grimwood, HudsonAlpha Institute for Biotechnology; Jerry Jenkins, HudsonAlpha Institute for Biotechnology; Jerry Tuskan, Oak Ridge National Laboratory; John Vogel, U.S. Department of Energy Joint Genome Institute; Daniel S. Rokhsar, DOE Joint Genome Institute

4:15 PM
Kbase Plants Update
Priya Ranjan, Oak Ridge National Laboratory

4:30 PM
Evolution of the Populus Genome: From a Reference to Holo- to Meta- to Pan-Genomes
Gerald A. Tuskan, Oak Ridge National Laboratory; Jerry Jenkins, HudsonAlpha Institute for Biotechnology; Wellington Muchero, Oak Ridge National Laboratory; Doug Hyatt, Oak Ridge National Laboratory; Piet Jones, Oak Ridge National Laboratory; Manesh Shah, Oak Ridge National Laboratory; Chris Schadt, Oak Ridge National Laboratory; Dale Pelletier, Oak Ridge National Laboratory; Rotem Sorek, Weizmann Institute of Science; Daniel Jacobson, Bioenergy Science Center and Biosciences Division, Oak Ridge National Laboratory; Jeremy Schmutz, HudsonAlpha Institute for Biotechnology

4:50 PM
Mining RNAseq Data to Determine Differential Gene Expression in Populus Transgenic Lines using Kbase
Jay Chen, Oak Ridge National Laboratory; Wellington Muchero, Oak Ridge National Laboratory; Sara S. Jawdy, Oak Ridge National Laboratory; Vasanth Singan, DOE Joint Genome Institute; Erika A. Lindquist, DOE Joint Genome Institute; Kerrie W. Barry, DOE Joint Genome Institute; Priya Ranjan, Oak Ridge National Laboratory; Jeremy Schmutz, HudsonAlpha Institute for Biotechnology; Jerry Tuskan, Oak Ridge National Laboratory

5:10 PM
A Genome-Wide Sequence-Indexed Collection of Brachypodium Mutants to Accelerate Grain and Biomass Crop Breeding
Richard Sibout, INRA-IJPB; Debbie Laudencia-Chingcuanco, USDA-ARS, Western Regional Research Center; John P. Vogel, DOE Joint Genome Institute

5:30 PM
Curation of Bioenergy-Relevant Families in the Switchgrass Genome
Laura Bartley, University of Oklahoma; Chengcheng Zhang, Univestiy of Oklahoma; Rashmi Jain, UC Davis/JBEI; Xiaolan Rao, University of North Texas; Kangmei Zhao, Carnegie Institute of Science; Juan Xie, South Dakota State University; Guotian Li, oint BioEnergy Institute; Manoj Sharma, ScJawaharlal Nehru University; Jerry Jenkins, HudsonAlpha Institute for Biotechnology; Richard Dixon, University of North Texas; Qin Ma, South Dakota State University; Bingyu Zhao, Virginia Tech; Pamela Ronald, Joint BioEnergy Institute (JBEI); Jeremy Schmutz, Hudson Alpha; Yuhong Tang, The Samuel Roberts Noble Foundation

5:50 PM
A RNA-Seq and Microarray Combined Gene Atlas Database for Perennial Bioenergy Crop Switchgrass
Yuhong Tang, The Samuel Roberts Noble Foundation; Chunman Zuo, University of Georgia; Manesh Shah, Oak Ridge National Laboratory; Ivone Torres-Jerez, The Samuel Roberts Noble Foundation; Kerrie W. Barry, DOE Joint Genome Institute; Jeremy Schmutz, HudsonAlpha Institute for Biotechnology; Michael K. Udvardi, Noble Research Institute; Daniel Jacobson, Bioenergy Science Center and Biosciences Division, Oak Ridge National Laboratory; Ying Xu, Department of Biochemistry and Molecular Biology, UGA

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