Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.)

Authors

  • Ji-Yi Zhang,

    1. Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA
    2. Department of Energy, BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA
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  • Yi-Ching Lee,

    1. Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA
    2. Department of Energy, BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA
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  • Ivone Torres-Jerez,

    1. Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA
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  • Mingyi Wang,

    1. Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA
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  • Yanbin Yin,

    1. Department of Energy, BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA
    2. Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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  • Wen-Chi Chou,

    1. Department of Energy, BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA
    2. Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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  • Ji He,

    1. Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA
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  • Hui Shen,

    1. Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA
    2. Department of Energy, BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA
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  • Avinash C. Srivastava,

    1. Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA
    2. Department of Energy, BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA
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  • Christa Pennacchio,

    1. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
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  • Erika Lindquist,

    1. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
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  • Jane Grimwood,

    1. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
    2. HudsonAlpha Genome Sequencing Center, Huntsville, AL, USA
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  • Jeremy Schmutz,

    1. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
    2. HudsonAlpha Genome Sequencing Center, Huntsville, AL, USA
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  • Ying Xu,

    1. Department of Energy, BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA
    2. Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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  • Manoj Sharma,

    1. Departments of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
    2. Department of Energy, The Joint Bioenergy Institute (JBEI), Emeryville, CA, USA
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  • Rita Sharma,

    1. Departments of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
    2. Department of Energy, The Joint Bioenergy Institute (JBEI), Emeryville, CA, USA
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  • Laura E. Bartley,

    1. Departments of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
    2. Department of Energy, The Joint Bioenergy Institute (JBEI), Emeryville, CA, USA
    Current affiliation:
    1. Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
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  • Pamela C. Ronald,

    1. Departments of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
    2. Department of Energy, The Joint Bioenergy Institute (JBEI), Emeryville, CA, USA
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  • Malay C. Saha,

    1. Department of Energy, BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA
    2. Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA
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  • Richard A. Dixon,

    1. Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA
    2. Department of Energy, BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA
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  • Yuhong Tang,

    1. Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA
    2. Department of Energy, BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA
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  • Michael K. Udvardi

    Corresponding author
    1. Department of Energy, BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA
    • Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA
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For correspondence (e-mail mudvardi@noble.org).

Summary

Switchgrass (Panicum virgatum L.) is a perennial C4 grass with the potential to become a major bioenergy crop. To help realize this potential, a set of RNA-based resources were developed. Expressed sequence tags (ESTs) were generated from two tetraploid switchgrass genotypes, Alamo AP13 and Summer VS16. Over 11.5 million high-quality ESTs were generated with 454 sequencing technology, and an additional 169 079 Sanger sequences were obtained from the 5′ and 3′ ends of 93 312 clones from normalized, full-length-enriched cDNA libraries. AP13 and VS16 ESTs were assembled into 77 854 and 30 524 unique transcripts (unitranscripts), respectively, using the Newbler and pave programs. Published Sanger-ESTs (544 225) from Alamo, Kanlow, and 15 other cultivars were integrated with the AP13 and VS16 assemblies to create a universal switchgrass gene index (PviUT1.2) with 128 058 unitranscripts, which were annotated for function. An Affymetrix cDNA microarray chip (Pvi_cDNAa520831) containing 122 973 probe sets was designed from PviUT1.2 sequences, and used to develop a Gene Expression Atlas for switchgrass (PviGEA). The PviGEA contains quantitative transcript data for all major organ systems of switchgrass throughout development. We developed a web server that enables flexible, multifaceted analyses of PviGEA transcript data. The PviGEA was used to identify representatives of all known genes in the phenylpropanoid–monolignol biosynthesis pathway.

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