The Amborella Genome Project

Project description
The origin and early diversification of flowering plants (angiosperms) had profound impacts on Earth's biota, providing the raw genetic material from which most crops and economically important plants were derived. The diversification of genes, genomes, and important traits cannot be adequately interpreted without a comparative framework firmly rooted with genome sequences from basal angiosperms. A genome sequence of Amborella trichopoda will provide a foundation for all comparative analyses of angiosperm gene content and genome structure. Among basal angiosperms, Amborella has the most extensive genomic resources, already possessing high-quality genomic libraries, a physical map, and a large expressed gene (transcriptome) database. These resources, along with its pivotal phylogenetic position and moderate genome size (870 million base pairs), make Amborella the singular choice for the first basal angiosperm to be fully sequenced.

The Amborella Genome Project will:

  1. Generate a high-quality draft genome sequence and gene annotation for Amborella trichopoda using a whole genome shotgun strategy.
  2. Extend and refine the large-scale physical map of Amborella using fluorescent in situ hybridization (FISH) and single molecule restriction mapping (i.e. optical mapping).
  3. Develop bioinformatic tools and a public access website to display the project data as it is produced, and support comparative analyses and data mining by the plant science community.

The Amborella genome, and the strategies used to obtain and analyze the genome, will provide a unique scientific resource broadly impacting plant biology as well as excellent opportunities to demonstrate the utility of comparative genomics across the biological sciences. A reference for angiosperm genome content and organization will benefit the analysis of all currently available angiosperm genome sequences and those that are obtained in the future. In addition to the scientific resources our project is generating, we will provide training and demonstration workshops on the utility of the tools and databases we are producing. We will hold develop teaching modules and hold outreach workshops for middle and high school teachers to enhance broad dissemination of project outcomes and the utility of comparative genomics. Our project will also provide training oportunities for undergraduate and graduate students and postdoctoral scholars. The project website (www.Amborella.org) will provide public access to all data, project results, and long-term repositories. All sequence data will be deposited to NCBI as they become available and image data will be deposited at Morphbank (http://www.morphbank.net/).

Read more about Amborella.

Funding
The Amborella Genome Project is funded by the National Science Foundation Plant Genome Research Program (Award number 0922742).

Participants
The Amborella Genome Project is a collaboration among scientists at Penn State University, University at Buffalo, University of Georgia, University of Florida, University of California Riverside, and Indiana University.

Principal Investigator:

  • Claude dePamphilis (Penn State University)
  • Co-Principal Investigators:

  • Victor A. Albert (University at Buffalo)
  • W. Brad Barbazuk (University of Florida)
  • James Leebens-Mack (University of Georgia, Athens)
  • Hong Ma (Pennsylvania State University)
  • Douglas E. Soltis (University of Florida)
  • Pamela S. Soltis (University of Florida)
  • Susan R. Wessler (University of California, Riverside)
  • Project Manager:

  • Joshua P. Der (Penn State University)
  • Key collaborators:

  • Jeffrey D. Palmer (Indiana State University)
  • Steven D. Rounsley (University of Arizona and Dow Agrosciences)
  • David Sankoff (University of Ottawa)
  • Stephan C. Schuster (Pennsylvania State University)
  • Rodney Wing (University of Arizona)
  • Other participants: additional contributors to the Amborella genome project include scientists from other universities in the United States, Canada, Mexico, China, Korea, Taiwan, Singapore, Germany, Italy, Denmark, France, and New Caledonia.

    Disclaimer: The Amborella Genome Project provides these data and tools in good faith, but makes no warranty, expressed or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used.