The Amborella Genome: A Reference for Plant Biology

01 Jul 2010 30 Jun 2018

Claude dePamphilis (PI) , Pamela S Soltis (CoPI), James H Leebens-Mack (CoPI), William B Barbazuk (CoPI), Victor A Albert (CoPI)


PI: Claude W. dePamphilis (Pennsylvania State University)

CoPIs: Victor A. Albert (University at Buffalo), W. Brad Barbazuk (University of Florida - Gainesville), James Leebens-Mack (University of Georgia - Athens), Hong Ma (Pennsylvania State University), Douglas E. Soltis (University of Florida - Gainesville), and Pamela S. Soltis (University of Florida - Gainesville)

Collaborators: Jeffrey D. Palmer (Indiana State University), Steven D. Rounsley (University of Arizona), Stephan C. Schuster (Pennsylvania State University), and Susan R. Wessler (University of Georgia - Athens)

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) complete the physical map of Amborella; 2) generate a high-quality draft sequence and assembly of the Amborella genome using "next generation" sequencing methods and a cost-effective strategy that has been tested on rice genomes and is superior to traditional sequencing methodologies; and 3) develop bioinformatic tools and public access websites to display the project database as it is produced, and support comparative analyses and data mining by the scientific community at large.

Broader Impacts: The Amborella genome, and the strategies being 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. Comparative genomics workshops for middle and high school teachers will be held and teaching modules for broad dissemination of project outcomes and the utility of comparative genomics will be created. In addition, the project will expand a successful cross-cultural scientific mentoring program involving minority undergraduate students at each of the participating universities, train postdoctoral scientists and graduate students, and create mentoring opportunities for inner-city high school students to help them consider careers in the plant sciences. Specific mentoring activities for the post-docs will enhance their professional development. 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/).