$7.3 million project to reveal genes of oldest flowering plant lineage

October 28, 2010

Unlocking the genetic secrets of Earth's most ancient living lineage of flowering plants -- the original source of genes for all economically important flowering crops -- is the goal of a new $7.3 million research project led by Claude W. dePamphilis, professor of biology at Penn State University. The 4-year Amborella Genome Project, funded by the National Science Foundation, involves scientists at five universities who will share the complex task of discovering the genetic structure of a rare plant species named Amborella, which has been found only on the island of New Caledonia in the southwest Pacific Ocean.

"Amborella is a very special plant because it is the only known living species on the earliest branch of the genetic tree of life of flowering plants," said dePamphilis. "After our research has revealed the complete genome of this critical species, scientists with diverse research goals will use it as the foundation for all comparative analyses of the gene content and genome structure of other flowering plants. Among the many investigations this research likely will benefit are efforts to understand how food crops such as corn, rice, and wheat, and other plants such as cotton, might adapt to our planet's warming climate."

The grant is one of 28 new awards, totaling $101.9 million, announced by the National Science Foundation's Plant Genome Research Program, now in its 13th year. The awards, which range from two to five years and from $634,000 to $9.6 million, support research and tool development to further knowledge of the structure and function of plant genomes. "Basic research leads to new discoveries that will improve the quality and yield of crop plants, and in the longer term, to innovations that will support the bio-based economy of the 21st century," said Joann Roskoski, acting assistant director for the biological sciences.

"Sequencing the Amborella genome and making it freely available to the scientific community on the project's website will allow us and other scientists to explore a large number of questions about how flowering plants originated, when important genes in flowering plants emerged, and whether genome duplication was a force that resulted in the incredible diversity of living varieties of flowering plants," dePamphilis said. During their research, the scientists of the Amborella Genome Project plan to use "next-generation" sequencing methods and a cost-effective strategy that has been tested on rice genomes and has proven to be superior to traditional sequencing methodologies. They also plan to make available on the project's website all currently available genome sequences of flowering plants, as well as those that will be obtained through future research.

"The Amborella genome, and the strategies we are using to obtain and analyze the genome, will provide not only a unique scientific resource with broad impacts in plant biology, but it also will provide excellent opportunities to demonstrate the utility of an evolutionary perspective across the biological sciences," said Victor A. Albert, the empire innovation professor of biological sciences at the University of Buffalo and a co-investigator on the research team. Other co-investigators include Hong Ma at Penn State and W. Brad Barbazuk, Douglas E. Soltis and Pamela S. Soltis at the University of Florida. Other scientists on the team include Steven D. Rounsley at the University of Arizona, Stephan C. Schuster at Penn State University, Susan R. Wessler at the University of Georgia, and Jeffrey D. Palmer at Indiana State University.

"In addition to the DNA sequence itself, we will develop tags to tie specific sequences to their physical locations on the chromosomes. This information will be invaluable in our analysis of the genome structure of Amborella," said Pamela Soltis, distinguished professor and curator at the Florida Museum of Natural History and a member of the UF Genetics Institute. "We also are going to host workshops and help to develop teaching modules on evolution and comparative genomics for middle-school and high-school teachers. Our project's website will provide public access to all data, project results, and long-term repositories of the genetic sequences that this research generates."

Plans for the Amborella Genome Project also include the expansion of a cross-cultural science-mentoring program involving minority undergraduate students at each of the participating universities, a suite of mentoring activities for postdoctoral researchers, the training of postdoctoral scientists and graduate students, and the creation of mentoring opportunities for inner-city high-school students with the goal of helping them consider careers in plant science.

The new research project builds on the results of two other efforts led by dePamphilis at Penn State: the Floral Genome Project, which began in 2001, and the Ancestral Angiosperm Genome Project, which began in 2007.

For more information, contact dePamphilis at 814-863-6412 or cwd3@psu.edu; Pamela Soltis at 352-273-1964 or psoltis@flmnh.ufl.edu; Albert at 716-881-7823 or vaalbert@buffalo.edu; or Barbara Kennedy, Penn State PIO, at 814-863-4682 or science@psu.edu.

For high-resolution images associated with this story, visit http://live.psu.edu/stilllife/2348 online. To watch a video associated with this story, visit http://www.youtube.com/watch?v=EbWlXay0By4 online.

More information about the Amborella Genome research project can be found at the research team's website, at http://www.Amborella.org/ online.

  • Flower of the Amborella trichopoda, which has been found only on the island of New Caledonia in the southwest Pacific Ocean. For a series of high-resolution images associated with this story, click on the image above.

    IMAGE: Sangtae Kim
Last Updated November 18, 2010