Walnut Creek, California
May 28, 2009
An enhanced version of
Phytozome.net, a web
portal for comparative plant genomics geared to advance biofuel,
food, feed, and fiber research, has been released by the
U.S. Department of Energy (DOE)
Joint Genome Institute (JGI).
Phytozome provides a central “hub” for web access to a rapidly
growing number of plant genomes, and includes tools for
visualization of plant genomes and associated annotations,
sequence analysis, and bulk, as well as targeted, plant data
retrieval. The gene families available in Phytozome, defined at
several evolutionarily significant epochs, provide a framework
for the transfer of functional information to important biofuel
and agricultural crops from model plant systems, as well as
allowing users to explore land plant evolution.
The 4.0 release of Phytozome now spans fourteen plant genomes,
including eight that have been sequenced at the DOE JGI:
- Populus trichocarpa,
the black cottonwood tree, the first tree sequenced and
being explored as a feedstock for a new generation of
cellulosic biofuels.
- Sorghum bicolor, a
drought-tolerant grass and the second most prevalent
biofuels crop in the U.S.
- Soybean (Glycine max),
the number two U.S. crop in both harvested acreage and sales
and the principal source of biodiesel, a renewable,
alternative fuel with the highest energy content of any
current alternative fuel.
- Chlamydomonas
reinhardtii, a single-celled green alga, a powerful
model system for the study of photosynthesis and source of
hundreds of genes associated with carbon dioxide capture and
generation of biomass.
- Brachypodium distachyon,
a temperate wild grass and model plant for temperate grasses
and herbaceous energy crops.
- Arabidopsis lyrata,
a close relative of the model plant Arabidopis thaliana and
a reference genome shedding light on the genetics,
physiology, development, and structure of plants in general
and how they respond to disease and environmental stress.
- Physcomitrella patens,
a moss widely recognized as an experimental organism of
choice not only for basic molecular, cytological, and
developmental questions in plant biology, but also as a key
link in understanding plant genome evolution.
- Selaginella
moellendorffii, a spikemoss with a compact genome that
is helping to define an ancient core of genes common to all
vascular plants.
Phytozome also includes the
completed sequences of rice, papaya, grape, Medicago (the
genus which includes alfalfa as a member), Arabidopsis
thaliana, as well as maize bacterial artificial chromosome
(BAC) sequences from the Maize Genome Sequencing Project.
Phytozome, accessible to the public at
www.phytozome.net, is a
collaboration between scientists at the DOE JGI, Lawrence
Berkeley National Laboratory, and the University of California,
Berkeley Center for Integrative Genomics. It was developed with
funding from the Department of Energy, the National Science
Foundation, the National Institutes of Health, and the Gordon
and Betty Moore Foundation.
The U.S. Department of Energy Joint Genome Institute,
supported by DOE’s Office of Science, is committed to advancing
genomics in support of DOE missions related to clean energy
generation and environmental characterization and cleanup. DOE
JGI, headquartered in Walnut Creek, Calif., provides integrated
high-throughput sequencing and computational analysis that
enable systems-based scientific approaches to these challenges.
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