2-Plants: Rice genome contains more genes than predicted
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TITLE: Twice as Many Predicted Genes in "Finished" Rice Chromosome
SOURCE: The Institute for Genomic Research, USA, Press Release
DATE: June 5, 2003
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Twice as Many Predicted Genes in "Finished" Rice Chromosome
The smallest rice chromosome has nearly twice as many predicted genes as
the draft DNA sequence had indicated, according to a new study.
The "finished" sequence and analysis of rice Chromosome 10, published in
the June 6 issue of Science , confirms that the rice genome is closely
similar to that of other grains, particularly sorghum and maize. The
study also offers a close look at the compacted short arm of the
chromosome, which is a gene-poor heterochromatic region of the rice genome.
Robin Buell, who leads the rice genome sequencing team at The Institute
for Genomic Research (TIGR), says the "finished" sequence - which helped
researchers identify about 1,700 additional rice genes -shows the
importance of completing a draft DNA sequence. "This work clearly
demonstrates the importance of finished sequence," says Buell. "The
finished Chromosome 10 sequence of rice will be a major component for
future comparative studies of other cereals, such as corn and wheat."
Chromosome 10 was sequenced by a U.S. group - led by Buell at TIGR and by
Rod A. Wing at the University of Arizona - with funding from the U.S.
Department of Agriculture, the National Science Foundation (NSF) and the
Department of Energy. That effort was part of the International Rice
Genome Sequencing Project (IRGSP), a public effort that is completing the
sequences of all 12 rice chromosomes, which have a total of 430 million
DNA base pairs.
Rice is one of the world's most important foods, providing more than half
of the daily calories for about a third of the world's population. The
IRGSP sequenced the genome of the japonica subspecies of rice (Oryza
sativa) that is cultivated in Japan, Korea and the United States. Another
rice subspecies, indica, has been sequenced by a Chinese institute.
The IGRSP public consortium announced in December 2002 that it had
completed an advanced, high-quality draft genome sequence of rice. The
data - freely available on the internet to all scientists worldwide - are
expected to help plant scientists develop improved rice strains that are
hardier and more productive. The draft sequence also provides an
important tool for scientists who focus their research on other cereal
crops (including maize, wheat and barley) with genomes that are colinear
Buell said that the new study predicts a total of about 3,500 genes on
Chromosome 10, which encompasses about 22 million DNA base pairs. The
previous estimate, based on the draft genome blueprint, had predicted
about half that number of genes.
The analysis of the "completed" genome - which still has seven gaps,
representing about 4 percent of the total chromosome sequence - also
found that the chromosome is "modular," with a long arm that is rich with
genes and a short arm that has relatively few genes. That short arm has
an abundance of heterochromatin, a stretch of highly compacted DNA with
few genes in it. Buell says this is the first large stretch of
heterochromatin in plants that has been studied in depth.
In an effort to determine the functions of many of the genes, Buell, Wing
and colleagues also compared the proteins encoded by the chromosome with
those encoded by the model plant Arabidopsis thaliana. They found matches
for about two-thirds of the proteins, indicating that some of the genes
were responsible for functions - such as producing enzymes and binding
nucleic acids - that are carried out by many plants.
Rice, setting a record for a single species, has been the focus of four
separate genome-sequencing initiatives, including the IRGSP and private
initiatives by agribusinesses Syngenta and Monsanto Co., both of which
have shared their rice sequence data with the public project. In
addition, a separate research project at the Beijing Genomics Institute
(BGI) has developed a draft sequence of subspecies indica 93-11, which is
the main subspecies grown in China and Southeast Asia.
Scientific papers by Japanese and Chinese IRGSP research groups detailing
the complete draft sequences of rice chromosomes 1 and 4 were published
last fall in the journal Nature, and IRGSP papers on the "complete"
sequences of the remaining rice chromosomes are planned. The final,
"finished" rice genome sequence is expected by 2004.
The rice project is an important part of TIGR's plant genomics program,
which includes other major research projects involving, maize (corn),
potato, and the model plant Arabadopsis thaliana and some of its close
relatives. TIGR had sequenced about one-third of the Arabadopsis genome
as part of an international consortium that published its results in
Nature in December 2000. TIGR is also conducting research involving pine,
barley, banana, and plant pathogens.
TIGR's president, Claire M. Fraser, Ph.D., said the rice genome sequence
is an important step towards better understanding one of the world's most
important crops and in gaining insight into related crops - such as
maize, wheat and barley - which have much larger genomes. "The rice
genome sequence will benefit a large number of plant genomics projects
and offers the potential to help millions of people across the globe,"
# # #
The Institute for Genomic Research (TIGR), which sequenced the first
complete genome of a free-living organism in 1995, is a not-for-profit
research institute based in Rockville, Maryland. TIGR conducts research
involving the structural, functional, and comparative analysis of genomes
and gene products in viruses, bacteria, archaea, and eukaryotes.
Robert Koenig, TIGR Public Affairs Manager, (+1-301) 838-5880,
C. Robin Buell, TIGR Assistant Investigator, (+1-301) 838-3558,
European NGO Network on Genetic Engineering
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