|
The
smallest rice chromosome has nearly twice as many predicted
genes as the draft DNA sequence had indicated, according
to a new study.
The
new "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,
particular 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 with rice.
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,"
Fraser said.
###
The
Institute for Genomic Research (TIGR) is a not-for-profit
research institute based in Rockville, Maryland. TIGR, which
sequenced the first complete genome of a free-living organism
in 1995, has been at the forefront of the genomic revolution
since the institute was founded in 1992. TIGR conducts research
involving the structural, functional, and comparative analysis
of genomes and gene products in viruses, bacteria, archaea,
and eukaryotes.
Additiona
Media Contact:
C. Robin Buell, TIGR Assistant Investigator
(301) 838-3558
rbuell@tigr.org |
