Washington, DC
November 19, 2008
Scientists
have developed a new tool that will help them accelerate the
assembly of the genome of any organism by identifying redundant
and irrelevant segments of DNA.
With funding from USDA’s Cooperative State
Research, Education, and Extension Service (CSREES) National
Research Initiative (NRI), scientists in Iowa developed a
computer software tool to identify the location and history of
troublesome transposable elements in an organism’s genome.
The genome of an organism contains all of the
hereditary information encoded in the DNA. Unfortunately, this
information may contain many repetitive sequences that are
historical artifacts that either no longer function or could
have been modified by evolution.
Transposable elements are mobile segments of DNA
that produce the repetitive segments. These elements exist
throughout the genome and can cause gene or chromosome
mutations. These changes can provide the mechanism that allows
gene functions to evolve.
Transposable elements vary between different
organisms, but their occurrence is high in many flowering
plants. For example, the human genome is composed of 45 percent
repeat sequences, while the corn genome contains 67 percent
repeat sequences. The segments are difficult for scientists to
sort out, because they tend to hide within themselves like
Russian nesting dolls. Little is known about the distribution
and history of formation of transposable elements across the
genome.
Brent Kronmiller and Roger Wise at Iowa State
University developed a software tool called TEnest that allows
scientists to identify all of the highly repetitive sequences in
the genome. It also allows scientists to unravel the nested
segments and reconstruct full-length repeats.
Transposable element populations replicate
throughout the genome independently, propagating and evolving.
With this new tool, the scientists can identify repeat
insertions in the genome, calculate their age since integration
into the DNA, and model their evolution.
TEnest is available for use both as a Web server
on the Resource for Plant Comparative Genomics,
www.PlantGDB.org, and as a stand alone downloadable version
available from
www.Wiselab.org.
To date, the tool has been applied to four
agriculturally important grains—maize, barley, wheat, and
rice—and an international effort to assemble the genome of each
grain is underway. Oat, sorghum, and soybean sequencing groups
have also expressed interest in developing organism specific
databases.
"Bioinformatic tools such as TEnest increase the
speed with which genomes are assembled and provide insight into
the evolution of the plant," Wise said. "Understanding the
genome of agricultural crops may allow scientists to develop
crops capable of growing in arid conditions and resistant to
pests."
CSREES funded this research project through the
NRI Plant Genome and Plant Biology programs. The Plant
Biological and Molecular Processes National Program of the
USDA’s Agricultural Research Service (ARS) also provided funds.
Through federal funding and leadership for research, education
and extension programs, CSREES and ARS focus on investing in
science and solving critical issues affecting people’s daily
lives and the nation’s future. For more information, visit
www.csrees.usda.gov and
www.ars.usda.gov/Research/Research.htm.
This impact is a service of the USDA Cooperative
State Research, Education, and Extension Service.
By Stacy Kish |
