New Tool Accelerates Genome Assembly

November 21, 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 the U.S. Department of Agriculture's Cooperative State Research, Education, and Extension Service's (CSREES) National Research Initiative, 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.

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.

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.

"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."
Reprinted from CSREES

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