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Sequencing Method Yields Fuller Picture

Study co-authored by USC College scientists unravels both chromosomes of sea creature, using method with potential to reveal parts of human genome.

By Carl Marziali
August 1, 2007

Sequencing Method Yields Fuller Picture

USC College biologists have developed a method for sequencing both chromosomes of an organism.

Their study appears in a recent issue of Genome Research.

The statistical method is significant because when researchers announce they have sequenced an organism’s genome, they really mean that they have created a mosaic of two chromosomes, said Lei Li of USC College's biological sciences and mathematics departments.

“A mosaic means it’s not real,” Li said.

Lead author and former graduate student Jong Hyun Kim, advised by Li and USC University Professor Michael Waterman, was able to infer a complete sequence of the chromosomes of Ciona intestinalis, a marine invertebrate commonly known as a sea squirt, from existing sequencing data.

Kim’s method exploited the high rate of genetic mutations in the microbe. Other organisms with high genetic variability, such as certain fish, also may be suitable.

Because the human genome has a relatively low mutation rate, the method cannot be applied to people.

However, Kim said, the method might be useful in sequencing parts of the human genome that display high variability.

As a by-product of their analysis, the researchers added to growing evidence that so-called junk DNA may have a function after all.

Recent studies have shown that junk DNA expresses proteins which may regulate gene function, and that sections of junk DNA have been highly conserved during evolution, suggesting that they play an important role.

The Genome Research study confirms that many short segments of junk DNA are highly conserved, Li and Kim said.

The study was funded by the Centers of Excellence in Genomic Science at the National Institutes of Health.