The discovery? Bring back a once-important but now rarely usedmolecular technique and combine it with newer cloning and DNAsequencing methods. The effect is a dramatic leap in efficiency.”It can reduce the cost of sequencing entire genomes by 50 to 95percent,” said Andrew Paterson, director of the UGA Plant Genome MappingLaboratory and a professor of crop and soil sciences, botanyand genetics.Staggering SavingsThat kind of savings could be staggering. Sequencing the sorghumgenome, used as an example to develop the new Cot-basedCloning and Sequencing (CBCS) method, would cost about $7.5million, compared to $20 million with the current “shotgun”approach.The difference is in the number of clones required to besequenced. Sequencing the onion genome would require 119 millionclones. CBCS slashes that to 15 million, eliminating the immensetime and $354 million in funding required to do the other 104million. For the sugar pine, CBCS cuts 281 million requiredclones to 60 million, knocking down costs by $750 million.The thing that drives up the time and cost to sequence a genomeis its vast number of relatively meaningless DNA sequences.Genetic Junk”Repetitive sequences complicate all aspects of gene and genomeresearch,” Paterson said.These highly repetitive sequences are, in essence, genetic junk,said Daniel Peterson, research coordinator of the Plant GenomeMapping Lab. There may be thousands, even millions, of copies ofa single sequence. For example, one such sequence is repeatednearly a million times in the human genome, accounting for nearly10 percent of human DNA.”Most of these are ancient viruses,” Peterson said. “They’re’selfish DNA,’ making up much of the bulk of a genome but addingnothing to its genetic complexity.” Daniel Peterson (left) and Andrew Paterson, keyplayers in a team of 10 University of Georgia scientists, reviewa presentation of Cot-Based Cloning and Sequencing, theirrevolutionary new approach to genome research. Photo: DanRahn Endless CopiesThe problem is that to sequence an entire genome, scientists haveto wade through these endless copies to get to the genes, whichvirtually always come in only one or a few copies each.A technique called Cot analysis makes the savings possible.Developed in the 1960s and widely used in the ’70s, it was allbut abandoned with the advent of molecular cloning methods. Inthe late ’80s and ’90s, research based on Cot analysis bottomedout.One reason it fell into disuse is that even in the rarefied worldof molecular biology, it’s a highly demanding process. “You haveto be very careful in interpreting the data,” Peterson said.Value of Cot AnalysisPeterson has been an ardent defender of the value of Cotanalysis. The method splits the double strands of DNA into singlestrands, or denatures them, and then allows them under controlledconditions to renature, or recouple into double strands.Cot analysis breaks down a complex genome into three populations:highly repetitive (HR), moderately repetitive (MR) and single- orlow-copy (SL) sequences. It’s based on the principle that themore highly repetitive sequences will renature faster. (You couldfind your date faster at the prom if there were millions ofcopies of her on the dance floor.)The BreakthroughThe UGA scientists’ breakthrough came when Paterson suggestedcloning the separate populations. That made it much easier toseparate out, and sequence, the low-copy DNA that includes mostof the genes and regulatory (“on-off”) switches. “It’s likeshooting fish in a barrel,” Peterson said.The approach allows researchers to focus their time and funds onthe single- and low-copy sequences, which comprise a small partof the genome but virtually all of its information content.Paterson, Peterson and eight other UGA scientists have publishedtheir CBCS findings in a May article in Genome Research. Susan Wessler,who specializes in the HR sequences, is named with Paterson andPeterson in UGA’s application for a patent on the CBCS method.