The discovery? Bring back a once-important but now rarely used
molecular technique and combine it with newer cloning and DNA
sequencing methods. The effect is a dramatic leap in
efficiency.
“It can reduce the cost of sequencing entire genomes by 50 to 95
percent,” said Andrew Paterson, director of the UGA
Laboratory and a professor of crop and soil sciences, botany
and genetics.
Staggering Savings
That kind of savings could be staggering. Sequencing the sorghum
genome, used as an example to develop the new
ot-based
Cloning and Sequencing (CBCS) method, would cost about $7.5
million, compared to $20 million with the current “shotgun”
approach.
The difference is in the number of clones required to be
sequenced. Sequencing the onion genome would require 119 million
clones. CBCS slashes that to 15 million, eliminating the immense
time and $354 million in funding required to do the other 104
million. For the sugar pine, CBCS cuts 281 million required
clones to 60 million, knocking down costs by $750 million.
The thing that drives up the time and cost to sequence a genome
is its vast number of relatively meaningless DNA sequences.
Genetic Junk
“Repetitive sequences complicate all aspects of gene and genome
research,” Paterson said.
These highly repetitive sequences are, in essence, genetic junk,
said Daniel Peterson, research coordinator of the Plant Genome
Mapping Lab. There may be thousands, even millions, of copies of
a single sequence. For example, one such sequence is repeated
nearly a million times in the human genome, accounting for nearly
10 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 adding
nothing to its genetic complexity.”
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Daniel Peterson (left) and Andrew Paterson, key
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Endless Copies
The problem is that to sequence an entire genome, scientists have
to wade through these endless copies to get to the genes, which
virtually 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 all
but abandoned with the advent of molecular cloning methods. In
the late ’80s and ’90s, research based on Cot analysis bottomed
out.
One reason it fell into disuse is that even in the rarefied world
of molecular biology, it’s a highly demanding process. “You have
to be very careful in interpreting the data,” Peterson said.
Value of Cot Analysis
Peterson has been an ardent defender of the value of Cot
analysis. The method splits the double strands of DNA into single
strands, or denatures them, and then allows them under controlled
conditions 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- or
low-copy (SL) sequences. It’s based on the principle that the
more highly repetitive sequences will renature faster. (You could
find your date faster at the prom if there were millions of
copies of her on the dance floor.)
The Breakthrough
The UGA scientists’ breakthrough came when Paterson suggested
cloning the separate populations. That made it much easier to
separate out, and sequence, the low-copy DNA that includes most
of the genes and regulatory (“on-off”) switches. “It’s like
shooting fish in a barrel,” Peterson said.
The approach allows researchers to focus their time and funds on
the single- and low-copy sequences, which comprise a small part
of the genome but virtually all of its information content.
Paterson, Peterson and eight other UGA scientists have published
their CBCS findings in a May article in
who specializes in the HR sequences, is named with Paterson and
Peterson in UGA’s application for a patent on the CBCS method.
