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Beckman Coulter Genomics Will Use Sanger Technology to Sequence Atlantic Salmon Genome

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By Monica Heger

This article was originally published December 14. It has been updated to correct that the ICSASG did, in fact, test 454’s paired-end approach. A member of the cod genome consortium had incorrectly suggested that they did not.

Under its new contract with the International Cooperation to Sequence the Atlantic Salmon Genome, Beckman Coulter Genomics will complete the first phase of the project using only Sanger sequencing — the only technology that can currently deliver a reference genome, according to a researcher involved in the project.

The ICSASG last week announced that it had awarded the project to Beckman Coulter Genomics — formerly Agencourt Bioscience and Cogenics (see In Sequence 12/8/2009). According to Doug Smith, director of science and technology at Beckman Coulter Genomics, the newer sequencing technologies are still not suitable for creating reference genomes, which is what the consortium aims to do. "They're improving, but they're still not good enough for that, especially for a large complex genome," he said.

Beckman Coulter Genomics will sequence the salmon genome to four-fold coverage, according to Pierre Meulien, Genome BC's chief scientific officer and member of the ICSASG. The $6 million first phase will be completed and made public by early 2011. A second request for proposals, for the second phase of the project, will be open to any and all sequencing technologies, said Meulien. The ultimate goal is to create a complete salmon genome that can act as a salmonid reference genome.

Smith said the company will use a mix of libraries, including high-copy plasmids, as well as BACs and fosmids for end-sequencing, that are 3.5 kilobases, 150 kilobases, and 40 kilobases long, respectively. They will likely use a variety of programs to assemble the genome, but primarily Arachne, he said.

The ICSASG had specified in its June request for proposal that it wanted the first phase to be done with Sanger technology or an equivalent (see In Sequence 6/23/2009). According to Meulien, the complexity of the salmon genome — it is around 3 gigabases long with many conserved repeat elements — and the fact that there is no current reference genome drove the consortium's decision to request Sanger technology, or an equivalent.

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The salmon genome is a "pseudo tetraploid genome, and it's the size of the human genome, so it's a very complex genome. It was felt by the review panel and scientists involved that the read lengths should be an average of 750 base pairs, and really, the Sanger technology is the only one currently that can give you robust read lengths of that nature," Meulien told In Sequence last week.

Ben Koop, director of the Centre for Biomedical Research at the University of Victoria in British Columbia and member of the ICSAG, agreed that the complexity of the salmon genome was a major factor in deciding to use Sanger technology.

Aside from the fact that the genome is a pseudo tetraploid, Koop said that researchers have also identified many repeat elements of around 1,500 base pairs in length. He said the consortium believes that there are between 10,000 to 100,000 of those elements, and that they are 90 percent to 98 percent similar to each other. The long reads that Sanger technology provides are key for sequencing these elements, he said: "Shorter reads become a major problem."

Additionally, there is no current reference genome for the salmon or a related species, Meulien said, which will add to the challenge of sequencing and assembling the genome. "We're starting from scratch here," he said. "So we were looking for a tried and tested technology that would be sure to deliver."
Last year, ICSASG members tested the 454 GS FLX platform for the project but concluded "that in its present form (average read length of 250 bp) the GS FLX technology is limited to gene mining and establishing a set of ordered sequence contigs with many gaps," according to the RFP.

In the meantime, however, a Norwegian research consortium has successfully sequenced and assembled the cod genome using the 454 technology only (see In Sequence 11/3/2009).

Kjetill Jakobsen, leader of the consortium that sequenced the cod genome and a professor of biology at the Centre for Ecological and Evolutionary Synthesis at the University of Oslo cited using a paired-end approach as a key to the success of 454. "We would not have been able to do the cod genome without the paired ends," he said.

William Davidson, professor of molecular biology and biochemistry at Simon Fraser University who is working on the salmon genome project, said that the group did use paired ends when they tested the 454 technology, but that it did not improve their contig length.

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Recent announcements of genomes being sequenced with second-generation sequencing platforms, including the cod genome with 454 and, this week, the giant panda genome with the Illumina GA (see In Sequence 12/14/2009), are demonstrating that the technology delivers high-quality genomes, Jakobsen said. "If you really want extremely long contigs, maybe the Sanger sequencing is better, but this is not entirely clear," he added. The Sanger technology is also much more expensive, and Jakobsen estimated that sequencing the salmon genome will be around ten times more expensive than the cost of sequencing the cod genome, which was about 3 million Norwegian kroners ($520,000) for consumables.

The ICSASG is made up of researchers, industry, and funding agencies from Canada, Chile, and Norway. Its goal is to produce a genome sequence of the Atlantic salmon that identifies and maps all of its genes and that can act as a reference genome for other salmonids. A sequenced genome could lead to better management of fish stocks and the identification of commercially valuable traits, as well as a better understanding of pathogens and disease resistance, the consortium said.

"It will be the first salmonid genome to be sequenced, so it will have great use both for the scientific community — evolutionary biologists, people working on rainbow trout, arctic char, other salmonid species — and will also hopefully give rise to some useful tools for the management of wild fisheries and aquaculture stocks," Meulien said.

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