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The Sweet Genome

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As researchers the world over search for alternative energy sources, many have looked to biology to power the world. One staple crop that has already been used as a source of bioethanol, and may be able to inform other work into biofuels, is sugarcane.

Sugarcane is a highly productive plant, says the University of Queensland's Robert Henry. "I think we are all trying to understand why sugarcane is so productive," he says, adding that it's "probably related to its high ploidy. We are all looking to see what can learn for wider application."

Sugarcane has long been an important crop, particularly in the tropics. But these days its importance beyond being a food source has emerged as sugarcane is increasingly piquing interests as a bioenergy source. According to the US Department of Energy, sugarcane has an annual worldwide production of roughly 140 million metric tons and a net value of nearly $30 billion. "Sugarcane is especially of interest because of the energy situation, and in the last few years bioenergy crops have become much more of interest," Henry says. "Sugarcane is probably the leading industrial crop in the world. … It's a prime candidate for further development as an energy crop."

While sugarcane is an economically important crop, it is a biologically difficult one to work with. Setting up a consortium to sequence the sugarcane genome was the brainchild of the University of São Paulo's Glaucia Souza — which is not so surprising, says Ray Ming at the University of Illinois at Urbana-Champaign, as Brazil produces more sugarcane than any country in the world. The US Department of Agriculture reports that Brazil has about 7.5 million hectares of land dedicated to sugarcane production — Australia has about 400,000 hectares, by comparison.

Souza hosted a two-day meeting in 2008 to gauge interest in a sugarcane sequencing consortium. On the first day, all of the researchers gave a presentation on their work toward sequencing the sugarcane genome. On the second, they discussed joining forces. The group has since met in Australia at a meeting hosted by Henry to continue to discuss who is going to do what and what the common goals are, Ming says. They are planning to have another meeting in France soon. It's slow going.

Biological difficulties

But that slowness is not without reason, as sugarcane is maddeningly difficult to study. There are a number of cultivars from different regions, the number of chromosomes spans a wide range, and it has a high and variable ploidy. All in all, not an easy organism to sequence. "The challenge with sugarcane is that it is a very complex genome because it has a high degree of ploidy in the presence of a number of progenitor species in the background of modern commercial cultivars," Henry says. "This is amongst the most challenging of genome sequences."

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So the consortium members have been focusing on creating and sequencing BACs from the sugarcane genome. "There's a BAC library being … distributed to the participants and we are sequencing a certain number of BACs each. We'll combine all the data to produce the sequences," Henry says. This is just an initial attempt — they won't get complete coverage of the genome this way, but it's a place to start. So far, Ming estimates that a couple hundred BACs have been sequenced, mainly by members of the Brazilian cohort. Henry says that they'll likely wind up with a couple hundred-fold coverage of the haploid genome. "Sugarcane is 12- to 14-ploid — therein lies the problem of how we sort out all those different analogs of the different chromosomes," Henry says. "That requires strategies we haven't quite worked through yet."

"Ideally, we would need 5,000 BACs to cover the gene space, and if we want to cover the entire genome, we cannot afford it," Ming adds. "It's too big."

However, the group may be able to take advantage of the recent sequencing of the sorghum genome, published in Nature in 2009 by a group of researchers including Ming, led by JGI's Daniel Rokhsar. Sorghum is closely related to sugarcane, sharing a common ancestor about 5 million years ago, but it is diploid and has a much smaller genome. "That is almost a reference genome because sorghum and sugarcane are closely related," Henry says.

Indeed, Ming published a paper in BMC Genomics in April comparing the sequences of 20 sugarcane BACs to those in the sorghum sequence. He and his colleagues report that the coding regions of the two genomes shared an average of 95.2 percent of their sequence, leading them to conclude that the sorghum would be an "excellent template" upon which to assemble the sugarcane genome.

In addition, the pain of sugarcane sequencing and assembly could be eased by technological advances — Ming hopes that third-generation sequencers with longer read lengths will help. "The third-generation DNA sequencing technologies hopefully will give us the breakthrough we need to assemble an autopolyploid genome — physical mapping is out of the question," he says.

Henry adds that the consortium may have to bide its time a bit until those technologies are ready. "It may be that we have to really await that third generation, or next-next-gen, for sugarcane. We may need these very long reads to reliably assemble sequence when we've got so many different homologs of the same chromosome," he says.

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On the same page

Another challenge is that the consortium researchers come from six different countries — Australia, Brazil, China, France, South Africa, and the United States — and each group has to agree on the consortium's aims. The entire consortium has met a few times — in Brazil and Australia, as well as at the Plant and Animal Genome conference held each January in San Diego — to hash out its goals. One of the main questions the group is still struggling with is which cultivar to focus on — each member country is partial to sequencing its own indigenous strain, Ming says.

"We've had lot of challenges on agreeing what to do, trying to identify which genotype to sequence," Henry adds. "That becomes quite difficult because everyone wants to sequence each genotype from their country as the reference."

They are, however, zeroing in on one strain, Ming says. The consortium has set its sights on a well-characterized French hybrid called R570 — Ming notes that all modern cultivars are hybrids, and R570 is likely a mix of clones from a high-sugar containing species, Saccharum officinarum, and from a low-sugar species, Saccharum spontaneum.

Ming says that he and others are considering sequencing other species as well. "Our vision has been focused on the species, the domesticated high-sugar species S. officinarum, and the two wild, low-sugar species S. robustum and S. spontaneum," he says. His group has been making BAC libraries of those species in conjunction with another collaboration, the International Consortium for Sugarcane Biotechnology. "The genomes of S. officinarum and S. spontaneoum should be sequenced before we try to tackle a hybrid genome, which is enormous and complex," he says. As an anueploid, R570 has about 115 chromosomes, while S. officinarum has 80 chromosomes and S. spontaneum has between 40 and 128 chromosomes.

Henry says that the researchers are quite aware that they must work together if they want a sugarcane genome sequence. It's just too difficult to do alone.

The Breakdown
Founder: Glaucia Souza,
University of São Paulo
Member countries: Australia, Brazil, China, France, South Africa, and the United States
Funding: Awarded internally by each member country

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