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Synthetic Genomics, ACGT Use Sanger, 454 to Sequence Jatropha Genome


Synthetic Genomics and the Asiatic Centre for Genome Technology, a subsidiary of a Malaysian oil palm plantation company, said this week that they have completed a first draft of the 400-megabase jatropha genome, a tropical tree that is one of the highest yielding oilseed plants.

The announcement comes less than two weeks after another private research partnership — between Roche's 454 Life Sciences, Synamatix, and Malaysian plantation company Sime Darby — said it had completed the oil palm genome (see In Sequence 5/19/2009). It may indicate that more agricultural companies are looking towards genome sequencing to help them improve their crops.

Synthetic Genomics and ACGT, a subsidiary of oil palm plantation company Asiatic Development Berhad, announced a year ago that they had completed a draft genome of the oil palm genome, a project they undertook independently from 454 and its partners.

Both the oil palm and jatropha projects are part of a 2007 joint venture between SGI and ACGT, which involved an investment of undisclosed amount by ACGT into San Diego-based SGI.

Both the jatropha and the oil palm genomes were sequenced by a mix of Sanger capillary sequencing and 454 sequencing, according to Helge Zieler, senior director of plant genomics at SGI.

"Taking a conservative approach that used Sanger technology as a primary source of gathering sequence made sense because of the read length," which helps with a high-quality assembly, Zieler said.

Sequencing for both projects was performed at the J. Craig Venter Institute in Rockville, Md., "our collaborator for all matters sequencing," he said. Craig Venter is the founder and CEO of Synthetic Genomics.

For the jatropha genome, the researchers generated eight-fold coverage by Sanger sequencing, using small-, medium-, and large-insert shotgun libraries, and two-fold coverage by 454 sequencing.

In contrast to the Sime Darby oil palm genome assembly, which is entirely based on 454 sequencing and used a combination of bacterial artificial chromosome and shotgun sequencing, the vast majority of Synthetic Genomics' jatropha assembly came from shotgun libraries.

"We stayed clear of excessive use of BACs" because those with highly repetitive content sometimes rearrange the DNA, Zieler said. "We do use BACs to some degree, but it's a very low amount."

Because the assemblies of both research consortia are proprietary, they did not disclose details about their quality, or the cost of their projects. Zieler said that he and his colleagues might publish the oil palm and jatropha genomes in the future but have no concrete plans to do so at the moment.

They have also sequenced ESTs to generate transcriptome data to annotate the jatropha genome, using a proprietary in-house approach that differs from commercially available transcriptome sequencing methods and "which, at reasonable cost, allows us to deeply sequence into the transcriptome and discover both commonly expressed and rare genes," he said.

Under a metagenomic program, the researchers have also sequenced and analyzed microbes associated with jatropha's roots, soil, and leaves to identify those that might be "useful for a variety of applications in the plantation."

This analysis involved "one or more" sequencing methods and differed, depending on the nature of each project, he said.

SGI and ACGT are "not immediately" planning to sequence additional crop genomes, Zieler said, but improving the oil palm and jatropha plants — the ultimate goal of the projects — will involve resequencing additional plants to track certain phenotypes.

"Sequencing will continue to be a big part in this project going forward, but not necessarily of the same scale or scope of what we just undertook, because once you have a reference genome in place, producing derivative sequences is much cheaper and could be done using other, less conservative approaches" that could involve "any of the currently available sequencing technologies," he said.

Having the genome sequence will also help with crop breeding because it can provide markers for certain traits. "The process of marker-assisted breeding can be very much streamlined and accelerated when a genome is available," he said. Specific genetic markers can, for example, identify regions in the genome that are associated with yield, oil content, disease resistant, or salt tolerance.

"But also, the genome gives an insight in general into the biology of the plant, into what may contribute to make it a productive oil seed crop," he said. "We are studying it to try to see if and what can be learned from it to achieve further gains in productivity."

But the genome is only the first step on the path to get there, he cautioned. "The genome is just the platform that makes a lot of new things possible. By itself, it will not give you an improved plant."