One of the challenges facing the world today is securing the food supply for everyone in the face of rising populations and environmental change. An important part of the solution is to analyze the DNA of crops in order to better understand what makes crops resistant to pests, drought, and other environmental stresses. That’s a huge challenge. The wheat genome is at least five times larger than the human genome and contains many repeated sequences. Bread wheat also has three distinct ancestral subgenomes, so trying to sequence and assemble the bread wheat genome is as difficult as sequencing and trying to interpret the genomes of a human, chimpanzee, and gorilla at the same time.
Genome Sequencing Powered by Intel Processors
The Genome Analysis Centre (TGAC) has taken on that challenge, using one of the largest SGI UV 2000 HPC systems in the U.K., which is powered by the Intel Xeon processor E5-4650L product family.
Laboratory data comes from high-throughput sequencers that analyze the physical matter DNA. After this primary analysis, the data is interpreted to read out the sequence of letters that represent each strand of DNA. It is then submitted to quality control, assembly, and annotation, where TGAC’s scientists can then start to interpret this data in order to understand each part of the genome.
Richard Leggett, project leader for quality control and primary analysis at TGAC, explains the assembly process: “We think of a ‘genome’ as a string of millions or billions of letters that represent four basic biological compounds — the wheat genome, for example, is represented by a string of 17 billion characters. But the most common DNA sequencing machines can only ‘read’ around 100 to 300 letters of DNA at a time, so when we sequence a genome we have to split it up into lots of smaller chunks. Assembly is the process of putting them back together again; unfortunately, there is no way to know where in the genome each sequenced chunk comes from. It’s a bit like taking 30 copies of a novel, cutting up all the words, putting them together in a big pile and then trying to re-create the novel. It requires a lot of computing power.”
Xeon Proves Vital to Sequencing
Lab operations can process between 2 and 4 TB of data per week — approximately 2 TB of which then needs to be stored. The SGI UV 2000 is a large shared memory platform, which, in combination with the Intel Xeon processor E5-4650L product family, makes up to 4,096 cores and 64 TB of coherent main memory for in-memory computing available in a single image system. TGAC is using 20 TB of coherent main memory, 2,560 cores, and 64 TB of RAM.
TGAC’s scientists have now sequenced and assembled 17 of the 21 chromosomes of the wheat genome. Researchers estimate that the full wheat genome sequence will be available within three years. It will help take the guesswork out of breeding new crops and give farmers rapid insight into which crops can resist local pathogens, so crop failures can be avoided.
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