SGI Powers University of Hawaii’s Papaya Genome Sequencing Project

An International Papaya Genome Consortium led by University of Hawaii (UH) researchers has completed the Papaya Genome Sequencing Project and, from the start, researchers relied on technology from SGI to provide the processing power and speed required to run the assemblies. The papaya genome was sequenced using a whole genome shotgun approach running on the combination of an SGI Altix system, SGI InfiniteStorage and Qube! scheduling software from PipelineFX. It has taken two years to construct the physical map and to sequence the 372 million base pairs. The disease-resistant ‘SunUp’ papaya is now the first fruit — and the first transgenic crop — to be sequenced, helping to pave the way for international export of genetically modified fruits and vegetables.

"Sequencing the papaya genome is the first large scale genome project done in Hawaii with international collaboration from 22 research institutes and will benefit the papaya research community, papaya farmers, and consumers for years to come," said Maqsudul Alam, Director of the Center for Advanced Studies in Genomics, Proteomics, and Bioinformatics, College of Natural Sciences, lead institute of the International Papaya Genome Consortium. "We chose the SGI Altix because of the configuration of the memory system, how quickly we can use the random memory, and also the scalability of the system, and of course, the price/performance. SGI technology has been instrumental in achieving this technological and scientific milestone."

The second largest crop in Hawaii, papaya was almost wiped out by the papaya ringspot virus a decade ago. Genetically modifying the papaya to create a ringspot-resistant transgenic or ‘hermaphrodite’ variety such as the SunUp saved the papaya from extinction on the islands. The Papaya Genome Project mapped papaya genes to improve the efficiency of agricultural cultivation, and to discover new applications for one of the most important edible fruit crops of tropical and subtropical regions worldwide. Papaya is also used in a wide range of medical, biotechnological and cosmetic applications that can be further developed now that a complete picture of the genomic sequence has been drawn.

When the project began over two years ago, Dr. Alam, who heads the multi-institution project housed at the UH Maui High Performance Computing Center (MHPCC) at University of Hawaii, looked for the fastest, and largest computer their budget would allow, one able to run for weeks without stopping during the 2-year-plus project. He also looked for a scalable backend-distributed processing solution with open API’s to develop Web-based interfaces, which allowed the development of custom processes, such as pre-loading standard databases into memory for faster searches. Another major consideration was the Project was going to generate a tremendous amount of data: a typical papaya base pairs assembly run can use as much as 40GB of memory and 150GB of disk space. Future plans of processing even larger genome sequencing projects will also require very large, highly scalable disk storage.

The SGI Altix system, with 32 CPUs of processing power, gave the team high throughput to their computing needs, allowing them to run highly multi-threaded applications concurrently. PipelineFX Qube!, used widely in digital media for game build engines and animation rendering, was uniquely set up as the Center’s backend software environment. PipelineFX Qube!, which handles distribution tasks, also managed the interactive Web site, Gbrowse, for national and international collaborators on the project.

The University of Hawaii used an SGI Altix 350 computer system, SGI InfiniteStorage TP9300 Fibre Channel storage, which has been upgraded over the course of the project to over 16TB, and PipelineFX Qube! render management and batch-queuing software for the Project. The complete system, purchased over two years ago, was integrated and sold through SGI Channel Partner CORESystems Hawaii.

"Because the SGI system architecture allows very large memory to be shared across all the processors, the Center personnel were able to write their own software that, every night, downloaded all the versions of the genomic databases, and the most common were uploaded into the Altix system’s shared memory for immediate access," said Deepak Thakkar, Higher Education and Research Solutions Manager, SGI. "SGI Altix systems and scalable storage solutions, with PipelineFX Qube!, made a unique genome analysis tool that got the job done. This is an exciting combination that has many other applications in biosciences."

The Hawaii Papaya Genome Project is a multi-institutional bioinformatics project. In Hawaii, participants include MHPCC, Hawaii Agricultural Research Center (HARC), Hawaii Papaya Industry Association, USDA Pacific Basin Agricultural Research Center, Pacific Telehealth and Technology Hui, and Hawaii Biotech. Nankai University in China is a major collaborator, as is University of Illinois and Maryland Biotechnology Institute.

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