Satellite link to supercomputer sequences genome while sailing
27 May 2014Tweet
A University of Florida researcher has become the first scientist to sequence the genome of fragile marine creatures on board a ship in real-time.
Because of the difficulties of storing or shipping their genetic material, it has hitherto been difficult to sequence the genomes of marine species. However, researchers at the University of Florida have got round this problem by deploying a fully-equipped genomic laboratory aboard a ship called the Copasetic and sending the initial data via a satellite link to the University's new HiPerGator supercomputer.
Aboard the Copasetic in early February and later in March-April, Professor Leonid Moroz, from the University of Florida, and his team where able to perform transcriptome sequencing of 22 organisms, among them rare comb jellies.
Moroz studies fragile marine pelagic organisms – comb jellies or ctenophores – for their ability to regenerate. Their wounds can heal in two to three hours and they can regenerate their elementary brains in three to five days. Another creature, sea slugs, may hold the key to the genomic basis for memory and neuronal evolution. While humans have learned to slow the progress of some diseases, Moroz said many sea creatures have already figured out how to reverse disease and injury.
On board ship, samples were immediately processed and sequenced using the Ion Torrent Personal Genome Machine System, which was linked via satellite to the university's new high-performance computer, HiPerGator.
HiPerGator is a Dell/AMD machine, with 16,384 processing cores; a Terascala HPC Storage Solution with a fast open-source parallel file system; and Mellanox’s FDR 56Gbps InfiniBand interconnects. The HiPerGator was purchased and assembled for for $3.4 million.
‘The real success of these two proof-of-concept trips is that we now know we can do high-throughput sequencing at any location on Earth,’ Moroz said. ‘This is the perfect example of collaboration and synergy between public and private institutions such as Ocean Research Corp, International SeaKeepers Society, Florida Biodiversity Institute, and Ocean Expedition (OceanX) programmes.’
Moroz said he was motivated to prove direct sequencing and real-time genomic analysis in the middle of the ocean would work because of past frustrations with field expeditions. Creatures shipped to a lab often arrive in degraded condition. Oversampling to compensate for those errors is a problem, too, because it leads to ‘killing these beautiful creatures’ said Moroz. But without enough samples to repeat experiments, researchers must undertake another costly field expedition.
The potential benefits are great: about 50 per cent of drugs today are derived from natural products. The globe is 70 per cent ocean, and scientists estimate 14 million to 20 million compounds remain to be discovered at sea. However they are disappearing quickly, it has been estimated that we lose an undiscovered species every 6 hours. ‘We need to deploy a sequencing fleet,’ Moroz said. ‘There are potentially unique solutions in nature for medicine, but they are disappearing.’
The first results of the sequencing at sea were presented at the international conference, Advances in Genome Biology and Technology, held at Marco Island in Florida in February.
‘We are in the midst of a genomic revolution,’ Moroz said. ‘We must take advantage of this great new computing facility, we are in a race to save species, in 20 years some won’t exist. Losing them would be like losing the Sistine Chapel’ said Moroz.