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Bridges helps preserve abalone species

Speed read
  • Abalone farming has ballooned to a $100 million+ industry
  • Memory-intensive Bridges supercomputer proves a key to conservation efforts
  • Genomic knowledge increases efficiency of abalone aquaculture businesses

Commercial abalone aquaculture — farming the shellfish in enclosures — has exploded to become a $100 million global industry over the past decade.

To improve and expand business operations, scientists at Iowa State University and the National Oceanic and Atmospheric Administration (NOAA) worked with the Pittsburgh Supercomputing Center (PSC) experts to assemble the DNA sequences of several species of abalone on the Bridges supercomputer.

Fishy business

Red abalone, a prized delicacy in much of the world, has also become more popular among American seafood eaters. This increased popularity is also driving growth in abalone farming, with abalone aquaculture becoming a major business in California, Korea, China, and in other areas around the world.

<strong>Delicate balance. </strong> Abalone popularity as a delicacy has relegated it to fisheries for mass production. Genomic sequencing will isolate desirable traits and increase industry efficiency. Courtesy Pittsburgh Supercomputing Center.

In part because wild abalone populations have been over-exploited and hit with disease, the shellfish is one of the few species in which farming, not fishing, dominates the global market.

Despite the value and volume of abalone culture, farmers still have a lot to learn about the shellfish. By breeding individuals with useful traits — like growth rate, disease resistance, and tolerance to temperature change — producers hope to grow it in a more cost-efficient manner.

Research on abalone DNA is also vital for plans to restore the endangered white and black varieties, and will likely play an important role in trying to save them from extinction.

That’s why Andrew Severin and Arun Seetharam of Iowa State University, along with colleagues John Hyde and Catherine Purcell at the NOAA Fisheries, Southwest Fisheries Science Center in La Jolla, California, decided to assemble the DNA sequences of several species of abalone.

“Researchers at Iowa State University have been working on similar projects to improve food production for the last 10 years in agriculture, and so we already had a sense of the best approaches to create genomic resources for a particular organism when you're trying to effectively breed it to maximize production,” says Severin.

Bridge to the future

The red abalone aquaculture species has a genome consisting of 1.8 billion DNA bases (letters in the genetic alphabet). Current sequencing technology reads DNA in fragments as small as 100 bases, and the investigators needed a powerful computer to mix and match billions of these overlapping reads to discover their proper genomic order.

Farmed abalone is genetically wild, with a lot of genetic variation between individuals. That’s good for a wild population, but can make assembling the DNA fragments harder because the same fragment in the genome can have different letters in different individuals.

Worse, abalone has a lot of repetition in its DNA sequence,which means the same fragment could match multiple places in the genome. All of this can quickly overwhelm the memory of a computer trying to reconstruct the full sequence.

Severin, who manages Iowa State’s Genome Informatics Facility, has been a Campus Champion with Extreme Science and Engineering Discovery Environment (XSEDE) since 2014. He knew that assembling the genomes of the five abalone species was going to take much more memory than available on most supercomputers.

He also knew where to find that kind of memory.

<strong>Friends in high places. </strong> Over-hunted nearly to the point of extinction, abalone have an HPC ally. Three TB of memory on the Bridges supercomputer made short work of genome assembly for five abalone species. Courtesy Iowa State University Genome Informatics Facility.

Working with XSEDE Extended Collaborative Support Service experts Phil Blood and David O’Neal at PSC, Severin's team ran assemblies on the large memory nodes of Bridges, an XSEDE-allocated system at PSC.

“We did the preliminary assemblies on Bridges for all five species,” says Seetharam.

“Our local supercomputing infrastructure was over-utilized, and XSEDE's Bridges supercomputer was the only place that would run all five genome assemblies at the same time.”

Today, they’ve completed rough assemblies of all five species and a 97 percent complete assembly for the commercially important red abalone.

Once the red abalone genome is finished, the scientists will compare the genes across all abalone species from different regions to identify which genes offer survival and growth benefits in different environments and growing conditions.

Thanks to the HPC resources and expertise provided through XSEDE and PSC, scientists have been able to provide crucial efficiency information to commercial abalone farms, while helping to restore the endangered white and black abalone.

Read the original article on PSC's website.

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