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Tracking the Tuna: How PacBio Sequencing Could Help Save the “King of the Sea”

Wednesday, November 28, 2018

Northern Bluefin Tuna

Their bodies are big, bony and… warm?

Unique among bony fish, Atlantic, Pacific and Southern bluefin tuna have a rare endothermic physiology that has garnered great interest among scientists. Like birds, mammals and some sharks, these kings of the sea are capable of conserving internally generated metabolic heat produced from their swimming muscles and viscera, and maintaining tissue temperatures above that of the environment.

The fish are also renowned among sushi enthusiasts for their delectable, fat-laden muscle, and prized by fisherman because of the high prices they command.

So the preservation of these species is paramount to many, and researchers are keen to monitor and manage their populations, which have suffered precipitous population decline and are now at the lowest levels of their spawning biomasses in recorded history. But progress is being hindered by a lack of knowledge about the evolutionary and genomic processes that have driven the physiological and ecological diversification of the bluefin tunas.

Conservation genomics using SMRT Sequencing could help.

In a recent webinar hosted by Nature, Barbara Block, the Charles and Elizabeth Prothro Professor in Marine Sciences at Stanford University, joined PacBio scientist Paul Peluso to describe a project to protect Pacific and Atlantic bluefin tuna by assembling their genomes and transcriptomes.

At the Monterey Tuna Research and Conservation Center, one of the world’s only captive bluefin centers, Block and colleagues are studying the physiology, energetics, hydrodynamics and transcriptomics of the fish. But tracking the activity of the fish in their natural habitat is also vital.

Among the questions they want to answer: How do these animals adapt to their ocean realms, and what is it about the bluefins that makes them uniquely different than all other tunas in their clade? What limits their performance in a warming world? How will they adapt to hypoxia, increased CO2 and ocean acidity?

“We’re interested in monitoring their genes and transcriptomes to help us understand the health of these tunas in an ocean, but that’s not easy,” Block said. “It’s not easy because the ocean is not transparent. When tunas slip beneath the surface, it becomes hard to follow them and to monitor their populations, their transcriptomics, their genomics, and where it is they go.”

Block said her lab uses a “fish and chips” approach. “We put computers on these animals that record their journeys beneath the sea along with the environmental conditions surrounding them,” she said. “By mapping the tunas on the globe, we are able to show visually, and spatially, how these animals use our planet.”

They’ve discovered that the fish travel far, able to go from Iceland to the Gulf of Mexico, or cross from North America to the Mediterranean, in just a few months. It is not so easy to tell populations apart, but genetics has helped.

As Peluso explained, the team generated approximately 118 Gb of sequence from just under 7 million reads for the Atlantic tuna (Thunnus thynnus), and 15 million reads, yielding just over 208 Gb of sequencing for the Pacific bluefin (Thunnus orientalis). Using FALCON-Unzip, they resolved haplotypes and identified structural variants along diploid assemblies of 1.6 Gb and 1.24 Gb, respectively.

Compared with an existing Pacific tuna (T. orientalis) genome from Japan assembled with short-read technology, the new PacBio assemblies contained much fewer fragments — around 2,000 contigs, compared to 16,802 for the Japanese assembly.

“It helped us to identify some genomic differences between these two species, as well as to develop a set of probes, or markers, that could be used to profile these species in a population scale across the globe,” Peluso said.

Further study could involve deeper dives into the assemblies to compare structural variants with gene models, such as correlations between the presence or absence of genes, as well as downstream implications of enhancer or promoter regions on gene expression.

“Having highly contiguous assemblies will help address these questions,” Peluso said.

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