In the basement of a lab at Baltimore’s Inner Harbor, The Chosen One was born.
At least, that’s what the researchers at the University of Maryland’s Center for Environmental Science called her. She was the blue crab who would be the foundation of a breakthrough scientific discovery — the first map of the species’ DNA.
Through a process known as genome sequencing, the scientists created a virtual blue crab encyclopedia, which appears on a computer screen as a color-coded network of thousands of nucleotides — the genetic building blocks that make a blue crab a blue crab.
The genome’s contents, researchers say, hold a range of potential clues to help them better understand and protect the state’s beloved crustacean. It could help pinpoint what mutations drive disease, for example, or track how climate change affects the species in the wild. It could even provide a blueprint on how to breed the meatiest crabs in a lab for Maryland picnic tables in summers to come.
Scientists had published genome assemblies for 67 different crustaceans, from the Chinese mitten crab to the shrimp. But until this year, the genetic road map of the blue crab remained largely a mystery.
Just sequencing the data took four researchers about four years. It’s an arduous process, but one that’s become more achievable thanks to technological advancements. By comparison, a first draft of the human genome was unveiled in 2000, but completing it took until this summer.
The work officially began on the waters of the Chesapeake Bay one day in 2014. UMCES professor J. Sook Chung boarded a crabber’s boat off Pasadena and harvested dozens of young female crabs to bring back to her lab at the Institute of Marine and Environmental Technology in downtown Baltimore.
After years of raising crabs in her lab, one question plagued her: Why is it that one mother crab can produce millions of eggs, but only a lucky few survive to adulthood?
Genomic sequencing could provide the answer.
To get there, the scientists had to raise the chosen crab, born in 2015 from one of the crabs harvested a year earlier. The next year, she gave birth in the lab to dozens of healthy babies, proving her genetic viability. Then, they extracted as much blood and soft tissue from that crab and sent those samples to a lab in Rockville for DNA extraction.
Then, Baltimore scientists received a trove of information from the Rockville lab that they had to piece together, bit by bit. It was terabytes upon terabytes of data, which had to be processed by a computer for five to six months at a time. That’s because the results were full of extra, repetitive genetic information, which they had to comb through to craft each individual chromosome.
“It’s a little bit like ads — when you’re watching Hulu and you get the same ads again and again,” said Tsvetan Bachvaroff, another professor at the University of Maryland center.
When the intricate jigsaw puzzle was complete, the group determined that blue crabs have 40 to 50 chromosomes. That’s nearly double the number in humans, but each one is considerably shorter than ours. There are still some small gaps in the blue crab genome, but future research could fill in the holes.
The scientists’ article was published last month in the peer-reviewed journal “G3: Genes, Genomes, Genetics.” The entire sequence will soon be available for public viewing.
The Maryland scientists are now able to compare the DNA of other blue crabs to the model they’ve created to understand what drives any differences between them. For instance, what genes decide the crabs’ size and color? What genetic differences separate a Maryland crab from one native to the waters of, say, Venezuela?
In Baltimore, they’ve already determined which part of the sequence encodes the hormone that controls molting, when crabs shed their shells so they can grow. Manipulating this gene could pave the way for improvements in large-scale blue crab farming, Chung said. That’s important because when blue crabs grow in a tank, they molt at different times. Crabs with soft bodies are vulnerable to their bloodthirsty brethren.
“Blue crabs are sort of notorious for cannibalistic behaviors. They don’t care if they’re siblings. If you culture them in a communal tank — thousands of them — eventually, there’s just one big crab. They will eat each other,” Chung said. “If you synchronize all of the animals sharing the water shedding the shell at the same time, you can remove those cannibalistic behaviors.”
Molting is also a vulnerable time for crabs in the wild, and the environment they’re in during that time has a profound impact on their future health and size, said Genine McClair, blue crab program manager for the Maryland Department of Natural Resources. Understanding more about what drives the process could help fisheries managers adjust harvest practices in pursuit of the best crabs, she said.
“Now, we have this starting point to ask all these questions, and researchers from all over the country can ask these questions, but they have to reference back to Maryland as where it all began,” she said.
All told, the sequencing project cost less than $250,000, much of which came from Maryland-based donors like Mike and Trish Davis of Severna Park. The couple, who ran a software company for decades before their retirement 12 years ago, was looking to support projects that might have trouble getting off the ground without an initial burst of donor funds.
“It’s just a tough project because we don’t know exactly what the benefits will be, and people don’t like to fund that sort of thing,” Mike Davis said.
Slowly, Davis and his wife assembled a group of donors, who collectively gave about $140,000 to the genome project, Davis said.
There was a competitive spirit that helped the scientists in Baltimore make their case, Davis said. The scientists joked about a general rivalry with counterparts in Virginia who also study blue crabs.
“They told us: ‘Well, it’s going to get mapped, it’s just a matter of who,’” Davis said. “We don’t want Virginia to do this, of course, as proud Marylanders.”
On a recent afternoon, Chung fed the lab’s latest crop of blue crabs from the bay, each stored in an orange Home Depot bucket, with oxygen tubes piping bubbles into their watery homes. It’s a seven-day-a-week job, she said, to keep the crabs healthy and note their progress.
Sporting a red T-shirt with an image of blue crab sewn on the back, Chung weaved between vast blue tanks to a dark corner of the lab, where minuscule baby crabs grow. Each with their own underwater cubicle, illuminated only by gentle red light, the dime-sized crabs are delicate creatures.
In a way, it’s fitting Chung was part of the genome sequencing work. Her first name, Sook, is another word for a mature female blue crab, as she’s quick to point out. And her earlier work had unveiled some of the creature’s more carefully guarded secrets. In 2014, for example, she was part of a team that discovered a new sex hormone in the eyestalks of female blue crabs.
But this recent project feels the most significant, she said — the equivalent of passing a baton to the relay runners of tomorrow.
“This is a digitized legacy to those who are coming — for the next generation of scientists,” she said. “That’s the way I see it. I left something behind.”