JAPANESE SCIENTISTS ARE on a mission to save the species of oyster responsible for producing the world’s most beautiful cultured pearls. The Japanese pearl oyster — Pinctada fucata — is fighting for its survival as viruses and red tides have taken a savage toll on oyster populations and, as a result, pearl production in Japan has shrunk by 70% over the past 20 years.

In an effort to preserve the future of the Japanese pearl industry, scientists have constructed a high-quality, chromosome-scale genome of the Pinctada fucata species, which they hope can be used to breed hardier, more resilient mollusks. The research was published recently in DNA Research.

“It’s very important to establish the genome,” said Dr. Takeshi Takeuchi, staff scientist in the Okinawa Institute of Science and Technology (OIST) Marine Genomics Unit. “Genomes are the full set of an organism’s genes — many of which are essential for survival. With the complete gene sequence, we can do many experiments and answer questions around immunity and how the pearls form.”

Scientists at the OIST, in collaboration with K. Mikimoto & Co.’s Pearl Research Institute and the Japan Fisheries Research and Education Agency, reconstructed 14 pairs of chromosomes (28 in total) and found key differences between the two chromosomes of one pair—chromosome pair 9. Notably, many of these genes were related to immunity.

“Different genes on a pair of chromosomes is a significant find because the proteins can recognize different types of infectious diseases,” said Dr. Takeuchi.

The scientists believe that the current state of the pearl farming industry is due partly to the lack of genetic diversity in the oyster population. Pearl farmers often breed oysters that have a higher rate or survival or ones that produce more beautiful pearls. But, researchers observed that after three consecutive inbreeding cycles, the genetic diversity was significantly reduced. Genetic deterioration due to the inbreeding of oysters with superior traits makes it difficult for the species to respond to various environmental changes and the emergence of pathogens.

“It is important to maintain the genome diversity in aquaculture populations,” concluded Dr. Takeuchi.

Akoya pearl production is currently 20,000kg (44,092 lbs) per year, down from 70,000kg (154,323 lbs) per year two decades ago. The scientists are hoping to restore an aquaculture industry that was generating 88 billion yen ($630 million) in annual revenue in the early 1990s. Despite diminished numbers, cultured pearls still rank as Japan’s second-most-exported marine product, after scallops.