In Japan, pearl oysters (Pinctada fucata) are an aquaculture staple. These precious baubles produced by tiny irritants trapped inside the mollusks are used to make jewelry around the world. Entrepreneur, farmer, and merchant Kokichi Mikimoto is widely credited with first developing cultured pearls 130 years ago and the legacy lives on. In 2019, pearls traded for about $5,810 (850,000 yen) per kilogram and prices surged as more and more people began to embrace wearing them.

However, over the last 20 years, a combination of diseases caused by viruses and red tides have hit the cultured pearl industry very hard. The production of Japan’s iconic pearls fell from over 150,000 pounds in the early 1990’s to just 44,092 pounds today.

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To learn more about oyster genetics with the hope of discovering more resilient strains, a team of researchers have built a high-quality, chromosome-scale genome of a pearl oyster. The team outlines their finding in a study published yesterday in the journal DNA Research.

“It’s very important to establish the genome,” study author Takeshi Takeuchi, staff scientist in Okinawa Institute of Science and Technology’s (OIST) Marine Genomics Unit, said in a statement. “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.”  

This work goes back to 2012, when Takeuchi and his collaborators published a draft genome of the Japanese pearl oyster. This was one of the first genomes assembled of a mollusk, and in the 10 years since, they have continued sequencing the genome to find a higher quality, chromosome-scale genome assembly.   

The oyster’s genome is made up of 14 pairs of chromosomes (28 total), one set inherited from each parent. The two chromosomes of each pair carry nearly identical genes, but there can be subtle differences and a diverse gene repertoire benefits their survival.  

Typically, when a genome is sequenced, this pair of chromosomes is merged together. This process works well for animals in a laboratory setting, since they normally have almost identical genetic information between the pair of chromosomes. However, wild animals like oysters have more variants in the genes that exist between chromosome pairs, and all of that variation can lead to a loss of genetic information.

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For this study the team sequenced both sets of chromosomes instead of merging them, possibly for the first time in a marine invertebrate. The genome sequence reconstructed all 28 oyster chromosomes and found key differences between the two chromosomes of one pair—chromosome pair 9. Importantly, many of the genes present on chromosome pair 9 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 Takeuchi.

According to Takeuchi, when the animal is cultured, there is often a strain that has a higher rate of survival or produces more beautiful pearls. Sometimes two animals with this strain can be bred together, but that leads to inbreeding and reduces genetic diversity. The study found that this important genetic diversity was significantly reduced after three consecutive inbreeding cycles.

The immunity of the oysters can then be impacted if the reduced diversity happens in the chromosome regions with genes related to immunity—like chromosome 9 in pearl oysters. “It is important to maintain the genome diversity in aquaculture populations,” added Takeuchi.

This kind of research will help the industry better prevent inbreeding so that the pearl oysters’ immune systems can fight off their increasing threats.