The hidden genetics of the embattled Japanese pearl oysters

Researchers trying to save the devastated Japanese pearl industry have delved deep into the pearl oyster’s genetics and found unexpected riches.

Pearls are the country’s second most exported marine product (after scallops). But this century, akoya pearl production has dropped from 70,000 kilograms per year to just 20,000.

Diseases and algal blooms called red tides, have devastated the Japanese pearl oyster (Pinctada fucata).

The researchers have used a high-quality genetic sequencing technique to learn the mollusc’s genome.

Read more on pearl oysters: Taking aquaculture offshore, beyond the blue horizon

“Genomes are the full set of an organism’s genes – many of which are essential for survival,” explains co-lead author of a report in DNA Research, Dr Takeshi Takeuchi, staff scientist in the Marine Genomics Unit at Okinawa Institute of Science and Technology, Japan.

“With the complete gene sequence, we can do many experiments and answer questions around immunity and how the pearls form.”

Takeuchi and colleagues first published a decade ago a draft genome of the Japanese pearl oyster’s 14 chromosome pairs.

They did this using a “typical” method of genomic sequencing: merging each chromosome pair  and reading a combination of the two chromosomes.

This method works well for creatures with little genetic diversity, but for wild animals with a lot of genetic variation, some information can be lost.

This time the researchers individually sequenced both sets of chromosomes and found some key differences between the pairs.

Two genetic sequencing diagrams. One has a mouse and two green haplotypes which are broken up and mixed together to make a single green haplotype. The second has a japanese pearl oyster and a blue and purple haplotype. When the haplotypes are broken up and mixed together again, the resulting genome is a mix of purple and blue. But when the haplotypes are broken up less using a technique labelled gdna fragmentation & long-read hifi sequencing, two pure haplotypes are the result - one blue, one purple
A set of genomic information derived from one parent is called a haplotype. (i) In experimental organisms with established strains or species with small genetic diversity, an individual possesses two sets of nearly identical genomes. Thus, the haplotype-merged genome assembly will be similar to both the two sets of genomes of the original individual. (ii) In organisms with high genetic diversity, such as wild animals, there are large differences in DNA sequences among haplotypes. Using conventional methods results in a genome assembly with a mixture of two haplotypes. It can lose genomic information. (iii) In this study, longer and more accurate DNA sequences were obtained by using the latest sequencer. The two haplotypes were reconstructed separately. Credit: OIST

Chromosome pair 9, specifically, had a lot of diverging genes – many of which 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,” says Takeuchi.

Pearl farmers will often select the oysters that produce the most beautiful pearls for breeding. After three generations, Takeuchi says, this inbreeding cycle can cause a loss in genetic diversity.

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“The findings of this research have shed light on this concern of pearl cultivation in Japan, and are of great industrial significance,” says Professor Shugo Watabe, a visiting professor at the Kitasato University, and professor emeritus at the University of Tokyo, Japan.

“Furthermore, many of the genes involved in the immune system have also been identified.

“This also provides insight into the mystery of pearl formation itself, as to why pearl oysters can form a nacreous layer in response to an externally introduced foreign object.”

Because this nacreous layer is how pearls are made, learning more about it could be beneficial to the industry.

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