Study reveal the molecular fingerprint behind beautiful pearls

A high-quality, chromosome-scale genome of pearl oysters.


In a new study, scientists- from the Okinawa Institute of Science and Technology (OIST), in collaboration with several other research institutes, including K. MIKIMOTO & CO., LTD, Pearl Research Institute, and Japan Fisheries Research and Education Agency- have reported a near-complete, haplotype-phased, genome assembly of the pearl oyster. This high-quality, chromosome-scale genome of pearl oysters could be used to find resilient strains.

The traditional method for genome sequencing involves merging the pair of chromosomes. However, this goes well for laboratory animals, which normally have almost identical genetic information between the pair of chromosomes. For wild animals, however, where there are numerous gene variations across chromosome pairs, this strategy results in a loss of information.

When sequencing the genomes for this investigation, the scientists decided not to combine the chromosomes. Instead, both sets of chromosomes were sequenced. This is the first research- focusing on marine invertebrates to use this method.

Pearl oysters have a total of 28 chromosomes because they have 14 pairs of them. Scientists then used advanced technology for genome sequencing. Later, they reconstructed all 28 chromosomes and found key differences between the two of one pair—chromosome pair 9. Notably, many of these genes were related to immunity.

Dr. Takeshi Takeuchi, staff scientist in OIST’s Marine Genomics Unit, said, “Different genes on a pair of chromosomes is a significant find because the proteins can recognize different types of infectious diseases.”

“When the animal is cultured, there is often a strain that has a higher rate of survival or produces more beautiful pearls. The farmers often breed two animals with this strain, which leads to inbreeding and reduces genetic diversity.”

After three consecutive inbreeding cycles, scientists found a significant reduction in the genetic diversity. If this reduced diversity occurs in the chromosome regions with genes related to immunity, it can impact the animal’s immunity.

genetic information necessary for an organism
The genetic information necessary for an organism to maintain its vital activities is called a genome. In genome decoding, DNA is extracted from individual cells, fragmented, and analyzed. The DNA sequence fragments are then reconstructed to obtain a genome assembly. Animals that reproduce sexually inherit one set of genomes from the mother and one from the father. 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.

“It is important to maintain the genome diversity in aquaculture populations.”

Prof. Shugo Watabe (Visiting Professor at the Kitasato University, professor emeritus at the University of Tokyo) said“Cultured pearls were developed for the first time in the world 130 years ago by Kokichi Mikimoto in Japan. Even today, they are the second most exported marine product produced in Japan, after scallops. However, the history of pearl aquaculture in Japan has been a battle against diseases in the aquaculture environment. The damage caused by the red discoloration disease, which emerged in 1996, was particularly severe.”

“The production of cultured pearls in Japan has declined significantly. In recent years, the pearl-farming industry is again facing major problems due to the spread of diseases caused by viruses. Although the details of the causes of diseases and countermeasures have not been established, it has been pointed out that pearl cultivation in Japan may be suffering from genetic deterioration due to the inbreeding of pearl oysters with superior traits, which makes it difficult to respond to various environmental changes and the emergence of pathogens.”

The results of this study have clarified the issue of pearl cultivation in Japan and have significant industrial implications. Many of the immune system‘s genes have also been identified, in addition. This explains why pearl oysters can produce a nacreous coating in response to an introduced foreign object from the outside, which sheds light on the mystery surrounding pearl production itself.

Journal Reference:

  1. Takeshi Takeuchi, Yoshihiko Suzuki, Shugo Watabe, et al. A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster. DNA Research. DOI: 10.1093/dnares/dsac035
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