The molecular fingerprint behind the beauty of Akoya pearls

Researchers have constructed a high-quality, chromosome-scale pearl oyster genome
.

• In Japan, pearl oysters are a key animal in aquaculture because they produce precious and beautiful pearls
  .
  

• Over the past 20 years, the production of Akoya pearls has declined from about 70,000 kilograms per year to just 20,000 kilograms
  per year due to various reasons, including disease.
  

• Researchers have built a high-quality, chromosome-scale genome of pearl oysters with the goal of discovering resilient variants and learning more about their underlying genetics
  .
  

• Using advanced technology, scientists have constructed the genome of not just one set of chromosomes, but two sets of chromosomes, revealing unexpected diversity
  in the gene pool within an individual.
  

• A crucial finding was the discovery of multiple genes responsible for immunity, suggesting that it is possible to grow resilient oyster varieties
  .
  

Pearl in an oyster shell
.
Pearl oysters are an important product in Japan because they produce beautiful pearls and are used to make necklaces, earrings and rings
.

In Japan, pearl oysters are an important aquaculture animal because they produce beautiful pearls that are used to make necklaces, earrings and rings
.
In the early 90s of the 20th century, this aquaculture industry brought in about 88 billion yen in revenue
per year.
However, over the past 20 years, new diseases and red tides have reduced Japan's pearl production from about 70,000 kilograms per year to just 20,000 kilograms
.

Now, the researchers have constructed a high-quality, chromosome-scale pearl oyster genome that they hope can be used to find resilient strains
.
The study was conducted by scientists from the Okinawa Institute of Science and Technology (OIST) in collaboration with K.
K.
A collaboration between MIKIMOTO & CO.
, LTD, Pearl Research Institute and a number of other research institutions, such as Japan's Fisheries Research and Education Agency, was recently published in the journal DNA Research
.

"Building the genome is very important," said
Dr.
Takeshi Takeuchi, one of the two first authors and a scientist in OIST's Marine Genomics Division.
The genome is the entire genome of an organism, many of which are essential
for survival.
With the complete genetic sequence, we can do a lot of experiments to answer questions
about immunity and how pearls form.
”

The genetic information necessary for an organism to sustain its vital activities is called the genome
.
In genome decoding, DNA is extracted from individual cells for fragmentation and analysis
.
DNA sequence fragments are then reconstructed to obtain genome assembly
.
Sexually reproducing animals inherit a set of genomes from their mothers and a set of genomes
from their fathers.
A set of genomic information from one parent is called haplotype
.
(i) In experimental organisms with established strains or species with less genetic diversity, individuals possess two sets of nearly identical genomes
.
Thus, haplotype merged genome assembly will be similar
to 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 between haplotypes.
Using traditional methods, genome combinations
of two haplotypes can be obtained.
It may lose genomic information
.
(iii) This study obtained longer and more accurate DNA sequences using the latest sequencers
.
The two haplotypes are reconstructed
separately.

In 2012, Dr.
Takeuchi and his collaborators published a draft genome of the Japanese pearl oyster (Pinctada fucata), one of the first species to assemble the genome of
mollusks.
They continued genome sequencing to build a higher-quality chromosome-scale genome assembly
.

Dr.
Takeuchi went on to explain that the oyster's genome consists of 14 pairs of chromosomes, one of which is inherited from both
parents.
Each pair of chromosomes carries nearly identical genes, but there are subtle differences
if different gene pools are conducive to their survival.

Traditionally, when genomes are sequenced, researchers merge pairs of chromosomes together
.
This works well for laboratory animals, which often have nearly identical genetic information
between chromosome pairs.
But for wild animals, there is a fair amount of genetic variation between chromosome pairs, and this approach leads to a loss
of information.

In this study, the researchers decided not to merge chromosomes
when sequencing the genome.
Instead, they sequenced both sets of chromosomes — a very rare method
.
In fact, this may be the first time this method has been used to study
marine invertebrates.

Because pearl oysters have 14 pairs of chromosomes, they have a total of 28 pairs of chromosomes
.
OIST researchers Mr.
Manabu Fujie and Ms.
Mayumi Kawamitsu sequenced the genome using state-of-the-art technology
.
Another first author, Dr.
Yoshihiko Suzuki, a former postdoctoral scholar of OIST's ecological and evolutionary genomics algorithm, now at the University of Tokyo, Dr.
Takeuchi reconstructed all 28 chromosomes and found key differences
between two chromosomes in a pair of 9.
Notably, many of these genes are associated with
immunity.

"The different genes on a pair of chromosomes is a major discovery because proteins can recognize different types of infectious diseases," Dr.
Takeuchi said
.

He noted that when the animals are cultured, one strain tends to have a higher survival rate or produce more beautiful pearls
.
Farmers often raise two animals with this strain, but this leads to inbreeding and reducing genetic diversity
.
The researchers found that after three consecutive inbreeding cycles, genetic diversity decreased
significantly.
If this reduction in diversity occurs in chromosomal regions of immune-related genes, it can affect the animal's immunity
.

Dr Takeuchi concluded: "It is important to
maintain the genomic diversity of aquaculture populations.

This research was supported
by the Bio-Oriented Technology Research Promotion Agency Project, a special program for the research and development of advanced technologies for the next generation.

130 years ago, Japan's Mikimoto Kokichi Mikimoto developed cultured pearls
for the first time in the world.
Even today, they are the second largest marine product exported by Japan, after scallops
.

However, the history of pearl farming in Japan has always been the history of fighting diseases in the
cultivation environment.
The damage caused by the appearance of red discoloration in 1996 was particularly severe
.
Production of cultured pearls in Japan has declined
significantly.
In recent years, the pearl farming industry has once again faced major problems
due to the spread of diseases caused by viruses.

Although the details of the cause of the disease and countermeasures have not yet been determined, it has been pointed out that pearl culture in Japan may undergo genetic degradation due to inbreeding of pearl oysters with superior traits, making it difficult to cope with various environmental changes and the emergence
of pathogens.

The results of this study shed light on this issue of pearl farming in Japan and are of great industrial significance
.
In addition, many genes involved in the immune system have also been identified
.
It also provides insight into the mysteries of pearl formation itself, such as why oysters can form a layer of nacre in response to foreign objects
introduced from outside.

The Akoya pearl produced by Japanese pearl oysters, with its unique and elegant luster, attracts people from all over the world, which is not found
in other pearl oyster varieties.
This study is expected to be the beginning of the genetic interpretation of this trait
.

References: A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster" by Takeshi Takeuchi, Yoshihiko Suzuki, Shugo Watabe, Kiyohito Nagai, Tetsuji Masaoka, Manabu Fujie, Mayumi Kawamitsu, Noriyuki Satoh and Eugene W Myers, 10 November 2022, DNA Research.