PacBio SMRT HiFi and Omni-C chromosome capture uncover the molecular fingerprints behind beautiful pearls

• Pearl oysters are an important farmed animal, and over the past 20 years, the production of akoya pearls has decreased from about 70,000 kilograms per year to only 20,000 kilograms
  per year due to a combination of diseases, red tides, and the environment.
  

• To further understand their underlying genes and hopefully discover strains with strong environmental adaptability, the researchers used PacBio single-molecule real-time (SMRT) HiFi long-read and Omni-C chromosome capture data to construct a high-quality, chromosome-scale pearl oyster genome – notably sequencing the two pairs of chromosomes separately without merging, revealing unexpected diversity
  in the gene pool in wild individuals 。 A very important finding is that the researchers found a genetic variant responsible for immunity, which suggests that there is hope for the development of a pearly oyster strain
  with strong environmental adaptability.
  

Pearl oysters are an important aquaculture animal in Japan because the beautiful pearls they produce are used to make necklaces, earrings and rings
.
In the early 90s of the 20th century, aquaculture brought in about 88 billion yen per
year.
However, over the past 20 years, a combination of new diseases and red tides has reduced Japan's pearl production from about 70,000 kilograms per year to just 20,000 kilograms
.
Researchers from the Okinawa Institute of Science and Technology (OIST) and K.
MIKIMOTO's Pearl Research Institute collaborated with other research institutions, including the Japan Fisheries Research and Education Institute, to build a high-quality, chromosome-scale pearl oyster genome that they hope can be used to find strains
that are more environmentally adaptable.
The study was recently published in DNA Research
.

"Building the genome is very important," said
Dr.
Takeshi Takeuchi, one of the study's two first authors and a staff member in OIST's Marine Genomics Division.
"The genome is the whole gene 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.
Back in 2012, Dr.
Takeuchi and his collaborators published a draft genome of Pinctada fucata, one of
the first genomes of this mollusk.
They continue genome sequencing to build a higher-quality, chromosome-scale genome assembly
.

The genome of this oyster is made up of 14 pairs of chromosomes
, one that inherits one from each parent.
The two chromosomes in each pair carry nearly identical genes, but there are subtle differences
if different gene pools favor their survival.
Usually when sequencing a genome, researchers merge a pair of chromosomes together
.
This works well for lab animals because their chromosomes often share nearly identical genetic information
between them.
But for wild animals, there is a lot of genetic variation between their chromosomal 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 the two sets of chromosomes separately — a very rare method
.
In fact, this may be the first study to study
marine invertebrates in this way.

Since pearl oysters have 14 pairs of chromosomes, they have a total of 28 chromosomes
.
OIST researchers Mr.
Manabu Fujie and Ms.
Mayumi Kawamitsu sequenced the genome using state-of-the-art PacBio single-molecule real-time (SMRT) HiFi long-read and Omni-C chromosome capture techniques for haplo-merged genome assembly, demonstrating that the quality and accuracy of haplophase assembly exceeds haplo-merged assembly, demonstrating that haplophase genome assembly strategies can effectively produce almost complete reference genomes
。 The pearl oyster genome reveals unexpected diversity between haplotypes, especially in non-communitic regions, which may play a vital role
in maintaining the innate immunity of pearl oysters.

Another first author, Dr.
Yoshihiko Suzuki, is a former postdoctoral scholar of OIST Ecological and Evolutionary Genomics Algorithms, now based at the University of
Tokyo.
He and Dr.
Takeuchi reconstructed all 28 chromosomes and found a key difference
between one of the pairs, the two chromosomes of the 9th pair.
Notably, many of these genes are associated with
immunity.

"The different genes on a pair of chromosomes is a major discovery because these proteins can recognize different types of infectious diseases," Dr.
Takeuchi said
.
He noted that when the animal is farmed, there is usually a strain that has a higher survival rate or produces more beautiful pearls
.
Farmers often raise two animals with this strain, but this leads to inbreeding and reducing genetic diversity
.
The researchers found a significant reduction
in genetic diversity after three consecutive cycles of inbreeding.
If this reduction in diversity occurs in chromosomal regions of immune-related genes, it affects the animal's immunity
.
"It is important
to maintain the genomic diversity of aquaculture populations.
"

DOI

10.
1093 / dnares / dsac035