By Nori Satoh
How beautiful pearls are. Pearls emit a complex pattern of brightness, each with completely different color combination. They have attracted human beings, especially women, for long time, but simultaneously they have attracted biologists with a long-standing question of how pearl oysters generate such beautiful biomineralized materials.
The pearl oyster has an organ called the mantle that secretes proteinous organic materials and forms shells. The luster layer in the inner part of the shell is called the ‘nacreous layer’ while the outer structure of the shell is called the ‘prismatic layer’. Pearl oysters are thought to secrete specific proteins selectively to form these two different shell layers. When the surface of the mantle is injured and some of its cells fall into the inner part of the tissue, the cells sometimes proliferate to form a sac-like structure. These cells may then secrete proteins and a hard material, which is made of identical components to the shell, thus forming a pearl. In 1892, taking advantage of this specific character of pearl oysters, Kokichi Mikimoto was the first in the world to succeed in aquaculture pearl production using the Japanese pearl oyster, Pinctada fucata. The nacreous layer is comprised of fine alternating layers of calcium carbonate about 0.4 micrometers thick and a thin organic layer about 0.02 micrometers thick. The nacreous layer is 1000 times tougher than pure calcium carbonate crystal, which has caught the attention of material scientists too. Aforementioned proteins play important roles in both pearl and shell formation, but not been revealed how pearl oysters form such a fine structure.
With an aid of next generation sequencers, the team of Okinawa Institute of Science and Technology has successfully decoded the genome of the Japanese pearl oyster Pinctada fucata in collaboration with other research groups including from the University of Tokyo and Mikimoto Co., Ltd. The genome of P. fucata is estimated to be 1.15 gigabases, relatively large among invertebrates and thus a huge challenge for sequencing. Their sequencing reached more than 40 times full coverage of the genome, which was reconstructed by high-performance cluster computer to obtain the genome assembly. As a result, it has been shown that the genome contains approximately 23,000 protein-coding genes, 70% of which are supported by corresponding expressed sequence tags. The genes include those for transcription factors and signal transduction molecules in numbers comparable with genomes of other metazoans, and those reported to be associated with bio-mineralization. Their success in deciphering the genome means that researchers now have all of the genetic information needed to uncover the secrets of how oysters generate beautiful pearls and shells. Great progress on pearl oyster research is therefore promised with this new genome data. Indeed, the decoded genome has stimulated research activity of mollusks biologists in Japan; they have already joined together twice to find out genes involved in every process of the pearl formation. It is now evident that the genome contains all the genes so far reported to be associated with the shell and pearl formation.
The researchers also found in the pearl oyster genome specific repetitive DNA sequences such as transposons and microsatellites, which occupy about 10% of the genome. These sequences are available as DNA markers, providing very useful tools in aquaculture industry for quality control of organisms, development of high-grade pearls, and parentage analysis. The genomic information will also benefit the study of pearl oyster ecology and physiology. Scientists can now analyze the impacts of environmental changes, such as increases in seawater temperature and acidification, on the marine organism.
The pearl oyster belongs to the phylum Mollusca, which is comprised of around 85,000 species, including oysters, abalones, squids, cuttle fish, octopuses, and snails. The mollusks are a highly diverse group, and their habitat extends from seawater to fresh water to land. Despite the fact that many mollusks are important organisms for the fishery industry, there has previously been no comprehensive genome data of this group of animals. This is partially because the genome size of molluscs is comparatively large, often more than several gigabases, which makes bivalve genome projects difficult to accomplish. The deciphered genome of the pearl oyster will therefore provide crucial information for understanding overall molluscan biology.
Noriyuki Satoh is a Professor at Okinawa Institute of Science and Technology Graduate University, and a Prof. Emeritus at Kyoto University. Graduated from Tokyo University Graduate School in 1994, the author specializes in developmental, environmental genomics and has won Alexander Kowalevsky Medal in 2005, and Edwin Conklin Medal in 2010. This piece refers to the Editor’s Choice paper “Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology” by Takeshi Takeuchi, Takeshi Kawashima, Ryo Koyanagi et al in the journal DNA Research, which you can read in full for a limited time.