We sequenced the genome of the pearl oyster Pinctada fucata
(Fig. A) with two major goals in mind. First, we sought to obtain genomic information that could be used in future studies of the molecular mechanisms underlying the biosynthesis of pearl in the bivalve mollusc. Pearls are of significant value industrially and as jewels; better understanding of the mechanism is essential to further improvement of pearl production in the fisheries industry. To date, mechanisms involved in the nacreous layer formation in the pearl oyster have been studied extensively.1–4
The shell of pearl oysters consists of two distinct structures: inner nacreous layers composed of aragonite and outer prismatic layers composed of calcite. An intriguing question in the field of bio-mineralization research is how the two polymorphs of calcium carbonate are produced in the same organism. Previous studies that explored these bio-mineralization processes identified and characterized a wide variety of genes and proteins; their functions have also been examined in association with shell formation.4–6
For example, Kinoshita et al
conducted an expressed sequence tag (EST) analysis of P. fucata
genes expressed in the pallial mantle, which forms the nacreous layer, and in the mantle edge, which forms the prismatic layer. That study generated 29 682 unique sequences, from which the authors succeeded in identifying multiple genes, some novel, that may play roles in the pearl formation. In spite of such extensive studies, however, we still have only a limited understanding of the molecular mechanisms underlying pearl oyster shell formation. Decoding the genome of pearl oysters is therefore essential for future genome-wide analyses of these mechanisms.
Figure 1. (A) The pearl oyster P. fucata and its pearl. Scale bar, 1 cm. (B) Flow cytometry of a mixture of sperm from Pinctata and Oryzias. The Pinctata genome, estimated to be ~1150 Mb in size, is slightly larger than the Oryzias genome (~1100 (more ...)
Our second goal was to improve our overall understanding of the biology of bivalve molluscs, specifically those features that characterize molluscs and their evolution among metazoans and/or lophotrochozoans.8–10
Lophotrochozoa is one of the largest clades of bilaterians, together with the Ecdysozoa and Deuterostomia. The core group of Lophotrochozoa includes molluscs, annelids, nemertines, lophophorates, and platyhelminths. Since these core groups show the greatest variety of adult body plans, the relationships among the lophotrochozoan taxa are still controversial.11
Although adult morphology varies vastly across the group, many core lophotrochozoans share spiral cleavage and a trochophore larval stage. Understanding the proposed repeated losses of both spiral cleavage and trochophore larvae in the Lophotrochozoa clade requires comparative studies of genes involved in the formation of body plans, performed on the basis of full genomic information.
The phylum Mollusca itself is one of the most diverse animal groups; mollusc species exhibit a range of morphologies and sizes, from microscopic bivalves to 1-m long giant clams.8–10
The phylum includes ~100 000 described and living species. Due to their hard exoskeletal shell, molluscs appear in the fossil record dating from the Cambrian era, and the major bivalves were established by the Middle Ordovician.12,13
However, the search for bivalve ancestors has proved less straightforward, mainly due to differing interpretations of the extant microfossils. Mollusca comprise seven or eight major lineages, and three majors are Bivalvia (clams and oysters), Gastropoda (snails and slugs), and Cephalopoda (squids and octopus). A recent phylogenetics of evolutionary relationship among Mollusca by Kocot et al
showed a sister-taxon relationship between Bivalvia and Gastropoda.
The class Bivalvia includes ~20 000 living species; their developing embryos pass through two larval stages, trochophore and verliger. Bivalves are characterized by their possession of two separate shells, called valves. It is thought that during evolution of molluscs leading to the bivalves, a single dorsal shell in the ancestor was doubled. Recently, Kin et al
examined genes involved in this prominent morphological transition in the Japanese spiny oyster Saccostrea kegaki
. They found that a member of transforming growth factor beta (TGF-β) family, dpp
, is expressed only in the cells along the dorsal midline, and plays an important role in establishing the characteristic shape of the bivalve shell anlagen.
The genome contains all the genetic information of a given organism; therefore, sequenced genomes provide an invaluable basis for studying every aspect of biology. Since the first sequencing of a metazoan genome, the nematode Caenorhabditis elegans16
in 1998, ~35 metazoan genome sequences have been reported. However, there is an apparent bias in the selection of targeted metazoan genomes. In contrast to vertebrates,17–19
ecdysozoans including Drosophila melanogaster22
and Apis mellifera
and the sponge,28
there have been no reports of sequenced genomes in lophotrochozoans, although planarians, annelids, and gastropod molluscs have been the subjects of their own genome projects.
With the aims described, in the context of the current status of genome sequencing efforts, we sequenced the genome of the pearl oyster P. fucata. Because of its comparatively large size, the assembly so far obtained is still comparatively short, but the draft genome will provide a platform sufficient for exploring the molecular basis of pearl biosynthesis.