The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.Oceans cover approximately 71% of the Earth's surface and harbour most of the phylum diversity of the animal kingdom. Understanding marine biodiversity and its evolution remains a major challenge. The Pacific oyster C. gigas (Thunberg, 1793) is a marine bivalve belonging to the phylum Mollusca, which contains the largest number of described marine animal species 1 . Molluscs have vital roles in the functioning of marine, freshwater and terrestrial ecosystems, and have had major effects on humans, primarily as food sources but also as sources of dyes, decorative pearls and shells, vectors of parasites, and biofouling or destructive agents. Many molluscs are important fishery and aquaculture species, as well as models for studying neurobiology, biomineralization, ocean acidification and adaptation to coastal environments under climate change 2,3 . As the most speciose member of the Lophotrochozoa, phylum Mollusca is central to our understanding of the biology and evolution of this superphylum of protostomes.As sessile marine animals living in estuarine and intertidal regions, oysters must cope with harsh and dynamically changing environments. Abiotic factors such as temperature and salinity fluctuate wildly, and toxic metals and desiccation also pose serious challenges. Filter-feeding oysters face tremendous exposure to microbial pathogens. Oysters do have a notable physical line of defence against predation and desiccation in the formation of thick calcified shells, a key evolutionary innovation making molluscs a successful group. However, acidification of the world's oceans by uptake of anthropogenic carbon dioxide poses a potentially serious threat to this ancient adaptation 4 . Understanding biomineralization and molluscan shell formation is, thus, a major area of interest 5 . Crassostrea gigas is also an interesting model for developmental biology owing to its mosaic development with typical molluscan stages, including trochophore and veliger larvae and metamorphosis.A complete genome sequence of C. gigas would enable a more th...

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