Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology

Abstract

The study of the pearl oyster Pinctada fucata is key to increasing our understanding of the molecular mechanisms involved in pearl biosynthesis and biology of bivalve molluscs. We sequenced ~1150-Mb genome at ~40-fold coverage using the Roche 454 GS-FLX and Illumina GAIIx sequencers. The sequences were assembled into contigs with N50 = 1.6 kb (total contig assembly reached to 1024 Mb) and scaffolds with N50 = 14.5 kb. The pearl oyster genome is AT-rich, with a GC content of 34%. DNA transposons, retrotransposons, and tandem repeat elements occupied 0.4, 1.5, and 7.9% of the genome, respectively (a total of 9.8%). Version 1.0 of the P. fucata draft genome contains 23 257 complete gene models, 70% of which are supported by the corresponding expressed sequence tags. The genes include those reported to have an association with bio-mineralization. Genes encoding transcription factors and signal transduction molecules are present in numbers comparable with genomes of other metazoans. Genome-wide molecular phylogeny suggests that the lophotrochozoan represents a distinct clade from ecdysozoans. Our draft genome of the pearl oyster thus provides a platform for the identification of selection markers and genes for calcification, knowledge of which will be important in the pearl industry.

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 Mb).

Figure 2.

Flow chart for sequencing and assembly of the P. fucata genome.

Figure 3.

Distribution of the contig lengths (Y-axis) and their coverage depth (X-axis) in the current P. fucata genome assembly. A coverage range between 1 and 50 is shown for convenience. The 100 longest contigs (44–18 kb) are plotted as red dots; all others are plotted as gray dots. Two significant peaks appeared near coverage depths 10 and 20, respectively. The difference in read coverage of the contigs is likely to be derived from heterozygosity in the genome. The majority of the longest contigs (89 out of the top 100) are covered more than 15 times. See also Supplementary Fig. S3 for further distribution analysis.

Figure 4.

Arrangement of P. fucata mitochondrial genes in (A) three contigs and (B) two cluster constructions of the genome.

Figure 5.

The GC content of the P. fucata assembled genome (500 bp sliding window). The vertical axis shows counts of DNA sequence reads; the horizontal axis, percentage of GC in the reads. The GC content of the pearl oyster genome was estimated to be ∼34%. The GC contents of genomes of C. elegans (34%), Strongylocentrotus pulpulatus (35%), B. floridae (40%), and H. sapiens (38%) are shown for comparison.

Figure 6.

Repeat elements in the P. fucata genome.

Figure 7.

Molecular phylogeny of the pearl oyster. A total of 77 547 aligned amino acid positions of proteins encoded by 409 genes were obtained from the triploblasts T. castaneum, D. melanogaster, A. gambiae, A. pisum, P. fucata, B. floridae, C. intestinalis, D. rerio, T. rubripes, M. domestica, G. gallus, A. carolinensis, M. musculus, and H. sapiens. The sequences were analysed using ML methods, with the diploblasts A. digitifera and N. vectensis serving as an outgroup. The scale bar represents 0.05 expected substitutions per site in the aligned regions. The topology was supported by 100% bootstrap value. This analysis shows the phylogenic position of molluscs obtained using genome-wide data from all of these species.