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.

Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana

“…We have identified genes that are potential candidates as biomarkers for ecotoxicological studies including those encoding enzymes putatively involved in the biotransformation of xenobiotics and those encoding enzymes of the antioxidant defence system. Since this study was initiated, two oyster genomes have been published (C. gigas and P. fucata) (Zhang et al, 2012a;Takeuchi et al, 2012), which have aided in the annotation process.…”

“…Clark et al, 2010;Craft et al, 2010;Hou et al, 2011;Joubert et al, 2010;Meyer et al, 2009), and so was applied here to the transcriptome of the mangrove oyster C. brasiliana. In the last few years, several oyster genomes have become available, including the Pacific oyster Crassostrea gigas (Zhang et al, 2012a) and Pearl oyster Pinctada fucata (Takeuchi et al, 2012), significantly enriching the genomic resources for this animal model.…”

Similar ratios of introns to intergenic sequence across animal genomes

“…Assemblies and annotations for Symbiodinium minutum (Shoguchi et al 2013), Pinctada fucata (Takeuchi et al 2012), Acropora digitifera (Shinzato et al 2011), Lingula anatina (Luo et al 2015), Ptychodera flava (Simakov et al 2015), and Octopus bimaculoides (Albertin et al 2015) were downloaded from the OIST Marine Genomics Browser (http:// marinegenomics.oist.jp/gallery/).…”

A History of the Cultured Pearl Industry

“…In pearl research, genome analysis is also making rapid progress (Shen and Morse, 1997;Kono et al, 2000;Zhang and Zhang, 2003;Wang et al, 2008Wang et al, , 2009, and there have been many significant studies in the field of biomineralization, such as the elucidation of the nacre-forming mechanism (Suzuki et al, 2009;Jackson et al, 2010;Joubert et al, 2010;Kinoshita et al, 2011;Fang et al, 2011;Gardner et al, 2011;Montagnani et al, 2011;Isowa et al, 2012;Marie et al, 2012;Wang et al, 2012). An important milepost was reached in 2012 when, in a world first, a group including the Okinawa Institute of Science and Technology Graduate University and others performed draft genome sequencing of the Japanese Akoya oyster (Takeuchi et al, 2012). Research on pearls is again entering a new era, and these types of basic research should contribute to the management of bioresources and the improvement of pearl culturing techniques, leading toward stable production of high quality pearls.…”