Journal Article

Draft Genome of the Pearl Oyster <i>Pinctada fucata</i>: A Platform for Understanding Bivalve Biology

Takeshi Takeuchi, Takeshi Kawashima, Ryo Koyanagi, Fuki Gyoja, Makiko Tanaka, Tetsuro Ikuta, Eiichi Shoguchi, Mayuki Fujiwara, Chuya Shinzato, Kanako Hisata, Manabu Fujie, Takeshi Usami, Kiyohito Nagai, Kaoru Maeyama, Kikuhiko Okamoto, Hideo Aoki, Takashi Ishikawa, Tetsuji Masaoka, Atushi Fujiwara, Kazuyoshi Endo, Hirotoshi Endo, Hiromichi Nagasawa, Shigeharu Kinoshita, Shuichi Asakawa, Shugo Watabe and Nori Satoh

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 19, issue 2, pages 117-130
Published in print April 2012 | ISSN: 1340-2838
Published online February 2012 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dss005

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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.

Keywords: pearl oyster; Pinctada fucata; draft genome

Journal Article.  6825 words.  Illustrated.

Subjects: Genetics and Genomics

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