Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology.
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.
Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.
Takeshi
T
Takeuchi
Takeshi
T
Kawashima
Ryo
R
Koyanagi
Fuki
F
Gyoja
Makiko
M
Tanaka
Tetsuro
T
Ikuta
Eiichi
E
Shoguchi
Mayuki
M
Fujiwara
Chuya
C
Shinzato
Kanako
K
Hisata
Manabu
M
Fujie
Takeshi
T
Usami
Kiyohito
K
Nagai
Kaoru
K
Maeyama
Kikuhiko
K
Okamoto
Hideo
H
Aoki
Takashi
T
Ishikawa
Tetsuji
T
Masaoka
Atushi
A
Fujiwara
Kazuyoshi
K
Endo
Hirotoshi
H
Endo
Hiromichi
H
Nagasawa
Shigeharu
S
Kinoshita
Shuichi
S
Asakawa
Shugo
S
Watabe
Nori
N
Satoh
D000483:Alleles; D000818:Animals; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics / Q000302:isolation & purification*; D020224:Expressed Sequence Tags; D016678:Genome; D008928:Mitochondria / Q000235:genetics; D005810:Multigene Family; D010802:Phylogeny; D049911:Pinctada / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
D018076:DNA, Complementary; D014157:Transcription Factors