Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology

被引：222

作者：

Takeuchi, Takeshi ^{[1
]}

Kawashima, Takeshi ^{[1
]}

Koyanagi, Ryo ^{[1
]}

Gyoja, Fuki ^{[1
]}

Tanaka, Makiko ^{[1
]}

Ikuta, Tetsuro ^{[1
]}

Shoguchi, Eiichi ^{[1
]}

Fujiwara, Mayuki ^{[1
]}

Shinzato, Chuya ^{[1
]}

Hisata, Kanako ^{[1
]}

Fujie, Manabu ^{[2
]}

Usami, Takeshi ^{[2
]}

Nagai, Kiyohito ^{[3
]}

Maeyama, Kaoru ^{[4
]}

Okamoto, Kikuhiko ^{[4
]}

Aoki, Hideo ^{[5
]}

Ishikawa, Takashi ^{[6
]}

Masaoka, Tetsuji ^{[7
]}

Fujiwara, Atushi ^{[8
]}

Endo, Kazuyoshi ^{[9
]}

Endo, Hirotoshi ^{[10
]}

Nagasawa, Hiromichi ^{[10
]}

Kinoshita, Shigeharu ^{[11
]}

Asakawa, Shuichi ^{[11
]}

Watabe, Shugo ^{[11
]}

Satoh, Nori ^{[1
]}

机构：

[1] Grad Univ, Marine Genom Unit, Okinawa Inst Sci & Technol, Onna, Okinawa 9040495, Japan

[2] Grad Univ, Gene Sequencing Sect, Okinawa Inst Sci & Technol, Uruma, Okinawa 9042234, Japan

[3] Mikimoto Co Ltd, Pearl Res Inst, Shima, Mie 5170403, Japan

[4] Mikimoto Pharmaceut Co Ltd, Ise, Mie 5168581, Japan

[5] Mie Prefecture Fisheries Res Inst, Shima, Mie 5176464, Japan

[6] Mie Univ, Fac Bioresources, Tsu, Mie 5170510, Japan

[7] Natl Res Inst Aquaculture, Fisheries Res Inst, Aquaculture Technol Div, Tamaki, Mie 5190423, Japan

[8] Natl Res Inst Fisheries Sci, Res Ctr Aquat Genom, Kanazawa Ku, Yokohama, Kanagawa 2378648, Japan

[9] Univ Tokyo, Grad Sch Sci, Dept Earth & Planetary Sci, Bunkyo Ku, Tokyo 1130033, Japan

[10] Univ Tokyo, Grad Sch Agr & Life Sci, Dept Appl Biol Chem, Bunkyo Ku, Tokyo 1138657, Japan

[11] Univ Tokyo, Grad Sch Agr & Life Sci, Dept Aquat Biosci, Bunkyo Ku, Tokyo 1138657, Japan

来源：

DNA RESEARCH | 2012年 / 19卷 / 02期

关键词：

pearl oyster; Pinctada fucata; draft genome; AMORPHOUS CALCIUM-CARBONATE; ACIDIC MATRIX PROTEIN; TRANSFER-RNA GENES; PRISMATIC LAYER; CIONA-INTESTINALIS; SHELL FORMATION; NACREOUS LAYER; PROGRAM; ANNOTATION; EVOLUTION;

D O I：

10.1093/dnares/dss005

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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 similar to 1150-Mb genome at similar to 40-fold coverage using the Roche 454 GS-FLX and Illumina GAllx 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 su;4:ests 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.

引用

页码：117 / 130

页数：14

共 76 条

[1] The genome sequence of Drosophila melanogaster [J].

Adams, MD ;

Celniker, SE ;

Holt, RA ;

Evans, CA ;

Gocayne, JD ;

Amanatides, PG ;

Scherer, SE ;

Li, PW ;

Hoskins, RA ;

Galle, RF ;

George, RA ;

Lewis, SE ;

Richards, S ;

Ashburner, M ;

Henderson, SN ;

Sutton, GG ;

Wortman, JR ;

Yandell, MD ;

Zhang, Q ;

Chen, LX ;

Brandon, RC ;

Rogers, YHC ;

Blazej, RG ;

Champe, M ;

Pfeiffer, BD ;

Wan, KH ;

Doyle, C ;

Baxter, EG ;

Helt, G ;

Nelson, CR ;

Miklos, GLG ;

Abril, JF ;

Agbayani, A ;

An, HJ ;

Andrews-Pfannkoch, C ;

Baldwin, D ;

Ballew, RM ;

Basu, A ;

Baxendale, J ;

Bayraktaroglu, L ;

Beasley, EM ;

Beeson, KY ;

Benos, PV ;

Berman, BP ;

Bhandari, D ;

Bolshakov, S ;

Borkova, D ;

Botchan, MR ;

Bouck, J ;

Brokstein, P .

SCIENCE, 2000, 287 (5461) :2185-2195

[2] Taking advantage of disorder: Amorphous calcium carbonate and its roles in biomineralization [J].

Addadi, L ;

Raz, S ;

Weiner, S .

ADVANCED MATERIALS, 2003, 15 (12) :959-970

[3]

[Anonymous], P 13 ANN INT C INT S

[4] Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes [J].

Aparicio, S ;

Chapman, J ;

Stupka, E ;

Putnam, N ;

Chia, J ;

Dehal, P ;

Christoffels, A ;

Rash, S ;

Hoon, S ;

Smit, A ;

Gelpke, MDS ;

Roach, J ;

Oh, T ;

Ho, IY ;

Wong, M ;

Detter, C ;

Verhoef, F ;

Predki, P ;

Tay, A ;

Lucas, S ;

Richardson, P ;

Smith, SF ;

Clark, MS ;

Edwards, YJK ;

Doggett, N ;

Zharkikh, A ;

Tavtigian, SV ;

Pruss, D ;

Barnstead, M ;

Evans, C ;

Baden, H ;

Powell, J ;

Glusman, G ;

Rowen, L ;

Hood, L ;

Tan, YH ;

Elgar, G ;

Hawkins, T ;

Venkatesh, B ;

Rokhsar, D ;

Brenner, S .

SCIENCE, 2002, 297 (5585) :1301-1310

[5] Tandem repeats finder: a program to analyze DNA sequences [J].

Benson, G .

NUCLEIC ACIDS RESEARCH, 1999, 27 (02) :573-580

[6] Whole-genome re-sequencing [J].

Bentley, David R. .

CURRENT OPINION IN GENETICS & DEVELOPMENT, 2006, 16 (06) :545-552

[7] Scaffolding pre-assembled contigs using SSPACE [J].

Boetzer, Marten ;

Henkel, Christiaan V. ;

Jansen, Hans J. ;

Butler, Derek ;

Pirovano, Walter .

BIOINFORMATICS, 2011, 27 (04) :578-579

[8]

Brusca RC., 2003, INVERTEBRATES

[9]

Carrol S.B., 2005, MOL GENETICS EVOLUTI

[10] Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis [J].

Castresana, J .

MOLECULAR BIOLOGY AND EVOLUTION, 2000, 17 (04) :540-552

← 1 2 3 4 5 6 7 8 →