Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology.
Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology.
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DOI：
10.1093/dnares/dss005
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发表时间：
2012-04
期刊：
影响因子：
--
通讯作者：
Satoh N
中科院分区：
文献类型：
--
作者：
Takeuchi T;Kawashima T;Koyanagi R;Gyoja F;Tanaka M;Ikuta T;Shoguchi E;Fujiwara M;Shinzato C;Hisata K;Fujie M;Usami T;Nagai K;Maeyama K;Okamoto K;Aoki H;Ishikawa T;Masaoka T;Fujiwara A;Endo K;Endo H;Nagasawa H;Kinoshita S;Asakawa S;Watabe S;Satoh N
合浦珠母贝的研究是提高我们对珍珠生物合成和双壳类软体动物生物学的分子机制的理解的关键。我们使用Roche 454 GS-FLX和Illumina GAIIx测序仪对11150-Mb基因组进行测序，覆盖率为140倍。将序列组装成N50 = 1.6kb的重叠群（总重叠群组装达到1024 Mb）和N50 = 14.5kb的支架。珍珠牡蛎基因组富含AT，GC含量为34%。DNA转座子、反转录转座子和串联重复元件分别占基因组的0.4%、1.5%和7.9%（共9.8%）。合浦岩藻基因组草图1.0版包含23257个完整的基因模型，其中70%由相应的表达序列标签支持。这些基因包括那些据报道与生物矿化有关的基因。编码转录因子和信号转导分子的基因的数量与其他后生动物的基因组相当。全基因组分子系统发育表明，lophotrochozoan代表了一个独特的分支从ecdysozoans。因此，我们的珠母贝基因组草图为识别钙化的选择标记和基因提供了一个平台，这方面的知识在珍珠产业中将是重要的。
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.
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