Large-scale DNA sequencing and its application

大规模DNA测序及其应用

• 批准号: 17020008
• 负责人: KOHARA Yuji
• 金额: $ 568.96万
• 依托单位: National Institute of Genetics
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research on Priority Areas
• 财政年份: 2005
• 资助国家: 日本
• 起止时间: 2005 至 2009
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-17020008/
• 关键词: ゲノム; cDNAライブラリー; 全ゲノムショットガン; EST; DNAシーケンサー; アッセンブラ; WGS(全ゲノムショットガン); ゲノムシーケンシング; フォスミド; SNP; 比較ゲノム; SAGE; whole genome shotgun sequencing

We established a large-scale (Sanger) DNA sequencing system through the review, improvement and cost reduction of the sequencing process step by step, leading to allow us to obtain 6 million (Sanger) reads per year. Based on the requests from the researchers in the grant group, we produced 3.4 million EST reads for 92 cDNA libraries from 16 organisms. We also produced 19.4 million reads for whole genome shotgun sequencing of 7 organisms including wild-derived mouse, a hemichordata, water bears, the choanoflagellate Monosiga ovata. Altogether 24 million reads were produced during the project period. To analyze the reads more closely, we developed a work-bench for genome finishing and a viewer for polymorphism identification. For the next generation DNA sequencing system, we set up a computer system with a security system that is essential for personal genomics and performed various DNA sequencing. Furthermore, we developed a viewer system for polymorphism identification and a system for cDNA full sequencing. Solexa multiplexing data analysis was also tested.

通过对测序过程的回顾、改进和成本的逐步降低，我们建立了大规模（桑格）DNA测序系统，导致每年可以获得600万（桑格）读数。根据研究人员的要求，我们从16种生物的92个cDNA文库中产生了340万个EST读数。我们还为7种生物的全基因组鸟枪测序产生了1940万个读段，包括野生来源的小鼠、半索动物、水熊虫、后领鞭毛虫卵单胞藻。在项目期间，共产生了2 400万个读数。为了更紧密地分析读数，我们开发了用于基因组整理的工作台和用于多态性鉴定的观察器。对于下一代DNA测序系统，我们建立了一个具有个人基因组学所必需的安全系统的计算机系统，并进行了各种DNA测序。此外，我们还开发了一个用于多态性鉴定的观察系统和一个用于cDNA全序列测定的系统。还测试了Solexa多路复用数据分析。

项目成果

Extensive analysis of EST sequences reveals that all cichlid species in Lake Victoria share almost identical transcript sets

• DOI: 10.1016/j.gene.2008.11.023
• 发表时间: 2009-07-15
• 期刊: GENE
• 影响因子: 3.5
• 作者: Kobayashi, Naoki;Watanabe, Masakatsu;Okada, Norihiro
• 通讯作者: Okada, Norihiro

The International Silkworm Genome Consortium: The genome of a lepidopteran model insect, the silkworm Bombyx mori.

国际家蚕基因组联盟：鳞翅目模式昆虫，家蚕 Bombyx mori 的基因组。

• 发表时间: 2008
• 期刊: Insect Biochem. & Mol. Biol 38

Genomic defense system against transposons in the silkworm, Bombyxmori

家蚕抗转座子的基因组防御系统

• 发表时间: 2008
• 期刊: Insect Biochemistry and Molecular Biology (Special Issue on Bombyx Genome) 38
• 作者: B. Ahsan;D. Kobayashi;T. Yamada;M. Kasahara;S. Sasaki;T. L. Saito;Y. Nagayasu;K. Doi;Y. Nakatani;W. Qu;T. Jindo;A. Shimada;K. Naruse;A. Toyoda;Y. Kuroki;A. Fujiyama;T. Sasaki;A. Shimizu;S. Asakawa;N. Shimizu;S. Hashimoto;J. Yang;Y. L;Shinpei Kawaoka
• 通讯作者: Shinpei Kawaoka

非分化性の社会性アメーバ、Acytostelium の遺伝子解析

Acytostelium（一种非分化的社会阿米巴原虫）的遗传分析

• 发表时间: 2010
• 作者: Kobayashi;H;Teiya Kijimoto;Naoki Kobayashi;Fuki Gyoja;Harumi Terasaki;漆原秀子
• 通讯作者: 漆原秀子

The medaka draft genome and new insights into vertebrate genome evolution

青鳉基因组草案和脊椎动物基因组进化的新见解

• 发表时间: 2007
• 期刊: Nature (印刷中)
• 作者: Kasahara;M.
• 通讯作者: M.