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Construction of an EST database for Bombyx mori

家蚕EST数据库的构建

基本信息

批准号：
10460027
负责人：
MITA Kazuei
金额：
$ 5.5万
依托单位：
National Institute of Radiological Sciences
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (B)
财政年份：
1998
资助国家：
日本
起止时间：
1998 至 2000
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-10460027/
关键词：
silkworm, Bombyx mori multi-cellular organism cDNA collection EST database cDNA library gene classification gene expression profile 多細胞生物系モデル生物 cDNA塩基配列決定

项目摘要

To build a foundation for the complete genome analysis of Bombyx mori, we have constructed an EST database. Since gene expression patterns deeply depend on tissues as well as developmental stages, we analyzed many cDNA libraries prepared from various tissues and different developmental stages to cover the whole set of Bombyx genes. So far, the Bombyx EST db contains 35,000 ESTs from 36 cDNA libraries, which are grouped into about 11,000 non-redundant ESTs with the average length of 1.25 kb. The comparison with FlyBase suggests that the present EST database, "SilkBase," covers more than 55% of all genes of Bombyx. The fraction of library-specific ESTs in each cDNA library indicates that we have not yet reached saturation, showing the validity of our strategy for constructing an EST database to cover all genes. To tackle the coming saturation problem, we have checked two methods, subtraction and normalization, to increase coverage and decrease the number of housekeeping genes, resulting in 5-11% increase of library-specific ESTs. The identification of a number of novel genes and comprehensive cloning of gene families have already emerged from SilkBase search. Direct links of SilkBase with FlyBase and WormBase provide ready identification of candidate Lepidoptera-specific genes.

为了为家蚕全基因组分析奠定基础，我们构建了EST数据库。由于基因表达模式很大程度上取决于组织和发育阶段，因此我们分析了从不同组织和不同发育阶段制备的许多cDNA文库，以涵盖整套家蚕基因。到目前为止，Bombyx EST db 包含来自 36 个 cDNA 文库的 35,000 个 EST，这些 EST 被分为约 11,000 个非冗余 EST，平均长度为 1.25 kb。与FlyBase的比较表明，现有的EST数据库“SilkBase”覆盖了家蚕所有基因的55%以上。每个 cDNA 文库中文库特异性 EST 的比例表明我们尚未达到饱和，这表明我们构建 EST 数据库以覆盖所有基因的策略的有效性。为了解决即将到来的饱和问题，我们检查了减法和归一化两种方法，以增加覆盖范围并减少看家基因的数量，从而使文库特异性 EST 增加 5-11%。 SilkBase搜索中已经出现了一些新基因的鉴定和基因家族的全面克隆。 SilkBase 与 FlyBase 和 WormBase 的直接链接提供了候选鳞翅目特异性基因的现成鉴定。