Construction of fish mitochondrial genome database

鱼类线粒体基因组数据库的构建

• 批准号: 13556028
• 负责人: NISHIDA Mutsumi
• 金额: $ 7.3万
• 依托单位: The University of Tokyo
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (B)
• 财政年份: 2001
• 资助国家: 日本
• 起止时间: 2001 至 2003
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-13556028/
• 关键词: Fishes; Mitochondrial genome; Database; On-line search; Biodiversity; DNA marker; Species identification; Phylogenetic analysis; mtDNA; 塩基配列

For organizing protection or management measures for biodiversity and biological resources in the aquatic ecosystems, indispensable is detailed genetic information on variability of populations, population structure, species identification of eggs, larvae, or other various kinds of materials, and so forth. However, only few facilities, such as online databases, have been available so far for genetic information on organisms in the wild.This project focused on the mitochondrial genome, which is known as a source of rich genetic information for such purposes, and aimed to construct an on-line database of the genome of fishes. Much data on the complete nucleotide sequence of the mitochondrial genome in fishes have been successfully generated and submitted to the international DNA database system by this project. On the basis of those and previously submitted data, the fish mitochondrial genome database was constructed as an international on-line database (http://mitofish.ori.u-tokyo.ac.jp/)This database "MitoFish" allows the users to know data.availability of complete nucleotide sequence of mitochondrial genome of fishes in the international DNA database system (DDBJ/GenBank/EMBL). If the users have partial nucleotide sequence data from fish mitochondrial genome, "MitoFish" also allows them to conduct homology search of the nucleotide sequence against the fish complete mitochondrial genome data in it. Using this search option, users can find what fish species or group(s) in the database is the most closely related to the material in their hand. This database has a lot of interlinks to useful international databases so that users are able to easily obtain various information on reference, specimen, taxonomy, and biology for the fish concerned. Through continuous update following the growth of the/international DNA databases, "MitoFish" will also grow into more and more unique and useful database of fish mitochondrial genome.

为了组织对水生生态系统中的生物多样性和生物资源的保护或管理措施，不可或缺的是关于种群变异性、种群结构、卵、幼虫或其他各种材料的物种鉴定等的详细遗传信息。然而，目前只有少数几种设施，如在线数据库，可用于收集野生生物的遗传信息。本项目以线粒体基因组为重点，旨在构建鱼类基因组在线数据库，线粒体基因组被认为是丰富遗传信息的来源。该项目已成功生成了大量鱼类线粒体基因组全序列数据，并提交给国际DNA数据库系统。在这些数据和以前提交的数据的基础上，建立了鱼类线粒体基因组数据库，作为一个国际在线数据库（http：//mitofish.ori.u-tokyo.ac.jp/）。如果用户拥有鱼类线粒体基因组的部分核苷酸序列数据，“MitoFish”还允许用户将该核苷酸序列与其中的鱼类线粒体基因组完整数据进行同源性检索，使用该检索选项，用户可以在数据库中找到与自己手中的材料最相关的鱼类物种或组。该数据库与许多有用的国际数据库相连接，因此用户能够容易地获得有关鱼类的参考、标本、分类和生物学的各种信息。随着国际DNA数据库的不断发展，通过不断更新，“MitoFish”也将成长为越来越独特和有用的鱼类线粒体基因组数据库。

项目成果

前川光司(編著): "サケ・マスの生態と進化"文一総合出版, 東京(印刷中). (2004)

Koji Maekawa（编辑）：“鲑鱼和鳟鱼的生态与进化”Bunichi General Publishing，东京（印刷中）。

Miya, M.: "Major patterns of higher teleostean phylogenies : a new perspective based on 100 complete mitochondrial DNA sequences."Molecular Phylogenetics and Evolution. 26. 121-138 (2003)

Miya, M.：“高等硬骨动物系统发育的主要模式：基于 100 个完整线粒体 DNA 序列的新视角。”分子系统发育与进化。

Inoue, J.G.: "Complete mitochondrial DNA sequence of the Japanese anchovy, Engraulis japonicus."Fisheries Science. 67. 828-835 (2001)

Inoue, J.G.：“日本凤尾鱼 Engraulis japonicus 的完整线粒体 DNA 序列。”渔业科学。

Ishikawa, S.: "Population structure of the Japanese eel Anguilla japonica as examined by mitochondrial DNA sequencing."Fisheries Science. 67. 246-253 (2001)

Ishikawa, S.：“通过线粒体 DNA 测序检查日本鳗鲡的种群结构。”渔业科学。

Inoue, Jun G.: "Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva."Molecular Phylogenetics and Evolution. (in press). (2004)

Inoue，Jun G.：“elopomorph 鱼类（Teleostei）单系性的线粒体基因组证据和 leptocephalus 幼虫的进化起源。”分子系统发育与进化。