Elucidation of the machinery of biodiversity on the basis of evolutionary genetics

基于进化遗传学阐明生物多样性机制

• 批准号: 10836024
• 负责人: GOJOBORI Takashi
• 金额: $ 2.18万
• 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 (C)
• 财政年份: 1998
• 资助国家: 日本
• 起止时间: 1998 至 1999
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-10836024/
• 关键词: evolution; biodiversity; complete genome sequences; genome duplication MHC; hitchhiking effect; operon; GC-content; GC含量; ゲノム; 大量解析; 重複領域; データベース; 系統樹

In this research project, from the viewpoint of evolutionary genetics we attempted to elucidate biodiversity that living organisms have acquired through evolution since the beginning of 3.5 billion years ago. Currently, a lot of complete genome sequences from a variety of species such as human are available, and hundreds of genome-sequencing projects are thought to be underway. Thus, these genomes gave us an opportunity to initiate the project of biodiversity analysis.In the first academic year we conducted detection of duplicated regions in eukaryotic genomes such as human. In order to improve the accuracy of the detection, we developed a new statistical method of finding significant duplicated regions. Consequently, we successfully identified 74 duplicated regions in human, 59 in yeast, and 197 in worm. We constructed a database for these results, so that anyone can access our data through Internet by using a graphical user interface. The times of duplication events were estimated so as to study what the duplication affect to evolution.In the second academic year, in order to analyze the MHC region of human in detail, a large DNA sequence (〜400 kb) in the region was newly determined. As a result, we found large genome duplication, and reconstructed the evolutionary process of the duplication. Moreover, high nucleotide diversity was found in non-coding regions, implying that hitchhiking effects might have occurred in the regions. Next, we extended our study to microbes, and could reveal that in general bacterial genome structures are quite unstable even in operons that are believed to be functionally important units. In addition, we developed a new method for the detection of evolutionary direction of GC-content change, which leads to high diversity of genomes.

在本研究项目中，我们试图从进化遗传学的观点来阐明生物体从35亿年前开始通过进化获得的生物多样性。目前，许多物种（如人类）的全基因组序列已经获得，数百个基因组测序项目正在进行中。因此，这些基因组给了我们一个机会，启动了生物多样性分析的项目。在第一学年，我们进行了检测真核生物基因组中的重复区域，如人类。为了提高检测的准确性，我们开发了一种新的统计方法来发现显着重复区域。因此，我们成功地确定了74个重复的区域在人类中，59个在酵母中，和197蠕虫。我们为这些结果构建了一个数据库，以便任何人都可以通过互联网使用图形用户界面访问我们的数据。在第二学年，为了对人类MHC区域进行详细的分析，新测定了该区域的一个大的DNA序列（约400 kb）。结果，我们发现了大的基因组重复，并重建了重复的进化过程。此外，在非编码区发现了高的核苷酸多样性，这意味着搭便车效应可能发生在该地区。接下来，我们将我们的研究扩展到微生物，并且可以揭示，通常细菌基因组结构非常不稳定，即使在被认为是功能重要单元的操纵子中。此外，我们开发了一种新的方法来检测GC含量变化的进化方向，这导致了基因组的高度多样性。

项目成果

Hatta, Y., Ohashi, J., Imanishi, T., Kamiyama, H., Iha, M., Simabukuro, T., Ogawa, A., Tanaka, H., Akaza, T., Gojobori, T., Juji, T., and Tokunaga, K.: "HLA genes and haplotypes in Ryukyuan suggest a recent gene flow to the Okinawa Islands."Human Biology.

Hatta, Y.、Ohashi, J.、Imanishi, T.、Kamiyama, H.、Iha, M.、Simabukuro, T.、Okawa, A.、Tanaka, H.、Akaza, T.、Gojobori, T.、

Itoh,T.: "A low rate of nucleotide changes in Escherichia coli K-12 estimated from a comparison of the genome sequences between two different substrains"FEBS Letters. 450. 72-76 (1999)

Itoh,T.：“通过比较两个不同亚株之间的基因组序列估计大肠杆菌 K-12 中核苷酸变化率较低”FEBS Letters。

Shiina, T.: "Multiple class I loci expressed by the quail MHC"Immunogenetics.. 49・5. 456-460 (1999)

Shiina, T.：“鹌鹑 MHC 表达的多个 I 类基因座”免疫遗传学.. 49・5（1999）。

Itoh, T.: "Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes"Mol. Biol. Evol.. 16・3. 332-346 (1999)

Itoh, T.：“通过完整微生物基因组的序列比较揭示操纵子结构的进化不稳定性”Mol. Evol. 16・3 (1999)。

五條堀孝: "つぎはぎだらけの生き物ゲノム"サイアス・朝日新聞出版局. 4・7. 20-23 (1999)

Takashi Gojo Hori：“生物的拼凑基因组”Cyas Asahi Shimbun Publishing Bureau 4/7（1999）。