Sequencing amd mapping of medaka cDNAs

青鳉 cDNA 的测序和作图

• 批准号: 11236203
• 负责人: MITANI Hiroshi
• 金额: $ 67.39万
• 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 on Priority Areas
• 财政年份: 1999
• 资助国家: 日本
• 起止时间: 1999 至 2003
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-11236203/
• 关键词: Medaka; Genome; Gene mapping; Evolution; Zebrafish; Fugu; Genome duplication; 染色体; cDNA; データーベース; シーケンス; マッピング; 魚類; EST; 遺伝子

Medaka (Oryzias latipes) is emerging as an important model fish that is phylogenically distant from zebrafish but closer to pufferfish. With the recent additions of the genetic toolkits such as BAC recourses and WGS sequences, the highly dense genome markers based on polymorphic inbred strains, which is essential for genome assembly with high quality come to be available by this research. This genomic map is a powerful tool for positional cloning of mutated genes in medaka and several of them are already cloned. About non-redundant 1200 genes and expressed sequence tags (ESTs) are mapped on a single meiotic backcross panel obtained from inbred strains.Gene duplication is thought to be important in the generation of the genetic diversity that determines the adaptability of a species to a changing environment and an additional ancient genome duplication has been proposed in ray-finned fishes based on comparative studies showing that many genes and gene clusters exist for which two copies … More are present in teleost compared to only one in other vertebrates. To compare the linkage relationships of orthologous genes among three species of vertebrates (medaka, zebrafish and human), we developed statistical method to identify the chromosomal similarity. The data suggests the number and content of the chromosomes of the last common ancestor of ray-fined fish and lobe-fined fish and that the extra whole genome duplication event in the ray-fin lineage occurred in the common ancestor of perhaps all euteleosts. For example, medaka LG2, LG21 and zebrafish LG6. LG9 share genes, which human homologues are located on human chromosome 2 and 21. And number of duplicated genes located on different medaka LG, suggests 20-30% of genes are duplicated in Medaka.Our comparative genomic analysis of medaka and zebrafish with reference to the human gene suggests that most teleost fish genomes mainly consist of paired chromosomes each pair derived from a single common proto-chromosome. And there may have been some chromosomal fission after the scrambling of gene order in the zebrafish linage, since zebrafish LG1 appeared to lack paired LG, and two cases of two to three LG-relationships between medaka and zebrafish were observed. This suggests that Medaka and zebrafish may have considerably different sets of genes with subfunctional or neofunction because the gene degeneration process after whole genome duplication would have affected different genes in the two fish lineage. Less

米达卡（Oryzias latipes）是一种重要的模式鱼，在系统发育上与斑马鱼相距较远，但与河豚鱼接近。随着BAC资源和WGS序列等遗传工具的增加，本研究提供了基于多态自交系的高密度基因组标记，这是高质量基因组组装的必要条件。该基因组图谱是定位克隆medaka突变基因的有力工具，其中一些突变基因已经被克隆。大约1200个非冗余基因和表达序列标签（est）被映射到从自交系获得的单个减数分裂回交面板上。基因复制被认为在遗传多样性的产生中起着重要的作用，而遗传多样性决定了物种对不断变化的环境的适应性。基于比较研究，人们提出在鳍状鱼类中存在另外一种古老的基因组复制，这表明许多基因和基因簇存在两个拷贝，硬骨鱼中存在更多的拷贝，而其他脊椎动物只有一个拷贝。为了比较三种脊椎动物（medaka，斑马鱼和人类）的同源基因连锁关系，我们建立了染色体相似性的统计方法。这些数据表明，鳍状鱼类和叶状鱼类的最后共同祖先的染色体数量和含量，以及鳍状谱系中额外的全基因组复制事件发生在可能所有真鱼动物的共同祖先中。例如，medaka LG2， LG21和斑马鱼LG6。LG9共有基因，其人类同源物位于人类2号和21号染色体上。不同藻属上的重复基因数量LG表明，藻属上有20-30%的重复基因。我们参照人类基因对medaka和斑马鱼进行的基因组比较分析表明，大多数硬骨鱼基因组主要由成对的染色体组成，每对染色体都来自一个共同的原染色体。在斑马鱼谱系中，基因顺序打乱后可能存在染色体分裂，因为斑马鱼LG1缺少配对的LG，在medaka和斑马鱼之间观察到2 - 3个LG关系的两例。这表明，Medaka和斑马鱼可能有相当不同的亚功能或新功能基因组，因为全基因组复制后的基因退化过程会影响两种鱼类谱系中的不同基因。少

项目成果

Shima, A., Himmelbauer, H., Mitani, H., Furutani-Seiki, M., Wittbrodt, J., Schartle, M.: "Fish genomes flying."EMBO reports. 4. 121-125 (2003)

Shima, A.、Himmelbauer, H.、Mitani, H.、Furutani-Seiki, M.、Wittbrodt, J.、Schartle, M.：“鱼类基因组飞行。”EMBO 报道。

Nishigaki, R. et al.: "Effect of cyclobutane pyrimidine dimers on apoptosis"Photochem. Pholobiol.. 70. 228-235 (1999)

Nishigaki, R. 等人：“环丁烷嘧啶二聚体对细胞凋亡的影响”Photochem。

Shima, A., Himmelbauer, A, Mitani, H., Furutani-Seiki, M., Wittbrodt., Schartl, M.: "Fish genomes flying-Symposium on Medaka genomics."EMBO reports. 4. 121-125 (2003)

Shima, A.、Himmelbauer, A、Mitani, H.、Furutani-Seiki, M.、Wittbrodt.、Schartl, M.：“鱼类基因组飞行 - 青鳉基因组学研讨会”。EMBO 报道。

Kondo, M., Nanda, I., Hornung, U., Asakawa, S., Shimizu, N., Mitani, H., Schmid, M., Shima, A., Schartl, M.: "Absence of the candidate male sex determining gene dmrt1b (Y) of medaka from other fish species."Current Biology. 13. 416-420 (2003)

Kondo, M.、Nanda, I.、Hornung, U.、Asakawa, S.、Shimizu, N.、Mitani, H.、Schmid, M.、Shima, A.、Schartl, M.：“候选人缺席

Kuwahara Y., Shimada A., Mitani H., Shima A.: "A Critical Stage in Spermatogenesis for Radiation-Induced Cell Death in the Medaka Fish, Oryzias latipes."Radiat. Res.. 157. 386-392 (2002)

Kuwahara Y.、Shimada A.、Mitani H.、Shima A.：“青鳉鱼（Oryzias latipes）辐射诱导细胞死亡的精子发生的关键阶段。”Radiat。