生物信息学现状和重要研究方向,陈润生E-mail : crssun5.ibp.ac.cnrunshengchotmail.com Tel: 86-10-64888543 Fax: 86-10-64871293凌伦奖E-mail : lingsun5.ibp.ac.cn Tel: 86-10-64888544中国科学院生物物理研究所 北京朝阳区大屯路15号,背景,Normal Male,FISH,Different probes used to mark each chomosome Computer identifies probe and give chromosome a false color,Trisomy 13 Patau Syndrome,Patau Syndrome,Cleft lip and palate Extra fingers & toes polydactylism Defects Heart Brain Kidney Most abort Live span 1 month,一. 什么是生物信息学？Genome informatics is a scientific discipline that encompasses all aspects of genome information acquisition, processing, storage, distribution, analysis, and interpretation. 它是一个学科领域，包含着基因组信息的获取、处理、存储、分配 、分析和解释的所有方面。 (The U.S. Human Genome Project: The First Five Years FY 1991-1995, by NIH and DOE) 从美国的三个国家计划说起：曼哈顿计划；阿婆罗计划；人类基因组计划。破译人类遗传密码就要读懂由30亿符号组成的100万页的“天书”,Genomes highlight the Finiteness of the “Parts” in Biology,Bacteria, 1.6 Mb, 1600 genes Science 269: 496,Eukaryote, 13 Mb, 6K genes Nature 387: 1,1995,1997,1998,Animal, 100 Mb, 20K genes Science 282: 1945,Human, 3 Gb, 100K genes ?,2000?,real thing, Apr 00,98 spoof,A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) Jun Yu,1,2,3,4 *Songnian Hu,1 *Jun Wang,1,2,5 * Gane Ka-Shu Wong,1,2,4 *Songgang Li,1,5 Bin Liu,1 Yajun Deng,1,6 Li Dai,1 Yan Zhou,2,7 Xiuqing Zhang,1,3 Mengliang Cao,8 Jing Liu,2 Jiandong Sun,1 Jiabin Tang,1,3 Yanjiong Chen,1,6 Xiaobing Huang,1 Wei Lin,2 Chen Ye,1 Wei Tong,1 Lijuan Cong,1 Jianing Geng,1 Yujun Han,1 Lin Li,1 Wei Li,1,9 Guangqiang Hu,1 Xiangang Huang,1 Wenjie Li,1 Jian Li,1 Zhanwei Liu,1 Long Li,1 Jianping Liu,1 Qiuhui Qi,1 Jinsong Liu,1 Li Li,1 Tao Li,1 Xuegang Wang,1 Hong Lu,1 Tingting Wu,1 Miao Zhu,1 Peixiang Ni,1 Hua Han,1 Wei Dong,1,3 Xiaoyu Ren,1 Xiaoli Feng,1,3 Peng Cui,1 Xianran Li,1 Hao Wang,1 Xin Xu,1 Wenxue Zhai,3 Zhao Xu,1 Jinsong Zhang,3 Sijie He,3 Jianguo Zhang,1 Jichen Xu,3 Kunlin Zhang,1,5 Xianwu Zheng,3 Jianhai Dong,2 Wanyong Zeng,3 Lin Tao,2 Jia Ye,2 Jun Tan,2 Xide Ren,1 Xuewei Chen,3 Jun He,2 Daofeng Liu,3 Wei Tian,2,6 Chaoguang Tian,1 Hongai Xia,1 Qiyu Bao,1 Gang Li,1 Hui Gao,1 Ting Cao,1 Juan Wang,1 Wenming Zhao,1 Ping Li,3 Wei Chen,1 Xudong Wang,3 Yong Zhang,1,5 Jianfei Hu,1,5 Jing Wang,1,5 Song Liu,1 Jian Yang,1 Guangyu Zhang,1 Yuqing Xiong,1 Zhijie Li,1 Long Mao,3 Chengshu Zhou,8 Zhen Zhu,3 Runsheng Chen,1,9 Bailin Hao,2,10 Weimou Zheng,1,10 Shouyi Chen,3 Wei Guo,11 Guojie Li,12 Siqi Liu,1,2 Ming Tao,1,2 Jian Wang,1,2 Lihuang Zhu,3 Longping Yuan,8 Huanming Yang 1,2,3 ,Science 2002 296: 79-92,A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) Jun Yu,1,2,3,4* Songnian Hu,1* Jun Wang,1,2,5* Gane Ka-Shu Wong,1,24*,Science 2002 296: 79-92 Rice is the most important crop for human consumption, providing staple food for more than half the worlds population. The euchromatic portion of the rice genome is estimated to be 430 Mb in size (1-3), which is the smallest of the cereal crops. It is 3.7 times larger than that of A. thaliana (4-6), and 6.7 times smaller than that of the human (7, 8). The well-established protocols for high-efficiency genetic transformation, widespread availability of high-density genetic and physical maps (9, 10), and high degrees of synteny among cereal genomes (11-15) combine to make rice a unique organism for studying the physiology, developmental biology, genetics, and evolution of plants. The International Rice Genome Sequencing Project (IRGSP) (16) has already delivered a substantial amount of sequence for the japonica (Nipponbare) subspecies, in bacterial artificial chromosome (BAC) and P1-derived artificial chromosome (PAC)-sized contigs. Working independently, Monsanto and Syngenta (17, 18) established proprietary working drafts for japonica, in April 2000 and February 2001, respectively. The Monsanto sequence has been used to assist in the efforts of the IRGSP.,Figure 9. Functional classification of rice genes, according to Gene Ontology Consortium, and assigned by homology to categorized A. thaliana genes. In this ontology, “biological process,“ “cellular location,“ and “molecular function“ are treated as independent attributes. Only 36.3% of the 25,426 predicted genes for A. thaliana are classified. For rice, only 20.4% of the 53,398 complete predictions, with both initial and terminal exons, could be classified.,计算机运算速度: 18个月增长一倍; DNA序列数据: 14个月增长一倍;,代表基因组研究进展的数据 近年来GenBank中的DNA碱基数目呈指数增加，大约每14个月增加一倍。到1999年12月其数目已达30亿，它们来自47000种生物。2000年4月DNA碱基数目是60亿。现在，2002年2月13日这一数目已达171亿（15465000记录）。各种生物的EST序列已达1082万条（2002年3月8日），其中人类的EST序列已超过417 万条（小鼠2525645），估计覆盖人类基因90以上；自1999年初单核苷酸多态性( SNPs,Single Nucleotide Polymorphisms )数据库出现以来，到2000年3月20日SNP的总数是26569，现在已超过412万（2002年1月24日）；自全长1.8Mb的嗜血流感杆菌（Haemophilus influenzae Rd）基因组序列于1995年发表（Fleischmann et al.，1995）以来，到2002年3月12日已有83个模式生物的完整基因组被测序完成，它们中有13个古细菌、63个原核真细菌、7个真核生物的完整基因组，其中包括酿酒酵母、线虫、拟南芥、果蝇和人。还有另外的100余个微生物基因组正在测试当中；,果蝇基因组包括1.2亿碱基对的编码区已于2000年2月测序并组装完成；人类基因组研究的标志性工作，包含三千三百万碱基对的人第22号染色体已于1999年11月完成测序，其结果发表在1999年12月2日的Nature 杂志上。从第22号染色体已鉴定出679个基因，其中55的基因是未知的。有35种疾病与该染色体突变相关，象免疫系统疾病、先天性心脏病和精神分裂症。作为人类基因组研究的里程碑性的工作，覆盖率为90的人完整基因组的“工作草图”已经在2000年4月底完成，到2003年将获得覆盖率为99的人类基因组全部序列。,