牡蛎全基因组序列图谱绘制完成

<正>近日,牡蛎基因组计划(Oyster Genome Project,OGP)项目组宣布,历时两年的牡蛎基因组序列图谱终于绘制完成。这是世界上第一张养殖贝类的全基因组序列图谱,标志着基于短序列的高杂合度基因组拼接和组装技     

人类的生命之谜即将破解

2000年6月26日,人类基因组“工作框架图”公布于世,人类基因组计划将在2003年完成。这个工程决不只是简单的科学探索,它是一个将控制各种基因密码破解的巨大国际工程,实际上完成了这个工程就等于解开了人类生老病死的秘密。 人类基因组计划是人类继曼哈顿原子弹计划、阿波罗登月计划之后最大的科学工程,是人类继洞开微观世界、宇观世界之后,首次全面地认识自我。人类基因组是人类所有基因和染色体的总和,含有生、长、病、老、死的全部遗传信息。     

Taurine牛基因组序列图：反刍动物生物学及其进化论的窗口

为了理解反刍动物的生物学和进化论,牛的基因组图被测定出有大约7倍区域（Genome sevenfold coverage）。整个序列含有最低限度22000个基因,有一套核心基因14345个,是7个哺乳动物种共享拥有的源祖同源基因或直系同源基因（Ortholog）,其中有1217个基因在非真哺乳动物亚纲（有袋目动物或单孔目动物）基因组图中不存在或没被检测到。牛染色体特有的进化演变区的片断复制的密度较高,重复元素丰富,并且这种种类特有的基因变异与产乳和免疫反应有关。表达代谢的基因一般是高度保守的,但是人类跟它们同源的5个参与代谢的源祖同源基因已丢失或广泛地发生了漂移。牛的基因组图谱就这样为理解哺乳动物进化和加速家畜泌乳和产肉的遗传改进提供了一种资源。     

比较基因组学揭示哺乳动物基因组脆性区域“产生与消亡”的过程

<正>一直以来基因组脆性区域被认为在进化过程中发挥关键性的作用。近期来自加州大学圣地亚哥分校的一项新生物信息学研究发现哺乳动物基因组的脆性区域经历了一个"产生与消亡"的过程。研究结果发表在2010年11月30日的《基因组生物学》(Genome Biology)杂志上。新研究发现有助于研究人员在人类基因组中鉴别     

马铃薯育种实现颠覆性突破

正近日,中国农业科学院深圳农业基因组研究所(以下简称"基因组所")黄三文团队最新研究成果实现了颠覆性创新,第一代基因组设计的杂交马铃薯问世,用二倍体育种替代四倍体育种,用杂交种子繁殖替代薯块繁殖。6月24日,国际学术期刊CELL(《细胞》)在线发表了题为"Genome design of hybrid potato(《杂交马铃薯的基因组设计》)"的研究成果。这标志着"优薯计划"实施以来取得了里程碑式突破。     

生物芯片技术

1998年线虫基因组的ＤＮＡ全序列测定已经完成。 2 0 0 0年 6月 2 6日 ,白宫宣布 :人类基因组草图已基本完成 ,这表明人类基因组计划将提前完成。美国加利福尼亚大学伯克利分校等 5个国际研究小组已测定了拟南芥 1 .2亿个碱基对中 1 .0 8亿个的顺序 ,原计划 2 0 0 4年完成的工作 ,提前到 2 0 0 0年 7月完成全序列的测定。因此 ,人们研究工作的重点已从基因结构的研究转向基因组功能的研究 ,进入了后基因组时代。为了揭示所有基因转录表达层次上的信息 ,人们需要一种更加高效快速且能同时测定基因组成千上万个基因活动的新方法。多学科 ,多技…     

前沿动态

中国完成白菜全基因组测序白菜类作物包括大白菜、小白菜、菜心和芜菁等形态各异的一大类蔬菜,是我国栽培面积和消费量最大的蔬菜作物。白菜全基因组测序是继黄瓜和马铃薯基因组测序项目后,由中国主导通过国际合作完成的又一重大成果,标志着我国在该领域基因组学研究中取得了国际领先地位。分析结果表明,白菜基因组大小约为485 Mb,包含约42 000个基因;     

林木功能基因组学及其研究策略

随着杨树等树木基因组测序的完成,林木育种进入了功能基因组学时代,林木功能基因组学研究面临的挑战是系统地对基因组中的所有预测基因进行注释和功能验证。林木功能基因组分析已经进入了高通量阶段,但要识别未知基因的确切功能,有必要了解每个基因在植物细胞所有基因活动网络中发挥的作用。因此,就必须了解各个基因在时间和空间上的表达模式。功能基因组学研究策略已经发展到能对这些成分细胞中基因的活性和浓度同时进行快速的测量。林木功能基因组学技术的最新研究进展能从全基因组进行功能分析,从而打开了林木未知基因功能研究的新途径。目前,广泛应用的林木功能基因组学研究策略有插入突变、FOX系统、蛋白质组学等。     

前沿扫描六则

正迄今最大规模的中国人基因组测序完成近日,中国研究人员领导的一个国际研究团队声称,他们完成了迄今最大规模的中国人基因组测序和分析,有助于揭示基因与生育的联系以及了解中国人口基因结构。这项发表在新一期美国《细胞》杂志上的研究显示,深圳华大基因研究院用"无创产前基因检测"技术收集了超过14万名中国孕妇的部分基因组样本。研究人员表示,这项研究的测序对象约占中国总人口的万分     

科技要闻

<正>中国主导完成马铃薯基因"蓝图"育种时间将减半以中国为首、14国科学家组成的"国际马铃薯基因组测序协作组",宣布马铃薯基因组序列框架图完成。这标志着人类将能够以马铃薯基因组序列为工具,把马铃薯新品种育种的速度从10~12年缩短到5年,并迅速提高其产量、品质和抗病性。     

The ENCODE (ENCyclopedia Of DNA Elements) Project

The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (approximately 1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. The results of this pilot phase will guide future efforts to analyze the entire human genome.     

Assessing the Human Genome Project: Effects on world agriculture

The Human Genome Project is the attempt to sequence the complement of human DNA. Its ultimate purpose is to understand and control human genetics. The social and ethical concerns raised by this attempt have been much debated, especially fears concerning human genetic engineering and eugenics. An almost completely neglected aspect of the genome project's potential effects is its impact on world agriculture. The Human Genome Project will provide source information to transform commercially and therapeutically valuable segments of the human genetic code into agricultural products using the newly extant technologies of gene farming. This application of developing genomic technologies has at least two foreseeable effects: 1) Transforming global agricultural markets and ecologies, raising possibilities of novel forms of neocolonialism and the further destruction of genetic diversity; and 2) transforming world health and society through new modes of pharmaceutical production and the unregulated expansion of medical access to novel and traditional therapeutics.Mark Lesney received his Ph. D. in plant pathology and has worked as an assistant professor of biotechnology research at the University of Florida. He is currently affiliated with the program in History of Science at the University of Florida, where he is studying the emergence of biotechnology research.     

Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques

To understand the demographic history of rhesus macaques (Macaca mulatta) and document the extent of linkage disequilibrium (LD) in the genome, we partially resequenced five Encyclopedia of DNA Elements regions in 9 Chinese and 38 captive-born Indian rhesus macaques. Population genetic analyses of the 1467 single-nucleotide polymorphisms discovered suggest that the two populations separated about 162,000 years ago, with the Chinese population tripling in size since then and the Indian population eventually shrinking by a factor of four. Using coalescent simulations, we confirmed that these inferred demographic events explain a much faster decay of LD in Chinese (r(2) approximately 0.15 at 10 kilobases) versus Indian (r(2) approximately 0.52 at 10 kilobases) macaque populations.     

Human genome. Storm erupts over terms for publishing Celera's sequence

A dispute has been raging behind the scenes for weeks over the conditions under which Celera Genomics is prepared to make its human genome sequence data publicly available. The argument went public on 6 December, when geneticist Michael Ashburner e-mailed an open letter to Science's board of reviewing editors and members of the press slamming an agreement on data release that Science had reached with Celera as a condition for accepting its paper for review. This spat is the latest round in an intense rivalry between Celera president J. Craig Venter and leaders of the Human Genome Project, a publicly funded consortium that has produced its own draft human genome sequence.     

Genomics. Rat genome off to an early start

The National Human Genome Research Institute has jump-started efforts to determine the order of the roughly 3 billion bases in the rat genome. The original plan had been to wait for funding, expected in fiscal year 2001. Instead, two of the 10 centers involved in sequencing the mouse genome are shifting to the rat now.     

Single-molecule DNA sequencing of a viral genome

The full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. A reference sequence enables the use of short read length. We report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously. A DNA polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual DNA molecules was monitored by fluorescence imaging. Read lengths of >25 bases and equivalent phred software program quality scores approaching 30 were achieved. We used this method to sequence the M13 virus to an average depth of >150x and with 100% coverage; thus, we resequenced the M13 genome with high-sensitivity mutation detection. This demonstrates a strategy for high-throughput low-cost resequencing.     

The composite genome of the legume symbiont Sinorhizobium meliloti

The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite 6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB megaplasmids. Genome sequence analysis indicates that all three elements contribute, in varying degrees, to symbiosis and reveals how this genome may have emerged during evolution. The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments.     

Mapping the human genome: current status

The human genome has already been the subject of extensive research activity even though the Human Genome Project is only just officially starting. This review and the accompanying wall chart attempt to provide an integrated, quantitative, and detailed summary of the status of knowledge on the human genome in mid-1990. The analysis has highlighted the rudimentary nature of many of the information links needed for the task. While this overview could not be fully comprehensive and required simplifying assumptions, the results have provided estimates of relative progress on a region-by-region basis throughout the genome.     

Human genome ultraconserved elements are ultraselected

Ultraconserved elements in the human genome are defined as stretches of at least 200 base pairs of DNA that match identically with corresponding regions in the mouse and rat genomes. Most ultraconserved elements are noncoding and have been evolutionarily conserved since mammal and bird ancestors diverged over 300 million years ago. The reason for this extreme conservation remains a mystery. It has been speculated that they are mutational cold spots or regions where every site is under weak but still detectable negative selection. However, analysis of the derived allele frequency spectrum shows that these regions are in fact under negative selection that is much stronger than that in protein coding genes.