着丝粒串联重复序列RCS2对亚洲栽培稻和非洲栽培稻的比较分析

为了揭示中高度重复序列在同为AA基因组的亚洲栽培稻和非洲栽培稻基因组中的差异以及重复序列在.栽培稻种的分化过程中可能起到的作用,利用水稻着丝粒串联重复序列RCS2作为探针分别对籼稻广陆矮4号、粳稻日本晴和非洲栽培稻的体细胞染色体进行荧光原位杂交(FISH)实验,并对其核型进行同源性聚类和比较分析,杂交结果显示:RCS2序列位于在3种栽培稻染色体组中,RCS2序列位于每条染色体的着丝粒位置,但有不同的分布特点,表明该3种栽培稻基因组的RCS2序列有不同的进化方向.探讨了RCS2序列结合Cot-1 DNA FISH方法对水稻染色体组进行核型分析的可行性和优势.     

真菌中DNA重复序列诱导点突变的研究进展

1987年,由Selker等在粗糙脉孢菌中首次发现重复序列诱导点突变(repeat-induced point mutation,RIP).在重复序列诱导点突变过程中,搜寻前减数分裂组织单倍体核中DNA的重复序列,然后发生众多的碱基C到T的突变,产生富碱基T+A片段,从而使重复序列中的G-C碱基对发生转换突变成为A-T碱基对.此外,发生RIP的序列多集中在着丝粒区域,主要是转座子甲基化后的遗迹.移动转座子是真核生物基因组进化的主要驱动力.对于真菌,重复序列诱导点突变(RIP)在减数分裂过程中通过突变多拷贝DNA,能最大限度地减少转座子的影响,因此对RIP的研究在一定程度上能有助于了解基因组进化的真谛.综述了重复序列诱导点突变的产生机制,以及真菌中重复序列诱导点突变的研究进展.     

在67种微生物基因组序列中都不存在的最短的碱基组合

对67种微生物基因组全序列进行分析，发现某些碱基组合(及其反向互补序列)在某些基因组中不存在，而这种不存在的概率很低；发现6个11bp的寡核苷酸序列(及其反向互补序列)--AGGGGGGGGTC(GACCCCCCCCT)、AGGGTCCCTG(CTAGGGACCCT)、ACGTACCTAGG(CCTAGGTACGT)、GACACACGTAG(CTACGTGTGTC)、CGCGTAACTAG(CTAGTTACGCG)、CTAGGGACCCA(TGGGTCCCTAG)在这67种基因组中都不存在。上述每个寡核苷酸序列(及其反向互补序列)在由这67种细菌基因组连接而成的DNA分子(长度为169660265bp)中不存在的概率至少小于2．5e-26。     

利用GISH和C0t-1DNA-FISH对稻属B，C，G基因组的比较分析

为探究稻属B,C,G基因组之间的关系以及研究中高度重复序列在稻属不同物种基因组进化中的作用,利用药用野生稻和斑点野生稻的中度和高度重序列C0t-1 DNA和总基因组作为探针,对疣粒野生稻进行了比较染色体原位杂交分析.该2种野生稻的总基因组和C0t-1 DNA在疣粒野生稻染色体上信号覆盖率分别为(72.39±0.11) %,(75.60±0.18) %,(47.93±0.16) %,(55.47±0.12) %. 此外,以C0t-1 DNA的杂交信号组成为依据,对疣粒野生稻染色体组进行了核型分析.结果表明:G基因组和B,C基因组之间的关系都比较远,其原因可能是G基因组要早于B,C基因组从稻属的祖先中发生分化,并在进化过程中发生加倍、重排和基因选择性丢失等现象,形成了各自种的特异基因组成分.稻属基因组中度和高度重复序列与功能基因一样,在不同种中也存在着相当的同源性和保守性,并在进化过程中得以保存下来.药用野生稻和疣粒野生稻基因组增大的重要原因之一,可能是基因组中度和高度重复序列加倍的结果.     

基于NCBI核酸数据库资源的产黄青霉微卫星序列的筛选

利用生物信息学方法在产黄青霉基因组中筛选微卫星序列,并对其基因组中微卫星数量和丰度进行了研究.利用SSRHunter1.3软件在长度为30 090 464 bp的产黄青霉基因组中共找到163个微卫星序列.其中以两碱基重复类型数目最多,为133个,占重复序列总数目的 81.60%;其次是三碱基重复为29个,占17.79%;最后是四碱基1个,占0.61%.在两碱基重复序列中,AT(44.79%)重复类别最多,其次是AG(23.92%).在三碱基重复序列中,共发现9种重复类别,其中以AAG和ACT重复类型最多,为6个(3.68%),其次是ACC(2.45%),最少的是AGC(0.61%).四碱基重复中,只有1种重复类别,为ATGT(0.61%).同时选取二碱基的重复次数在7以上和三碱基的重复次数在6以上的微卫星序列,利用Primer Premier 5.0软件设计了引物,共得到30对引物.本研究不仅为后续产黄青霉微卫星标记的筛选奠定了基础,也丰富了其基因组学资源,对产黄青霉的种群遗传结构分析、分子标记选育和遗传多样性有重要意义.     

病毒基因组中的对称性

病毒基因组中的重复序列比率很低,因为其核酸序列大都是编码区域.如果出现一段同向对称或者是反向对称序列在病毒基因组中,它往往代表一个调控元件,或者是一个信号因子.我们总结了病毒中的一些对称序列,并阐明它的特点,分布及功能.     

山羊和藏羚羊全基因组微卫星分布规律及其生物信息学分析

本文利用生物信息学方法搜索和统计了山羊和藏羚羊全基因组中完整型SSRs序列,并对其生物信息学特征进行比较分析.山羊和藏羚羊全基因组中SSRs总数量分别为920 300个和913 059个,占其全基因组长度的比例分别为5.56‰和5.39‰.山羊和藏羚羊全基因组SSRs六种重复类型的数量、比例、丰度和密度分布模式如下:单核苷酸SSRs二核苷酸SSRs三核苷酸SSRs五核苷酸SSRs四核苷酸SSRs六核苷酸SSRs,这六种重复类型SSRs特征相互比较有显著差异,而相同重复类型SSRs特征基本一致.山羊基因5′端非翻译区和外显子区均是三核苷酸SSR丰最丰富,其次依次是单核苷酸、二核苷酸、四核苷酸、五核苷酸和六核苷酸;而其3′端非翻译区和内含子区均是单核苷酸SSR最丰富,其次依次是二核苷酸、四核苷酸、三核苷酸、五核苷酸和六核苷酸.山羊第1条染色体上SSRs数量最多,其次依次是第2条、X染色体、第6条、第4条和第8条染色体,而较少的是第25、28条染色体,所有染色体上SSRs丰度不存在显著差异.山羊和藏羚羊全基因组各重复类型优势SSRs序列基本一致,并与牛、绵羊全基因组中不同重复类型SSRs优势序列相一致.     

萼花臂尾轮虫(Brachionus calyciflorus)的ISSR引物筛选及其多态性检验

采用简单重复序列区间(ISSR:一种基于微卫星的分子标记,无需预知遗传背景即可研究基因组中微卫星序列的变异,适合大规模的种群遗传研究)的方法对萼花臂尾轮虫(Brachionus calyci florus)进行PCR扩增,优化出适宜的ISSR-PCR反应体系,并从100条引物中筛选出16条具有良好多态性和重复性的ISSR引物.研究结果显示,萼花臂尾轮虫简单重复序列以(AC)和(AG)的两碱基重复为主,筛选出的ISSR引物扩增共得到114个位点,66个多态位点,多态性高达57.89%,高于常用于该物种分子生态学研究的线粒体COI基因的多态性.     

原核CRISPR-Cas系统的结构功能及应用

CRISPR-Cas系统是新近在原核生物中发现的一种抵御外来DNA入侵的免疫机制,由一个成簇规则间隔的短回文重复序列(CRISPR)和附属的蛋白质(Cas)组成,广泛分布于真细菌和古菌中.CRISPR由重复序列及其间隔序列组成,间隔序列来自于过去的入侵DNA,并插入到细菌的CRISPR排列中.一旦出现新的入侵,CRISPR转录,其RNA经过加工后与Cas蛋白质组成一个核蛋白复合体,该复合体通过RNA与入侵DNA序列之间的互补配对,结合目标序列,最后Cas蛋白质将入侵DNA降解.此外,基于CRISPR系统中的Cas9蛋白,发展了一种新的基因组编辑技术,在不同的细胞中均能获得高效的基因定点打靶,展现出巨大的潜力.     

生物序列比对算法的简述

基因组和蛋白质组的研究极大地依赖于数据库的搜索,寻求更快更灵敏的生物序列相似性比对算法一直是生物信息学研究的热点,文章介绍了相似性比对的得分算法和各种数据库搜索工具,并对各种算法的优缺点进行了讨论与比较.     

利用乙醇脱氢酶基因证据揭示稻属CCDD异源四倍体中染色体组的起源

对稻属异源四倍体中染色体组C和D以及稻属现存的所有二倍体染色体组A、B、C、E、F的乙醇脱氢酶基因（Adh1）片段分别进行PCR扩增、克隆和序列测定，并以G染色体组序列作为外类群，采用PAUP运算软件中的简约性方法对所测定的序列进行了系统发育分析．结果表明：（1）3个CCDD四倍体是同一次杂交事件的产物；（2）四倍体中的C染色体组和亚洲二倍体中的C染色体组表现出更近的系统发育关系；（3）D染色体组和E染色体组表现出较近的亲缘关系，二者可能有共同的祖先．     

Initial sequencing and comparative analysis of the mouse genome

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.     

A physical map of the chicken genome

Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can aid genome assemblies, generally starting with low-resolution cytogenetic maps and ending with the highest resolution of sequence. Fingerprint clone maps are based upon complete restriction enzyme digests of clones representative of the target genome, and ultimately comprise a near-contiguous path of clones across the genome. Such clone-based maps are used to validate sequence assembly order, supply long-range linking information for assembled sequences, anchor sequences to the genetic map and provide templates for closing gaps. Fingerprint maps are also a critical resource for subsequent functional genomic studies, because they provide a redundant and ordered sampling of the genome with clones. In an accompanying paper we describe the draft genome sequence of the chicken, Gallus gallus, the first species sequenced that is both a model organism and a global food source. Here we present a clone-based physical map of the chicken genome at 20-fold coverage, containing 260 contigs of overlapping clones. This map represents approximately 91% of the chicken genome and enables identification of chicken clones aligned to positions in other sequenced genomes.     

A physical map of the mouse genome

A physical map of a genome is an essential guide for navigation, allowing the location of any gene or other landmark in the chromosomal DNA. We have constructed a physical map of the mouse genome that contains 296 contigs of overlapping bacterial clones and 16,992 unique markers. The mouse contigs were aligned to the human genome sequence on the basis of 51,486 homology matches, thus enabling use of the conserved synteny (correspondence between chromosome blocks) of the two genomes to accelerate construction of the mouse map. The map provides a framework for assembly of whole-genome shotgun sequence data, and a tile path of clones for generation of the reference sequence. Definition of the human-mouse alignment at this level of resolution enables identification of a mouse clone that corresponds to almost any position in the human genome. The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy.     

The complete genome of an individual by massively parallel DNA sequencing

The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2-40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'.     

SARS冠状病毒的起源和进化初探

发展了一种研究基因序列进化的随机替代模型，根据一组从某个最近共同祖先演化而来的若干序列，可以预测此共同祖先序列，并计算随机替代概率矩阵，确定了从祖先序列的各个碱基到进化序列的各个碱基之间的替代概率。将这一模型应用于分析包括SARS冠状病毒在内的4种冠状病毒全基因组的演化规律，确定了在若干较保守的编码蛋白基因序列中同义替代位点的最近共同祖先序列以及分歧进化后的累计同义替代数目。结果表明，SARS病毒和其他几种已知的冠状病毒具有相当的进化历程，但存在不同的进化途径，支持了SARS病毒在造成此次大规模感染人体之前已经历了较长的进化历程的猜测。     

Genome sequence of the plant pathogen Ralstonia solanacearum

Ralstonia solanacearum is a devastating, soil-borne plant pathogen with a global distribution and an unusually wide host range. It is a model system for the dissection of molecular determinants governing pathogenicity. We present here the complete genome sequence and its analysis of strain GMI1000. The 5.8-megabase (Mb) genome is organized into two replicons: a 3.7-Mb chromosome and a 2.1-Mb megaplasmid. Both replicons have a mosaic structure providing evidence for the acquisition of genes through horizontal gene transfer. Regions containing genetically mobile elements associated with the percentage of G+C bias may have an important function in genome evolution. The genome encodes many proteins potentially associated with a role in pathogenicity. In particular, many putative attachment factors were identified. The complete repertoire of type III secreted effector proteins can be studied. Over 40 candidates were identified. Comparison with other genomes suggests that bacterial plant pathogens and animal pathogens harbour distinct arrays of specialized type III-dependent effectors.     

Filamentous phage integration requires the host recombinases XerC and XerD

Many bacteriophages and animal viruses integrate their genomes into the chromosomal DNA of their hosts as a method of promoting vertical transmission. Phages that integrate in a site-specific fashion encode an integrase enzyme that catalyses recombination between the phage and host genomes. CTX phi is a filamentous bacteriophage that contains the genes encoding cholera toxin, the principal virulence factor of the diarrhoea-causing Gram-negative bacterium Vibrio cholerae. CTX phi integrates into the V. cholerae genome in a site-specific manner; however, the approximately 6.9-kilobase (kb) CTX phi genome does not encode any protein with significant homology to known recombinases. Here we report that XerC and XerD, two chromosome-encoded recombinases that ordinarily function to resolve chromosome dimers at the dif recombination site, are essential for CTX phi integration into the V. cholerae genome. The CTX phi integration site was found to overlap with the dif site of the larger of the two V. cholerae chromosomes. Examination of sequences of the integration sites of other filamentous phages indicates that the XerCD recombinases also mediate the integration of these phage genomes at dif-like sites in various bacterial species.     

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.     

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.