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1.
Juqing Jia Guangrong Li Cheng Liu Jianping Zhou Zujun Yang 《Frontiers of Agriculture in China》2010,4(2):137-144
Abstract In order to develop a molecular marker for the detection of alien chromatin, an allele-specific primer targeting
pyruvate dehydrogenase (PDHA1) gene was used to analyze 12 taxa representing different basic genomes in Triticeae. Ampli....cation products with different
sizes were generated among species. The sequence alignments indicated that the PDHA1 genes contained some deletions/insertions of Miniature Inverted-repeat Terminal Elements (MITE) and simple sequence repeats
(SSRs), thus suggesting that the Triticeae genomes have been rapidly evolving during speciation. The genome-specific amplicons
and chromosomal location of PDHA1 gene on Triticeae genomes can be used to trace the corresponding alien chromatins from Aegilops, Secale and Dasypyrum species in wheat background. 相似文献
2.
Knowledge of the rhesus macaque genome sequence enables reconstruction of the ancestral state of the human genome before the divergence of chimpanzees. However, the draft quality of nonhuman primate genome assemblies challenges the ability of current methods to detect insertions, deletions, and copy-number variations between humans, chimpanzees, and rhesus macaques and hinders the identification of evolutionary changes between these species. Because of the abundance of segmental duplications, genome comparisons require the integration of genomic assemblies and data from large-insert clones, linkage maps, and radiation hybrid maps. With genomic triangulation, an integrative method that reconstructs ancestral states and the structural evolution of genomes, we identified 130 human-specific breakpoints in genome structure due to rearrangements at an intermediate scale (10 kilobases to 4 megabases), including 64 insertions affecting 58 genes. Comparison with a human structural polymorphism database indicates that many of the rearrangements are polymorphic. 相似文献
3.
The type of RNA editing found in the kinetoplast-mitochondria of trypanosomes and related protozoa, involving uridylate insertions and deletions, creates translatable messenger RNAs (mRNAs) out of nonsense pre-edited RNAs by correcting encoded defects that vary from simple frameshifts to large "cryptic" regions. However, any evidence for translation of these mRNAs in the kinetoplast has been missing for decades. We identified a kinetoplast-encoded protein, apocytochrome b, whose mRNA is edited in the 5' region. The determined amino-terminal sequence of the protein coincides with the predicted sequence derived from the edited region, demonstrating that the cognate apocytochrome b mRNA is translated into a functional protein. This finding represents the first direct evidence for a functional translation system in the kinetoplasts. 相似文献
4.
Clark AG Glanowski S Nielsen R Thomas PD Kejariwal A Todd MA Tanenbaum DM Civello D Lu F Murphy B Ferriera S Wang G Zheng X White TJ Sninsky JJ Adams MD Cargill M 《Science (New York, N.Y.)》2003,302(5652):1960-1963
Even though human and chimpanzee gene sequences are nearly 99% identical, sequence comparisons can nevertheless be highly informative in identifying biologically important changes that have occurred since our ancestral lineages diverged. We analyzed alignments of 7645 chimpanzee gene sequences to their human and mouse orthologs. These three-species sequence alignments allowed us to identify genes undergoing natural selection along the human and chimp lineage by fitting models that include parameters specifying rates of synonymous and nonsynonymous nucleotide substitution. This evolutionary approach revealed an informative set of genes with significantly different patterns of substitution on the human lineage compared with the chimpanzee and mouse lineages. Partitions of genes into inferred biological classes identified accelerated evolution in several functional classes, including olfaction and nuclear transport. In addition to suggesting adaptive physiological differences between chimps and humans, human-accelerated genes are significantly more likely to underlie major known Mendelian disorders. 相似文献
5.
Gresham D Ruderfer DM Pratt SC Schacherer J Dunham MJ Botstein D Kruglyak L 《Science (New York, N.Y.)》2006,311(5769):1932-1936
A central challenge of genomics is to detect, simply and inexpensively, all differences in sequence among the genomes of individual members of a species. We devised a system to detect all single-nucleotide differences between genomes with the use of data from a single hybridization to a whole-genome DNA microarray. This allowed us to detect a variety of spontaneous single-base pair substitutions, insertions, and deletions, and most (>90%) of the approximately 30,000 known single-nucleotide polymorphisms between two Saccharomyces cerevisiae strains. We applied this approach to elucidate the genetic basis of phenotypic variants and to identify the small number of single-base pair changes accumulated during experimental evolution of yeast. 相似文献
6.
【目的】了解我国西南地区不同玉米地方品种的遗传多样性,为合理利用这些玉米种质资源提供参考。【方法】以西南地区12份玉米地方品种为材料,对Glb1基因片段进行克隆、测序及序列比对,分析其遗传多样性。【结果】12份玉米材料Glb1基因序列长度为1138-1149 bp,其序列一致性为96.21%。12份材料Glb1基因序列间存在较多的变异位点,大于等于3 bp的插入/缺失有8个,主要位于第81-84、122-128、161-164、368-371、428-442、668-680、966-976和1003-1011 bp。不同玉米地方品种材料间的遗传相似系数为96.50%-100.00%,平均为98.58%。根据聚类分析结果可将12份材料分为五大类,且来源于同一地区的玉米材料趋向于聚为一类。【结论】Glb1基因具有较高的保守性,所选材料间Glb1基因序列存在一定的遗传多样性,利用Glb1基因序列可作为鉴定不同玉米地方品种的一种理想分子标记。 相似文献
7.
采用最邻近算法对同源建模中的缺失值进行填充,由此扩大传统同源建模方法的研究尺度.在序列结构比对中,氨基酸的插入（删除）会引起数据缺失,传统的同源建模法不能处理这部分结构.结合最邻近算法、期望值最大化方法和主成分分析,抽取蛋白质结构演化的主要信息,构建蛋白质保守结构的低维取样空间.与标准的主成分分析相比,该方法能利用更多的演化信息,涵盖更多的具有遗传信息的区域,构造更大尺度的蛋白质取样空间.取样空间的精度用目标蛋白质结构与其在取样空间上的投影的均方根偏差评价.将该方法应用于33个蛋白质超家族,结果表明,扩大后的取样空间精度达到测定蛋白质结构的X-ray实验精度,满足后续的蛋白质结构研究. 相似文献
8.
为了认识节节麦5t+12t亚基品质表现突出的分子基础,利用SDS-PAGE分析研究了该亚基组合中12t亚基的电泳迁移率并克隆和测序了该亚基基因。结果表明,该12t亚基在SDS-PAGE上的电泳迁移率与普通小麦中的Dy12具有一致的电泳迁移率,但与Dy10的电泳迁移率差异明显。而氨基酸序列比较结果显示,12t亚基的分子序列与Dy10的相似程度非常高,二者仅存在4个氨基酸的替换,而它与Dy12的分子序列存在较大的差异,不但包括12个氨基酸的替换,同时包括2个六肽氨基酸和另外4个氨基酸部位的插入和缺失变化。本研究结果表明,节节麦高分子量谷蛋白Dx5t+Dy12t亚基赋予小麦优良加工品质的主要原因可能与12t亚基与小麦Dy10非常相似,导致这一亚基组合更倾向与Dx5+Dy10有一定关系。 相似文献
9.
10.
对来自福建、浙江和北京地区的中华蜜蜂囊状幼虫病毒(Chinese Sac Brood Virus,CSBV)进行了PCR鉴定,并对来自北京地区的病毒株CSBV-BJ/2010结构基因片段进行了克隆及系统进化分析.结果表明:RT-PCR方法获得了426 bp的cDNA片段;所获得序列与GenBank中CSBVLN/200... 相似文献
11.
气味结合蛋白(odorant-binding proteins,OBPs)和化学感受蛋白(chemosensory proteins,CSPs)在菜粉蝶(Pieris rapae)气味识别的过程中发挥着重要作用。通过本地BLAST等方法在菜粉蝶基因组中找到了推测的OBPs和CSPs蛋白序列,采用多序列比对、半胱氨酸模式序列识别、进化发育树构建等方法,鉴定出了24个PrOBPs和38个PrCSPs基因。其中,PrOBP1-PrOBP17这17个OBPs属于Classic OBPs蛋白家族,PrOBP19-PrOBP24属于Minus-C OBPs蛋白家族。鉴定出的38个PrCSPs都具有鳞翅目CSPs的半胱氨酸模式识别序列。本实验通过对菜粉蝶基因组中OBPs和CSPs基因的查找鉴定,丰富了昆虫OBPs和CSPs基因数据库,可为菜粉蝶气味识别和化学感受相关实验和应用提供参考。 相似文献
12.
参考GenBank中PEDV经典CV777毒株基因组序列设计特异性引物,采用RT-PCR方法对临床采集的疑似PEDV样品进行S基因扩增、克隆和测序,拼接获得30条完整S基因序列,并进行遗传进化及同源性分析。结果显示,获得的30条PEDV S基因与25个参考株S基因的核苷酸相似性介于93.6%～99.8%;且各流行毒株与经典毒株比较,具有多处的点突变、插入和缺失。与其他参考株相比,S1区存在157个氨基酸突变位点,占总数的65.7%（157/239）,暗示PEDV的 S1区域比S2区域易发生变异;表明目前中国PEDV流行株已经发生了变异,在一定程度揭示了免疫猪群仍然发病的原因。 相似文献
13.
植物同源异型枢基因(Homeobox gene,HBG)广泛存在,是一类重要的转录因子编码基因,在生物进化中具有很强的保守性。利用GenBank登录的拟南芥、苜蓿、豌豆、烟草、番茄等同源异型枢基因保守区序列设计简并引物,通过RT-PCR技术,从马铃薯萌动的幼芽中获得了一个homeobox的cDNA基因,命名为StKN1,GenBank登录号为DQ494855.1。该基因片段长971 bp,经序列分析比对,与其他植物的HBG具有很高的序列相似性。系统进化分析将StKN1基因归入homeobox KNOX基因家族。 相似文献
14.
Janssen A van der Burg M Szuhai K Kops GJ Medema RH 《Science (New York, N.Y.)》2011,333(6051):1895-1898
Various types of chromosomal aberrations, including numerical (aneuploidy) and structural (e.g., translocations, deletions), are commonly found in human tumors and are linked to tumorigenesis. Aneuploidy is a direct consequence of chromosome segregation errors in mitosis, whereas structural aberrations are caused by improperly repaired DNA breaks. Here, we demonstrate that chromosome segregation errors can also result in structural chromosome aberrations. Chromosomes that missegregate are frequently damaged during cytokinesis, triggering a DNA double-strand break response in the respective daughter cells involving ATM, Chk2, and p53. We show that these double-strand breaks can lead to unbalanced translocations in the daughter cells. Our data show that segregation errors can cause translocations and provide insights into the role of whole-chromosome instability in tumorigenesis. 相似文献
15.
Identification of a chromosome 18q gene that is altered in colorectal cancers 总被引：141，自引：0，他引：141
E R Fearon K R Cho J M Nigro S E Kern J W Simons J M Ruppert S R Hamilton A C Preisinger G Thomas K W Kinzler 《Science (New York, N.Y.)》1990,247(4938):49-56
Allelic deletions involving chromosome 18q occur in more than 70 percent of colorectal cancers. Such deletions are thought to signal the existence of a tumor suppressor gene in the affected region, but until now a candidate suppressor gene on this chromosomal arm had not been identified. A contiguous stretch of DNA comprising 370 kilobase pairs (kb) has now been cloned from a region of chromosome 18q suspected to reside near this gene. Potential exons in the 370-kb region were defined by human-rodent sequence identities, and the expression of potential exons was assessed by an "exon-connection" strategy based on the polymerase chain reaction. Expressed exons were used as probes for cDNA screening to obtain clones that encoded a portion of a gene termed DCC; this cDNA was encoded by at least eight exons within the 370-kb genomic region. The predicted amino acid sequence of the cDNA specified a protein with sequence similarity to neural cell adhesion molecules and other related cell surface glycoproteins. While the DCC gene was expressed in most normal tissues, including colonic mucosa, its expression was greatly reduced or absent in most colorectal carcinomas tested. Somatic mutations within the DCC gene observed in colorectal cancers included a homozygous deletion of the 5' end of the gene, a point mutation within one of the introns, and ten examples of DNA insertions within a 0.17-kb fragment immediately downstream of one of the exons. The DCC gene may play a role in the pathogenesis of human colorectal neoplasia, perhaps through alteration of the normal cell-cell interactions controlling growth. 相似文献
16.
Many evolutionary studies use comparisons across species to detect evidence of natural selection and to examine the rate of character evolution. Statistical analyses in these studies are usually performed by means of a species phylogeny to accommodate the effects of shared evolutionary history. The phylogeny is usually treated as known without error; this assumption is problematic because inferred phylogenies are subject to both stochastic and systematic errors. We describe methods for accommodating phylogenetic uncertainty in evolutionary studies by means of Bayesian inference. The methods are computationally intensive but general enough to be applied in most comparative evolutionary studies. 相似文献
17.
One of the long-standing problems in modern astronomy is the curious division of Galactic globular clusters, the "Oosterhoff dichotomy," according to the properties of their RR Lyrae stars. Here, we find that most of the lowest metallicity ([Fe/H] < -2.0) clusters, which are essential to an understanding of this phenomenon, display a planar alignment in the outer halo. This alignment, combined with evidence from kinematics and stellar population, indicates a captured origin from a satellite galaxy. We show that, together with the horizontal-branch evolutionary effect, the factor producing the dichotomy could be a small time gap between the cluster-formation epochs in the Milky Way and the satellite. The results oppose the traditional view that the metal-poorest clusters represent the indigenous and oldest population of the Galaxy. 相似文献
18.
Genetic variation in HTLV-III/LAV over time in patients with AIDS or at risk for AIDS 总被引：89，自引：0，他引：89
B H Hahn G M Shaw M E Taylor R R Redfield P D Markham S Z Salahuddin F Wong-Staal R C Gallo E S Parks W P Parks 《Science (New York, N.Y.)》1986,232(4757):1548-1553
In a study of genetic variation in the AIDS virus, HTLV-III/LAV, sequential virus isolates from persistently infected individuals were examined by Southern blot genomic analysis, molecular cloning, and nucleotide sequencing. Four to six virus isolates were obtained from each of three individuals over a 1-year or 2-year period. Changes were detected throughout the viral genomes and consisted of isolated and clustered nucleotide point mutations as well as short deletions or insertions. Results from genomic restriction mapping and nucleotide sequence comparisons indicated that viruses isolated sequentially had evolved in parallel from a common progenitor virus. The rate of evolution of HTLV-III/LAV was estimated to be at least 10(-3) nucleotide substitutions per site per year for the env gene and 10(-4) for the gag gene, values a millionfold greater than for most DNA genomes. Despite this relatively rapid rate of sequence divergence, virus isolates from any one patient were all much more related to each other than to viruses from other individuals. In view of the substantial heterogeneity among most independent HTLV-III/LAV isolates, the repeated isolation from a given individual of only highly related viruses raises the possibility that some type of interference mechanism may prevent simultaneous infection by more than one major genotypic form of the virus. 相似文献
19.
The CRISPR/Cas9 induces large genomic fragment deletions of MSTN and phenotypic changes in sheep 
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下载免费PDF全文 DING Yi ZHOU Shi-wei DING Qiang CAI Bei ZHAO Xiao-e ZHONG Shu JIN Miao-han WANG Xiao-long MA Bao-hua CHEN Yu-lin 《农业科学学报》2020,19(4):1065-1073
The CRISPR/Cas9 system has been extensively used to engineer genetic loci for the generation of knockouts, insertions, and point mutations in animal models. However, many mutations that have been reported in animals are small insertions or deletions. This study used the CRISPR/Cas9 system to induce large DNA fragment deletions in MSTN via three guide RNAs in sheep. This successfully achieved the precise gene editing of the ovine MSTN gene by injecting both Cas9 m RNA and sg RNAs into embryos at the one-cell stage. Of 10 edited animals, 3 animals(30%) exhibited large genomic fragment deletions(～5 kb). Furthermore, the body weights of these 3 animals were significantly different(P_00.0001, P_(15)=0.001, P_(30)=0.005, P_(60)=0.027) between lambs with large deletions and wildtype lambs. In addition, the edited lambs were also significantly different(P_00.0001, P_(15)0.0001, P_(30)=0.002, P_(60)=0.011) compared with wildtype. These results suggest that the generated MSTN knockout sheep is a reliable and effective animal model for further study. Furthermore, this method is time-and labor-saving, and efficient for the creation of animal models for agriculture, biology, and medicine. 相似文献
20.
牛线粒体D-loop的序列分析及进化关系 总被引：1，自引：0，他引：1
牦牛存在两处10bp和7bp的缺失．10个品种的20条D-loop序列中共有18种单倍型，共检测到164个突变位点，346个突变碱基，其中转换突变235个，颠换突变55个，插人和缺失突变56个．基于聚类分析显示本试验所检测的黄牛中除了鲁西黄牛以外都起源于欧洲原牛，鲁西黄牛来源于两个母系，一个是欧洲原牛，另一个是瘤牛型原牛．牦牛与黄牛起源于不同的母系． 相似文献