拟南芥DNA全序列测定与分析完成

在 2 0 0 0年 1 2月 1 4日英国出版的ＮＡＴＵＲＥ杂志上 (Ｖｏｌ.4 0 8:796～ 81 5) ,发表了植物分子遗传研究的模式开花植物拟南芥 1 1 5.4Ｍｂ的全序列图谱 ,原文的中文译名为“开花植物拟南芥的基因组序列分析”。拟南芥ＤＮＡ全长 1 2 5Ｍｂ ,只剩下 1 0Ｍｂ的中心着丝区ＤＮＡ ,因为多重复序列所含基因很少 ,还未全测出。拟南芥全基因组ＤＮＡ包含 2 5498个功能基因组及其所对应的 1 1 0 0 0个蛋白质家族。这是人类首次全部破译出一种高等植物的全基因序列 ,是在分子水平上向植物生命奥秘探索的又一里程碑式的工作。拟南芥植物基因组…     

水稻（Oryza sativa L.）核基因组存在叶绿体psbA基因的同源 …

序列比较说明、重复ＤＮＡ顺序ｐＲＲＤ９＾＊与水稻叶绿体基因组中编码ＱＢ蛋白的ｐｓｂＡ基因存在高度的同源。用ｐＲＢＤ９亚克隆片段ｐＲＲＤ９Ｒ和片段ｐＲＲＤ９Ｌ对水稻的叶绿体和核ＤＮＡ进行Ｓｏｕｔｈｅｒｎ杂交分析,揭示了ｐｓｂＡ基因同源片段在某个进化时期由叶绿体基因组转移到水稻核基因组,而且两者在水稻进化过程中的变异程度存在明显的差异。     

可转座基因与植物基因组多样性

高等植物基因组含有大量各式各样的串联重复序列和出现频率很高的散布重复序列,如转座子、反转座子、短散布核元件和一些新发现的小型转座子等,它们当中的大多数是具有移动能力的可转座基因.这些可转座基因在漫长的进化过程中对基因和基因组多样性的形成所起的作用,成为近年来分子生物学领域中的重要研究内容.     

植物线粒体DNA质料研究进展

本文列出了已发现的高等植物中的线粒体ＤＮＡ质粒,按分子形状分为线粒体环状ＤＮＡ质粒和线粒体线状ＤＮＡ质粒,环状线粒体ＤＮＡ质粒的特征是分子较小,序列中有正向／反向重复序列,ＯＲＦ一般较小。线状线粒体ＤＮＡ质粒的特征是分子较大,末端有重复序列,５’端与蛋白质共价结合,有较长的ＯＲＦ。还分别介绍了它们的复制机制、转录和起源。质粒间及质粒及核基因组、线粒体基因组、叶绿体基因组的同源性也作了介绍。最后,综     

自私DNA及其功能

自私ＤＮＡ及其功能李子银,胡会庆（华中农业大学农学系,武汉４３００７０）真核生物基因组的一个显著特点就是含有大量的非编码序列,这些ＤＮＡ序列包括高度重复序列,特别是占总ＤＮＡ１—３０％的卫星ＤＮＡ（ＳａｔｅｌｌｉｔｅＤＮＡ）;中度重复序列（如哺乳动物...     

纤毛虫大核发育过程中程序化的DNA消除

纤毛虫大核发育过程中发生程序性的ＤＮＡ消除,被消除的序列为内在删除顺序非编码区。消除以后,大核胚基中的ＤＮＡ发生片段化,在腹毛目纤毛虫中,ＤＮＡ断裂成为只有基因大小的ＤＮＡ分子;在四膜虫中,ＤＮＡ断裂成为平均长度约６００ｋｂ的片段,在断裂位点发现一个１５ｂｐ的顺序,为断裂位点的标志信号。通过对四膜虫小核基因组某一内在删除顺序的研究,发现此序列的删除受两套顺式作用顺序的控制。     

鲫鱼Hind Ⅲ高重复DNA序列的分子克隆

基因组DNA高重复序列的研究有助于解释许多重要的生命现象 ,如基因调节、基因转座、基因进化等 ,还可以用于进行种群的遗传分析。鱼类的DNA高重复序列研究资料较少 ,曾在鲤科鱼类发现HindⅢ高重复序列家族。本研究用HindⅢ内切酶消化 ,从鲫鱼 (Carassiusauratusauratus)基因组DNA也克隆出一种独特的高重复序列。序列测定揭示该重复序列长度为 175bp ,在单倍体基因组的拷贝数为 1× 10 5。鲫鱼HindⅢ高重复序列与鲫鱼属 (Carassius)其它同类已知的高重复序列存在某种程度的变异 ,而与鲤科其它属的已知的HindⅢ高重复序列完全不同     

水稻重复DNA顺序克隆pRRD3的研究

用ＤＮＡ复性动力学方法克隆到一个水稻（ＯｒｙｚａｓａｔｉｖａＬ．）中度重复ＤＮＡ顺序。不同限制性内切酶消化和Ｓｏｕｔｈｅｒｎ杂交分析显示,这段重复ＤＮＡ顺序以串联加散布的形式存在于水稻基因组中;序列分析表明在它内部含有一个典型的植物启动子序列ＴＧＴＡＴＡＡＡＴＡ;以ｐＲＲＤ３克隆片段作探针,对水稻３４个品种进行拷贝数测定,在野生稻与栽培稻、籼稻与粳稻之间均存在拷贝数上的明显差异;对ＡＡ基因组不同亚型水稻ＤＮＡ进行Ｓｏｕｔｈｅｒｎ杂交分析,得到基因组亚型特异的杂交带谱,说明该重复顺序是研究水稻进化和分类的一个有用探针。     

一种快速有效的识别DNA重复序列的方法

按统计的相应分析方法设计和编制了基因组重复序列的识别软件。经众多Ａｌｕ序列的回顾性分析,错报率为４．８％,漏报率为５．８％,又地剪入编码区的Ａｌｕ序列的细致检查和对Ｔ细胞受体基因组的Ａｌｕ序列的大尺度搜索,证实本程序是一种快束速和良好的识别ＤＮＡ重复序列的工具。     

黄瓜线粒体DNA类质粒pC1的性质和核酸序列研究

津研四号黄瓜线粒体中除主环ＤＮＡ外,还有４种ＤＮＡ类质粒：ｐＣ１、ｐＣ２、ｐＣ３、ｐＣ４。将环形类质粒ｐＣ１ｌｐｋ ｇｃ ｐＵＣ１９的ＥｃｏＲⅠ位点上,克隆至Ｅ．ｃｏｌｉ ＪＭ１０９中。以克隆的ｐＣ１为探针,进行同源性检测,ｐＣ１与津研四号黄瓜的核基因组、叶绿体基因组、线粒体基因组和线粒体中其他类质粒不同源。对ｐＣ１进行序列测定和分析,ｐＣ１长度２ ８８９ｂｐ,含有多个正向和反向重复序列,有３个８     

A new middle repetitive sequence of Nicotiana plumbaginifolia genome

A middle repetitive sequence NPR18 was isolated from Nicotiana plumbaginifolia nuclear genome [8]. Sequences homologous to the repeat are dispersed through genomes of several Nicotiana species. compute-assisted data analysis of NPR18 primary sequence reveals several features attributed to mobile genetic elements: an AT content higher than average for nuclear DNA of genus Nicotiana plants; a number of direct and inverted repeats. Some of the repeats displayed homology to the terminal and subterminal repeats of Ac/Ds-like plant elements.     

Identification of the Mitochondrial Genome in the Chrysophyte Alga Ochromonas danica

ABSTRACT. Analysis of total DNA isolated from the Chrysophyte alga Ochromonas danica revealed, in addition to nuclear DNA, two genomes present as numerous copies per cell. The larger genome (?120 kilobase pairs or kbp) is the plastid DNA, which is identified by its hybridization to plasmids containing sequences for the photosynthesis genes rbcL, psbA, and psbC. The smaller genome (40 kbp) is the mitochondrial genome as identified by its hybridization with plasmids containing gene sequences of plant cytochrome oxidase subunits I and II. Both the 120- and 40-kbp genomes contain genes for the small and large subunits of rDNA. The mitochondrial genome is linear with terminal inverted repeats of about 1.6 kbp. Two other morphologically similar species were examined, Ochromonas minuta and Poteriochromonas malhamensis. All three species have linear mitochondrial DNA of 40 kbp. Comparisons of endonuclease restriction-fragment patterns of the mitochondrial and chloroplast DNAs as well as those of their nuclear rDNA repeats failed to reveal any fragment shared by any two of the species. Likewise, no common fragment size was detected by hybridization with plasmids containing heterologous DNA or with total mitochondrial DNA of O. danica; these observations support the taxonomic assignment of these three organisms to different species. The Ochromonas mitochondrial genomes are the first identified in the chlorophyll a/c group of algae. Combining these results with electron microscopic observations of putative mitochondrial genomes reported for other chromophytes and published molecular studies of other algal groups suggests that all classes of eukaryote algae may have mitochondrial genomes < 100 kbp in size, more like other protistans than land plants.     

Double-strand breaks increase the incidence of genetic deletion associated with intermolecular recombination in bacteriophage T7

An in vitro DNA replication system based on extracts prepared from Escherichia coli cells infected with bacteriophage T7 was used to study deletion associated with the repair of double-strand breaks. The gene for T7 ligase was interrupted by a DNA insert which included 17-bp direct repeats. Deletion between the repeats restored the reading frame of the gene, and these DNA molecules could be detected by their ability to give rise to ligase-positive phage after in vitro packaging. T7 genomes that had a pre-existing double-strand break located between the direct repeats were incubated together with intact genomes which had the same direct repeats. Genetic markers placed on either side of the insert in the ligase gene allowed identification of the source of DNA molecules that underwent deletion between the direct repeats. This allowed an assessment of the participation of the molecules with strand breaks in the deletion process, under conditions where any mechanism could contribute to deletion. Approximately three-quarters of the T7 molecules that had lost the region between the direct repeats contained one or both of the partial genomes originally introduced into the reactions. About 50% of the genomes which had undergone deletion had recombined markers between the partial and intact genomes. The data demonstrate that double-strand breaks substantially enhance the contribution of intermolecular recombination to deletion. Received: 19 November 1996 / Accepted: 26 February 1997     

DNA transposition – a major contributor to plant chromosome structure

Higher plant nuclear genomes contain many families of dispersed repeats that change during evolution. Recent evidence from studies on genetically defined transposable elements raises the possibility that many of the dispersed repeats are remnants of such elements. Transposition of DNA has also occurred between mitochondria, chloroplasts and nuclei, a fact that underlines the major role played by DNA transposition in determining the structure of plant genomes.     

Molecular and structural evolution of Citrus satellite DNA

Highly repeated satellite DNA (stDNA) of citric plants was characterized by cloning and sequencing 10–14 repeats of each plant (Citrus limon, C. sinensis, C. ichangensis, Poncirus trifoliata). The monomers are mostly 181 bp in length with a GC-content between 60% and 68% (significantly higher than the average GC-content of the citrus group genomes). Similarity among the repeats indicates that they belong to a satellite family that underwent species-specific modifications, which are reflected in the phylogenetic relationships. Curvature provoked by dA-stretches of the repeats analyzed by gel shifts revealed structural conservation, even though the nucleotide sequences vary among species, thereby probably supporting the heterochromatic structure of stDNA. We show that the species-specific modification of the satellite consensus involves changes in the position and number of dA tracts. The molecule shapes of satellite oligomeres predicted by computer modelling indicate a superhelical structure of the tandem repeats which is in a good agreement with the satellite sequence dendrogram. The contribution of DNA bending elements to the evolution of plant satellite repeats is discussed. Received: 27 November 2000 / Accepted: 12 January 2001     

Assessing Diversity of DNA Structure-Related Sequence Features in Prokaryotic Genomes

Prokaryotic genomes are diverse in terms of their nucleotide and oligonucleotide composition as well as presence of various sequence features that can affect physical properties of the DNA molecule. We present a survey of local sequence patterns which have a potential to promote non-canonical DNA conformations (i.e. different from standard B-DNA double helix) and interpret the results in terms of relationships with organisms'' habitats, phylogenetic classifications, and other characteristics. Our present work differs from earlier similar surveys not only by investigating a wider range of sequence patterns in a large number of genomes but also by using a more realistic null model to assess significant deviations. Our results show that simple sequence repeats and Z-DNA-promoting patterns are generally suppressed in prokaryotic genomes, whereas palindromes and inverted repeats are over-represented. Representation of patterns that promote Z-DNA and intrinsic DNA curvature increases with increasing optimal growth temperature (OGT), and decreases with increasing oxygen requirement. Additionally, representations of close direct repeats, palindromes and inverted repeats exhibit clear negative trends with increasing OGT. The observed relationships with environmental characteristics, particularly OGT, suggest possible evolutionary scenarios of structural adaptation of DNA to particular environmental niches.     

Genome modifications in protoplast-derived tobacco plants: Contents of repetitive DNA sequences

Plasticity of the tobacco genome was studied by testing the DNAs of protoplast-derived regenerants with three different repetitive DNA sequences by the method of quantitative DNA/DNA hybridizations. A large population of 91 regenerants belonging to 35 different protoclones was analysed and a high degree of heterogeneity in the contents of the different DNA repeats was detected. The contents of middle repetitive sequences of two types were more stable or changed in the same direction, while the highly repetitive sequence varied independently and displayed a significant reduction in comparison with the two other sequences. Comparing the variation within the subpopulations of plants of the same clonal origin and the variation among the protoclones led to a conclusion that the pre-existing DNA variability in the starting plant material and/or thein vitro stress during the very early stages of protoclone regeneration played a decisive role in the formation of modified genomes in regenerants.     

Abundance and DNA sequence of two-base repeat regions in tropical tree genomes

Tandem DNA repeats of two-base pairs are potentially important tools for population genetic studies because of their abundance and length variation. As part of our research into the ecology of tropical forest plants, we began a study of dinucleotide repeat regions in several genera of tropical trees. Genomic libraries in bacteriophage lambda were screened with the oligonucleotide probes poly(GT) and poly(AG). Both types of repeat regions were abundant in the genomes of all six plant species examined. Using the size of inserts in the phage libraries and number of phage screened, we estimated that there were 5 x 10(3) to 3 x 10(5) poly(AC) sites per genome, with slightly more AG than AC sites. When libraries were made from smaller fragments of genomic DNA, abundance estimates were higher, suggesting that two-base repeat sites were clustered in the genome. Poly(AC) sites were 16-22 bp in length, and four of the five sequenced were adjacent to either poly(AG)or poly(AT) sites. Other repeat region s appeared in DNA flanking the AC sites. This further demonstrated that two-base repeats and other repetitive DNA were clustered in the genome. Two-base repeats are abundant in plant genomes and could provide a large number of polymorphic markers for studies of plant population genetics.     

FORRepeats: detects repeats on entire chromosomes and between genomes

MOTIVATION: As more and more whole genomes are available, there is a need for new methods to compare large sequences and transfer biological knowledge from annotated genomes to related new ones. BLAST is not suitable to compare multimegabase DNA sequences. MegaBLAST is designed to compare closely related large sequences. Some tools to detect repeats in large sequences have already been developed such as MUMmer or REPuter. They also have time or space restrictions. Moreover, in terms of applications, REPuter only computes repeats and MUMmer works better with related genomes. RESULTS: We present a heuristic method, named FORRepeats, which is based on a novel data structure called factor oracle. In the first step it detects exact repeats in large sequences. Then, in the second step, it computes approximate repeats and performs pairwise comparison. We compared its computational characteristics with BLAST and REPuter. Results demonstrate that it is fast and space economical. We show FORRepeats ability to perform intra-genomic comparison and to detect repeated DNA sequences in the complete genome of the model plant Arabidopsis thaliana.     

Repetitive DNA and chromosome evolution in plants

Most higher plant genomes contain a high proportion of repeated sequences. Thus repetitive DNA is a major contributor to plant chromosome structure. The variation in total DNA content between species is due mostly to variation in repeated DNA content. Some repeats of the same family are arranged in tandem arrays, at the sites of heterochromatin. Examples from the Secale genus are described. Arrays of the same sequence are often present at many chromosomal sites. Heterochromatin often contains arrays of several unrelated sequences. The evolution of such arrays in populations is discussed. Other repeats are dispersed at many locations in the chromosomes. Many are likely to be or have evolved from transposable elements. The structures of some plant transposable elements, in particular the sequences of the terminal inverted repeats, are described. Some elements in soybean, antirrhinum and maize have the same inverted terminal repeat sequences. Other elements of maize and wheat share terminal homology with elements from yeast, Drosophila, man and mouse. The evolution of transposable elements in plant populations is discussed. The amplification, deletion and transposition of different repeated DNA sequences and the spread of the mutations in populations produces a turnover of repetitive DNA during evolution. This turnover process and the molecular mechanisms involved are discussed and shown to be responsible for divergence of chromosome structure between species. Turnover of repeated genes also occurs. The molecular processes affecting repeats imply that the older a repetitive DNA family the more likely it is to exist in different forms and in many locations within a species. Examples to support this hypothesis are provided from the Secale genus.