Global transposable characteristics in the complete DNA sequence of the yeast

Global transposable characteristics in the complete DNA sequence of the Saccharomyces cevevisiae yeast is determined by using the metric representation and recurrence plot methods. On the basis of the correlation distance of nucleotide strings, 16 chromosome sequences of the yeast, which are divided into 5 groups, display 4 kinds of the fundamental transposable characteristics: a short increasing period, a long increasing quasi-period, a long major value and hardly relevant.

Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation

The vegetation of the northeast Qinghai-Tibetan Plateau is dominated by alpine meadow and desert-steppe with sparse forests scattered within it. To obtain a better understanding of the phylogeography of one constituent species of the forests in this region, we examined chloroplast trnT-trnF and trnS-trnG sequence variation within Juniperus przewalskii, a key endemic tree species. Sequence data were obtained from 392 trees in 20 populations covering the entire distribution range of the species. Six cpDNA haplotypes were identified. Significant population subdivision was detected (G(ST) = 0.772, N-ST = 0.834), suggesting low levels of recurrent gene flow among populations and significant phylogeographic structure (N-ST > G(ST), P < 0.05). Eight of the nine disjunct populations surveyed on the high-elevation northeast plateau were fixed for a single haplotype (A), while the remaining, more westerly population, contained the same haplotype at high frequency together with two low frequency haplotypes (C and F). In contrast, most populations that occurred at lower altitudes at the plateau edge were fixed or nearly fixed for one of two haplotypes, A or E. However, two plateau edge populations had haplotype compositions different from the rest. In one, four haplotypes (A, B, D and E) were present at approximately equivalent frequencies, which might reflect a larger refugium in the area of this population during the last glacial period. Phylogenetic analysis indicated that the most widely distributed haplotype A is not ancestral to other haplotypes. The contrasting phylogeographic structures of the haplotype-rich plateau edge area and the almost haplotype-uniform plateau platform region indicate that the plateau platform was recolonized by J. przewalskii during the most recent postglacial period. This is supported by the findings of a nested clade analysis, which inferred that postglacial range expansion from the plateau edge followed by recent fragmentation is largely responsible for the present-day spatial distribution of cpDNA haplotypes within the species.

Mitochondrial DNA hypervariable region-1 sequence variation and phylogeny of the concolor gibbons, Nomascus

The still little known concolor gibbons are represented by 14 taxa (five species, nine subspecies) distributed parapatrically in China, Myanmar, Vietnam, Laos and Cambodia. To set the stage for a phylogeographic study of the genus we examined DNA sequence

Mitochondrial DNA variation, effective female population size and population history of the endangered Chinese sturgeon, Acipenser sinensis

The anadromous Chinese sturgeon (Acipenser sinensis), mainly endemic to the Yangtze River in China, is an endangered fish species. The natural population has declined since the Gezhouba Dam blocked its migratory route to the spawning grounds in 1981. In the near future, the completion of the Three Gorges Dam, the world's largest hydroelectric project, may further impact this species by altering the water flow of the Yangtze River. Little is currently known about the population genetic structure of the Chinese sturgeon. In this study, DNA sequence data were determined from the control region (D-loop) of the mitochondrial genome of adult sturgeons (n = 106) that were collected between 1995-2000. The molecular data were used to investigate genetic variation, effective female population size and population history of the Chinese sturgeon in the Yangtze River. Our results indicate that the reduction in abundance did not change genetic variation of the Chinese sturgeon, and that the population underwent an expansion in the past. AMOVA analysis indicated that 98.7% of the genetic variability occurred within each year's spawning populations, the year of collection had little influence on the diversity of annual temporary samples. The relative large effective female population size (N-ef) indicates that good potential exists for the recovery of this species in the future. Strikingly, the ratio of N-ef to the census female population size (N-f) is unusually high (0.77-0.93). This may be the result of a current bottleneck in the population of the Chinese sturgeon that is likely caused by human intervention.

Cloning and analysis of 16 Rab genes from macronuclear DNA of Euplotes octocarinatus

Rab proteins belong to the largest family of the Ras superfamily of small GTPase that play an important role in intracellular vesicular traffic. So far, almost 60 members of Rab family have been identified in mammalian cells. To further study the diversity and function of Rab protein in evolution, unicellular protozoa ciliates, Euplotes octocarinatus, were used in this study, Rab genes were screened by PCR method from macronuclear DNA of E. octocarinatus. Sixteen Rab genes were obtained. They share 87.6 - 99.5% identities. Highly conserved GTP-binding domains were found. There are some hot regions that diverse sharply in these genes as well.

DNA diagnosis by capillary electrophoresis and microfabricated electrophoretic devices

DNA diagnosis is experiencing an impressive progression towards the development of novel technology to identity various clinically relevant categories of genetic changes and to meet the exponential growth of genomics. The introduction of capillary electrophoresis has dramatically accelerated the completion of the first draft of the human DNA sequence in the Human Genome Project, and thus, has become the method of choice for analysis of various genetic variants. The recent development of microfabricated electrophoretic devices has led to the possibility of integrating multiple sample handling with the actual measurement steps required for automation of molecular diagnostics. This review highlights the most recent progress in capillary electrophoresis and electrophoretic microdevices for DNA-based diagnostics, including the important areas of genotyping for point mutation, single nucleotide polymorphisms, short tandem repeats and organism identification. The application of these techniques for infectious and genetic disease diagnosis, as well as forensic identification purpose, are covered. The promising development and the challenges for techinical problems are also discussed.

attB site disruption in marine Actinomyces sp M048 via DNA transformation of a site-specific integration vector

An efficient conjugation method has been developed for the marine Actinomyces sp. isolate M048 to facilitate the genetic manipulation of the chandrananimycin biosynthesis gene cluster. A phi C31-derived integration vector pIJ8600 containing oriT and attP fragments was introduced into strain M048 by bi-parental conjugation from Escherichia coli ET12567 to strain M048. Transformation efficiency was (6.38 +/- 0.41) x 10(-5) exconjugants per recipient spore. Analysis of eight exconjugants showed that the plasmid pIJ8600 was stably integrated at a single chromosomal site (attB) of the Actinomyces genome. The DNA sequence of the attB was cloned and shown to be conserved. The results of antimicrobial activity analysis indicated that the insertion of plasmid pIJ8600 seemed to affect the biosynthesis of antibiotics that could strongly inhibit the growth of E. coli and Mucor miehei (Tu284). HPLC-MS analysis of the extracts indicated that disruption of the attB site resulted in the complete abolition of chandrananimycin A-C production, proving the identity of the gene cluster. Instead of chandrananimycins, two bafilomycins were produced through disruption of the attB site from the chromosomal DNA of marine Actinomyces sp. M048.

Self-similarity limits of genomic signatures

It is shown that metric representation of DNA sequences is one-to-one. By using the metric representation method, suppression of nucleotide strings in the DNA sequences is determined. For a DNA sequence, an optimal string length to display genomic signature in chaos game representation is obtained by eliminating effects of the finite sequence. The optimal string length is further shown as a self-similarity limit in computing information dimension. By using the method, self-similarity limits of bacteria complete genomic signatures are further determined.

木根麦冬rRNA基因进化的研究

木根麦冬（Ophiopogon xylorrhizus Wang et Dai）属于铃兰科（Convallariaceae）或广义百合科（Liliaceae s.l.）沿阶草族（Ophiopogoneae）沿阶草属（Ophiopogon Ker-Gawl.），属于典型的濒危植物。前人已从细胞学、种群生态学、生殖生物学和遗传结构与多样性等方面对木根麦冬进行了研究，但在分子进化和分子细胞遗传学水平上的研究近为空白。本文运用染色体的荧光原位杂交(FISH)、PCR扩增和克隆、DNA测序、系统发育重建等方法，对18S rDNA作了染色体原位定位，研究了木根麦冬的Ss rRNA基因结构特点，并重建了该基因的系统发育树，探讨了5S rRNA多基因家族的分子进化模式和木根麦冬的濒危机制。主要结果如下： 1．对木根麦冬三个居群七个个体、及其最近姐妹种林生麦冬（Ophiopogon svlvicola Wang et Tang）一个个体的5S rRNA基因进行了PCR扩增和TA克隆，在两个种中共得到1085个具有插入片段的阳性克隆。 2．对木根麦冬三个居群六个个体的294个SS rRNA基因克隆，及林生麦冬一个个体的45个克隆，总计339个克隆进行了DNA序列测定，这是目前已完成的最大的单个物种的5S rRNA数据。结果表明：两个种的序列高度多样化，在339个拷贝中仅仅有13对(3.8%)是相同的，序列长度变化在307bp-548bp之间，长度变异主要发生在间隔区，单个碱基的插入和缺失(indel)频率很高，5bp以上片段的插入，缺失有11个，插入的序列通常是其两侧序列的重复和倒位。术根麦冬序列的分化指数（sequence differentiation index，SDI）是0.078，林生麦冬是0.032，两个物种间是0.149，木根麦冬的序列之间的分化明显大于林生麦冬。 3．以PAUP程序对339个5S rRNA基因拷贝的DNA序列（包括编码区和间隔区）作了系统发育分析，结果如下：在得到一个唯一的最俭约树中，所有木根麦冬的拷贝被聚成一支，而林生麦冬的则被聚到另一支，统计支持率(bootstrap)达到lOO%，表明这两个物种所有的的5S rRNA基因拷贝分别来自各自的一个祖先拷贝（建立者拷贝），而其共同祖先的其它拷贝则在物种形成中或之后丢失：在多基因家族中如此长期而单一的拷贝偏选( sorting)过程尚未有前人报道;由此基因系统发育树可以看出，在这两个物种形成之后，“建立者拷贝”经历了多次扩增过程而形成了一个直系的（orthologous）多基因家族。 4．在木根麦冬分支中，很少有亚分支是全部由一个居群或一个个体的拷贝组成的，不同居群、不同个体的拷贝混合在同一个亚分支中;对基因系统发育树、序列多样性和序列分化指数分析表明，5S rRNA基因家族内一致化（homogeruzation）过程很弱，不同拷贝是独立进化的，这在串联．重复的多拷贝基因家族中是不寻常的;由上述分析我们推测，在术根麦冬的进化历史上，居群间的基因交流远远比今天频繁，可能是某些外在因素在近期发生变化，导致自交和自交衰退，并进而导致濒危。 5．利用荧光原位杂交技术，成功地将18S rRNA基因定位在木根麦冬减数分裂期的染色体上，两对强信号和一对弱信号分别位于三对二价体染色体上。

栽培牡丹起源研究

牡丹在中国被称作“花中之王”。我国不仅是全部野生牡丹的原产地，也是栽培牡丹最早的驯化地。野生牡丹共有8个种，分布于云南、四川、湖北、甘肃、陕西、山西、安徽、河南和西藏等9省区，因其具有很大的观赏和药用价值，而在中国和世界温带地区广泛栽培。本研究利用形态特征和4个核基因片段（三个Adh 基因和GPAT基因片断）的核苷酸序列变异对牡丹组的种间系统发育关系进行了分析，并对我国栽培牡丹四个品种群的101个代表品种的可能祖先进行了形态学鉴定和分子诊断标记研究。在此基础上，利用核编码叶绿体表达的GPAT基因的（大内含子）部分序列和叶绿体基因组的trnS – trnG 和 rpS16 – trnQ两个基因间隔区的DNA序列变异重建了栽培牡丹37个代表品种和26个野生居群间的谱系关系。结果表明：（1）GPAT基因树是迄今得到的分辨率最好，并具有很高自展值支持的牡丹组种间系统发育关系树;（2）GPAT基因树和形态学证据一致支持银屏牡丹（P. suffruticosa ssp. yinpingmudan）, 凤丹（P. ostii）, 紫斑牡丹（P. rockii）, 卵叶牡丹（P. qiui）, 和矮牡丹 （P. jishanensis） 参与了栽培牡丹的起源;（3）叶绿体DNA单倍型网络树（network）进一步证实上述5个祖先类群的4个（矮牡丹除外）可能参与了栽培牡丹的母系起源。37个品种的GPAT基因谱系和叶绿体DNA单倍型网络树一致表明银屏牡丹是栽培牡丹最主要的祖先，其次是紫斑牡丹、凤丹、和卵叶牡丹;（4）我们的分子证据不支持形态学证据关于矮牡丹是栽培牡丹最主要的野生祖先的推测;（5）形态学和分子诊断标记证据表明，101个品种中有65.35 % 的品种具有两个以上野生种的特征，18.81 % 品种同时具有 Eco R I (+) 和 InDel51(+)物种特异分子标记。对37个品种的GPAT基因谱系和叶绿体DNA谱系比较发现，其中35个可能是杂种起源。另外，对7个古代牡丹品种（据文献记载）的GPAT基因的不同克隆类型进行测序和谱系分析，结果表明其中4 个为杂种起源。上述证据充分表明杂交和（或）渗入杂交在牡栽培牡丹的起源和进化中发挥了重要作用。根据本研究的结果，结合现有的形态学数据、考古记录，以及有关牡丹栽培和驯化历史的记载，我们对栽培牡丹的起源和驯化历史总结如下。牡丹的栽培迄今有1,600 – 2,000年，栽培牡丹最迟起源于1，500年前。最初通过驯化和对突变的选择获得原始品种。由于牡丹品种可以通过无性和（或）有性方式进行繁殖，其后新的品种通过如下方式产生：（1）对突变的选择，（2）对栽培类型和野生种之间或栽培类型之间杂交和（或）渗入杂交产生的实生苗的选择。由于绝大部分（如果不是全部）早期的原始品种已绝灭，现有栽培牡丹是起源于各种人工和自然进化力共同作用的结果，其中包括多次驯化、人工选择、突变、杂交和渗入杂交等。据作者所知，栽培牡丹的这种 ‘compilospecies’ 起源和驯化模式是目前已研究过的主要栽培作物中未见报道的。 因此，本研究不仅为栽培牡丹的多系起源和驯化历史提供了可信的分子证据，同时也为利用单拷贝基因的内含子序列构建栽培作物及其近缘野生祖先间的种系发生关系提供了成功的例子。另外，本研究也为同时利用核和叶绿体基因组的非编码DNA序列研究杂交在栽培作物的起源和进化的中作用提供了成功的例子。