通过多基因组比较的方法在5种绿球蓝细菌中识别基因组岛(英文)

为探索水平基因转移在绿球蓝细菌基因组多样性中的作用,5个高光适应性绿球蓝细菌基因组被比较.先用BLASTP两两最佳匹配搜索和基因位置保守性的方法预测直系同源基因,并进一步计算每个基因组中所有基因在其他4种绿球蓝细菌基因组中直系同源基因的数量,从而达到识别外源基因的目的;而基因组岛是指由1个或几个连续外源基因组成的区域.结果表明:在5个绿球蓝细菌基因组中共识别出了16至52个不等的基因组岛,它们中的许多基因在病毒基因组或富含病毒的环境样本中都有同源基因.以上这些结果显示,在绿球蓝细菌中,病毒可能介导了基因的水平转移,从而导致了基因组的多样性.     

Selection on major components of angiosperm genomes

Angiosperms are a relatively recent evolutionary innovation, but their genome sizes have diversified remarkably since their origin, at a rate beyond that of most other taxa. Genome size is often correlated with plant growth and ecology, and extremely large genomes may be limited both ecologically and evolutionarily. Yet the relationship between genome size and natural selection remains poorly understood. The manifold cellular and physiological effects of large genomes may be a function of selection on the major components that contribute to genome size, such as transposable elements and gene duplication. To understand the nature of selection on these genomic components, both population-genetic and comparative approaches are needed.     

Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.     

高等植物线粒体基因组测序和序列分析

线粒体是真核细胞内的重要细胞器,是一种遗传上半自主性的细胞器,编码与自身功能相关的部分基因,参与生命活动一些过程。植物的线粒体基因组较动物的更为复杂,且与植物细胞质雄性不育和物种进化密切相关。本文概述了植物线粒体基因组测序工作,并在此基础上,综述了植物线粒体基因组的大小、组成形式、基因组序列的结构特征、基因组成,分析表达特点、RNA编辑、序列重组,以及线粒体基因组进化、线粒体相关的雄性不育机理研究的研究进展。     

Introduction of genetic material into plant cells

The tumor-inducing (Ti) plasmid of the soil microorganism Agrobacterium tumefaciens is the agent of crown gall disease in dicotyledonous plants. The Ti plasmid contains two regions that are essential for the production of transformed cells. One of these regions, termed transfer DNA, induces tumor formation and is found in all established plant tumor lines; the other, termed the virulence region, is essential for the formation but not the maintenance of tumors. Transfer DNA, which transfers to the plant genomes in a somewhat predictable manner, can be increased in size by the insertion of foreign DNA without its transferring ability being affected. The tumor-causing genes can be removed so that they no longer interfere with normal plant growth and differentiation. This modified Ti plasmid can thus be used as a vector for the transfer of foreign genes into plants.     

The nature and dynamics of bacterial genomes

Though generally small and gene rich, bacterial genomes are constantly subjected to both mutational and population-level processes that operate to increase amounts of functionless DNA. As a result, the coding potential of bacterial genomes can be substantially lower than originally predicted. Whereas only a single pseudogene was included in the original annotation of the bacterium Escherichia coli, we estimate that this genome harbors hundreds of inactivated and otherwise functionless genes. Such regions will never yield a detectable phenotype, but their identification is vital to efforts to elucidate the biological role of all the proteins within the cell.     

高粱CMS材料线粒体基因组DNA指纹研究

应用限制性核酸内切酶片段分析（REFA）和随机扩增多态性DNA（RAPD）技术，分析了6个Milo型细胞质来源的高粱细胞质雄性不育系的线粒体基因组（Mitochondrial genome)的指纹图谱。RAPD分析共使用10nt随机引物50个，其中22个得到扩增到多态性。各种试材的REFA指纹亦不相同。结果表明具有相同细胞质（Milo)来源的高粱雄性不育系的线粒体基因组已经产生了异质性。     

A physical map of the Escherichia coli K12 genome

A physical map of a genome is the structure of its DNA. Construction of such a map is a first step in the complete characterization of that DNA. The restriction endonuclease Not I cuts the genome of Escherichia coli K12 into 22 DNA fragments ranging from 20 kilobases (20,000 base pairs) to 1000 kilobases. These can be separated by pulsed field gel electrophoresis. The order of the fragments in the genome was determined from available E. coli genetic information and analysis of partial digest patterns. The resulting ordered set of fragments is a macrorestriction map. This map facilitates genetic and molecular studies on E. coli, and its construction serves as a model for further endeavors on larger genomes.     

An age-induced switch to a hyper-recombinational state

There is a strong correlation between age and cancer, but the mechanism by which this phenomenon occurs is unclear. We chose Saccharomyces cerevisiae to examine one of the hallmarks of cancer--genomic instability--as a function of cellular age. As diploid yeast mother cells aged, an approximately 100-fold increase in loss of heterozygosity (LOH) occurred. Extending life-span altered neither the onset nor the frequency of age-induced LOH; the switch to hyper-LOH appears to be on its own clock. In young cells, LOH occurs by reciprocal recombination, whereas LOH in old cells was nonreciprocal, occurring predominantly in the old mother's progeny. Thus, nuclear genomes may be inherently unstable with age.     

实时荧光定量PCR技术在乳品微生物学中的应用研究进展

越来越多的基因组测序给特异性引物和探针的设计带来了极大的支持。最近有研究表明,基于定量聚合酶链式反应（qPCR）方法的技术成功应用于发酵过程中的微生物计数以及乳制品中益生菌数量的计算。基于qPCR方法的技术进步包括实时荧光定量PCR技术,不仅可以计数活菌数量,还可以在单一反应体系中检测多个微生物菌群数量,且能构建高通量PCR流程。实时荧光定量PCR技术在食品工业中的应用已证明其可靠性,尽管如此,该技术在乳品工业中的广泛使用还需要更多的技术支持和标准化方法。综述了实时荧光定量PCR技术及其在乳品微生物学中的最新研究与应用进展。     

Sequence variations of <Emphasis Type="Italic">PDHA1</Emphasis> gene in Triticeae species allow for identifying wheat-alien introgression lines

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.     

The rise of the angiosperms: a genecological factor

In the primitive angiosperms, closed carpels are believed to have evolved as protection for ovules, which would otherwise be injured by animal pollinators. The hypothesis is presented that, whatever the origin and other functions of angiosperms, insect pollination and closed carpels may, in combination, reduce the influence of random variation on pollen tube competition, thus enhancing the ability of natural selection to act on the gametophytic phase of the life cycle. The microgametophytic phase represented by vast numbers of haploid individuals can then serve, by insect pollination and closed carpels, as a screen against any genome not functioning with a high degree of metabolic vigor. Poorly balanced genomes could thus be eliminated at relatively little cost. Insect-pollinated angiosperms would therefore benefit from positive aspects of sexual recombination. Such a system may have allowed the angiosperms to undergo their rise to dominance.     

Genome-wide experimental determination of barriers to horizontal gene transfer

Horizontal gene transfer, in which genetic material is transferred from the genome of one organism to that of another, has been investigated in microbial species mainly through computational sequence analyses. To address the lack of experimental data, we studied the attempted movement of 246,045 genes from 79 prokaryotic genomes into Escherichia coli and identified genes that consistently fail to transfer. We studied the mechanisms underlying transfer inhibition by placing coding regions from different species under the control of inducible promoters. Our data suggest that toxicity to the host inhibited transfer regardless of the species of origin and that increased gene dosage and associated increased expression may be a predominant cause for transfer failure. Although these experimental studies examined transfer solely into E. coli, a computational analysis of gene-transfer rates across available bacterial and archaeal genomes supports that the barriers observed in our study are general across the tree of life.     

Mutation pressure and the evolution of organelle genomic architecture

The nuclear genomes of multicellular animals and plants contain large amounts of noncoding DNA, the disadvantages of which can be too weak to be effectively countered by selection in lineages with reduced effective population sizes. In contrast, the organelle genomes of these two lineages evolved to opposite ends of the spectrum of genomic complexity, despite similar effective population sizes. This pattern and other puzzling aspects of organelle evolution appear to be consequences of differences in organelle mutation rates. These observations provide support for the hypothesis that the fundamental features of genome evolution are largely defined by the relative power of two nonadaptive forces: random genetic drift and mutation pressure.     

Characterization and molecular cloning of a human parvovirus genome

The genome of the small human virus serologically associated with erythrocyte aplasia and erythema infectiosum (fifth disease) is shown to be a linear, nonpermuted, single-stranded DNA molecule with self-priming hairpin termini, properties which are characteristic of the genomes of the family Parvoviridae. This human parvovirus chromosome was molecularly cloned into bacterial plasmid vectors and the cloned DNA was used to explore its relatedness to other mammalian parvovirus serotypes by DNA:DNA hybridization. It is not related to the human adeno-associated viruses but does show a distant evolutionary relationship to genomes of the helper-independent parvoviruses of rodents. This strongly suggests that it is an autonomous parvovirus, and as such is the first example of a member of this group of common animal pathogens to cause disease in man.     

Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes

Although common among bacteria, lateral gene transfer-the movement of genes between distantly related organisms-is thought to occur only rarely between bacteria and multicellular eukaryotes. However, the presence of endosymbionts, such as Wolbachia pipientis, within some eukaryotic germlines may facilitate bacterial gene transfers to eukaryotic host genomes. We therefore examined host genomes for evidence of gene transfer events from Wolbachia bacteria to their hosts. We found and confirmed transfers into the genomes of four insect and four nematode species that range from nearly the entire Wolbachia genome (>1 megabase) to short (<500 base pairs) insertions. Potential Wolbachia-to-host transfers were also detected computationally in three additional sequenced insect genomes. We also show that some of these inserted Wolbachia genes are transcribed within eukaryotic cells lacking endosymbionts. Therefore, heritable lateral gene transfer occurs into eukaryotic hosts from their prokaryote symbionts, potentially providing a mechanism for acquisition of new genes and functions.     

水稻线粒体中与细胞质雄性不育有关的类质粒DNA（综述）

对水稻细胞质雄性不育的遗传机理研究已经积累了一些资料。在线粒体类质粒ＤＮＡ研究方面，已经明确了不育系和保持系间、不同的不育系间的线粒体类质粒ＤＮＡ存在着差异；类质粒ＤＮＡ在核基因组中存在同源序列；类质粒ＤＮＡ在正常可育栽培种中出现的频率有随进化阶段升高而降低的趋势；类质粒ＤＮＡ的存在与细胞质雄性不育性的表达有关。