链霉菌的rep-PCR基因指纹分析

对重复片段PCR(repPCR)基因指纹分析应用于链霉菌分子分型进行研究,结果表明repPCR基因指纹分析具有分辨率高、稳定、重现性好、简便易行等特点,在一定程度上与16S rDNA 序列比较结果相一致,是一种快速而有效的DNA指纹技术,能反映出链霉菌种和菌株水平的基因型、系统发育和分类学关系,可应用于种及以下水平的分类和快速鉴定,尤其适用于分析大量的菌株或分离株。     

Network-Based Interpretation of Genomic Variation Data

Advances in sequencing technologies are allowing genome-wide association studies at an ever-growing scale. The interpretation of these studies requires dealing with statistical and combinatorial challenges, owing to the multi-factorial nature of human diseases and the huge space of genomic markers that are being monitored. Recently, it was proposed that using protein–protein interaction network information could help in tackling these challenges by restricting attention to markers or combinations of markers that map to close proteins in the network. In this review, we survey techniques for integrating genomic variation data with network information to improve our understanding of complex diseases and reveal meaningful associations.     

Genomic Fingerprinting of Virulent and Avirulent Strains of Clavibacter michiganensis subspecies sepedonicus

Genomic fingerprints of C. michiganensis subsp. sepedonicus were generated by CHEF gel electrophoresis of restriction digested high-molecular weight DNA. Low levels of intra-subspecific variation were detected by cluster analysis of the fingerprints. Four haplotypes were identified by genomic fingerprinting with HindIII, and eight were identified with EcoRI. Haplotypes generated with HindIII were less similar than those generated by EcoRI. Haplotypes generated with HindIII formed groups that corresponded well with plant reactions of the strains, but similar types of groupings were less apparent with haplotypes generated with EcoRI. When disease severity in eggplant and potato, population size in potato, and ability to induce a hypersensitive response (HR) in tobacco were overlaid onto dendograms of genetic similarity, avirulent HR-negative strains clustered separately from virulent HR-positive strains in both EcoRI and HindIII profiles. Avirulent HR-positive strains that lack pCS1 clustered with avirulent HR-negative strains in a EcoRI dendogram, but clustered with virulent HR-positive strains in a HindIII dendogram. Genomic fingerprinting of high-molecular weight DNA fragments provided a means for detecting genomic variability associated with virulence in C. michiganensis subsp. sepedonicus. Received: 1 March 2001 / Accepted: 7 June 2001     

AFLP Fingerprinting for Assessing Intraspecific Variation and Genome Mapping in Mites

Molecular genetic techniques have come a long way in the last decade. With the advent of PCR, genetic markers are now accessible for all organisms, including mites. However, there is usually a trade-off between the accuracy of the molecular technique or genetic marker and expediency. In mites, many molecular techniques are not applicable due to their small size. Here we describe a relatively new molecular fingerprinting technique, amplified fragment length polymorphism (AFLP), which is currently used widely in plant genomic research. We outline the AFLP procedure adapted for mites, show results using this technique from our own research and discuss the benefits and limitations of AFLPs for assessing genetic variation and for genome mapping. It is our intention to highlight the possible use of AFLPs as genetic markers with a broad application in acarological research.     

水稻Rim2/Hipa 超级家族的基因组变异和基于Rim2/Hipa 展示的水稻资源的系统进化和指纹分析

水稻Rim2/Hipa是最近鉴定的一个受逆境诱导的转座因子超级家族.研究表明,Rim2的核心序列在不同来源的水稻材料中存在显著的差异,暗示Rim2家族的长期进化历程.基于Rim2因子间的差异性以及该因子的静止状态,开发出一种利用Rim2因子展示的新的分子指纹技术,可以灵敏地区分不同水稻资源以及它们的遗传关系.仅用5对引物就可以清楚地将53个栽培稻和普通野生稻材料鉴定出来,并可将它们分为不同的系统进化组.研究表明不仅在水稻资源而且在野生稻种质间均存在明显的多样性.野生稻可以被单独分组,或者分散在粳稻中间.这种新的指纹技术还可以将水稻的杂交子代和它们的亲本区分出来,并可用于种子纯度的鉴定,在水稻基因组进化研究、水稻育种和种子生产中有很好的应用前景.     

Variation in Genomic Recombination Rates Among Heterogeneous Stock Mice

We used a large panel of pedigreed, genetically admixed house mice to study patterns of recombination rate variation in a leading mammalian model system. We found considerable inter-individual differences in genomic recombination rates and documented a significant heritable component to this variation. These findings point to clear variation in recombination rate among common laboratory strains, a result that carries important implications for genetic analysis in the house mouse.THE rate of recombination—the amount of crossing over per unit DNA—is a key parameter governing the fidelity of meiosis. Recombination rates that are too high or too low frequently give rise to aneuploid gametes or prematurely arrest the meiotic cell cycle (Hassold and Hunt 2001). As a consequence, recombination rates should experience strong selective pressures to lie within the range defined by the demands of meiosis (Coop and Przeworski 2007). Nonetheless, classical genetic studies in Drosophila (Chinnici 1971; Kidwell 1972; Brooks and Marks 1986), crickets (Shaw 1972), flour beetles (Dewees 1975), and lima beans (Allard 1963) have shown that considerable inter-individual variation for recombination rate is present within populations. Recent studies examining the transmission of haplotypes in human pedigrees have corroborated these findings (Broman et al. 1998; Kong et al. 2002; Coop et al. 2008).Here, we use a large panel of heterogeneous stock (HS) mice to study variation in genomic recombination rates in a genetic model system. These mice are genetically admixed, derived from an initial generation of pseudorandom mating among eight common inbred laboratory strains (DBA/2J, C3H/HeJ, AKR/J, A/J, BALB/cJ, CBA/J, C57BL/6J, and LP/J), followed by >50 generations of pseudorandom mating in subsequent hybrid cohorts (Mott et al. 2000; Demarest et al. 2001). The familial relationships among animals in recent generations were tracked to organize the mice into pedigrees. In total, this HS panel includes ∼2300 animals comprising 85 families, 8 of which span multiple generations. The remainder consists of nuclear families (sibships) that range from 1 to 34 sibs, with an average of 9.6 sibs (Valdar et al. 2006) (Mott et al. 2000; Demarest et al. 2001; Shifman et al. 2006).

TABLE 1

Heterogeneous stock mouse pedigrees

Genomic DNA Fingerprinting of Oenococcus oeni Strains by Pulsed-Field Gel Electrophoresis and Randomly Amplified Polymorphic DNA-PCR

Genetic diversity of 60 Oenococcus oeni strains from different wines was evaluated by numerical analysis of (i) pulsed-field gel electrophoresis (PFGE) patterns with endonuclease ApaI and (ii) randomly amplified polymorphic DNA (RAPD)-PCR fingerprints with four oligonucleotide primers. Sixty-two percent of the strains could be distinguished by PFGE, whereas most strains were identified by distinct RAPD-PCR profiles and associated according to the geographical origin. Because of its rapidity and reliability, RAPD-PCR appeared to be a suitable method for typing and monitoring O. oeni strains in winemaking. Received: 3 November 1999 / Accepted: 8 December 1999     

Variation in Heterozygosity Predicts Variation in Human Substitution Rates between Populations,Individuals and Genomic Regions

The “heterozygote instability” (HI) hypothesis suggests that gene conversion events focused on heterozygous sites during meiosis locally increase the mutation rate, but this hypothesis remains largely untested. As humans left Africa they lost variability, which, if HI operates, should have reduced the mutation rate in non-Africans. Relative substitution rates were quantified in diverse humans using aligned whole genome sequences from the 1,000 genomes project. Substitution rate is consistently greater in Africans than in non-Africans, but only in diploid regions of the genome, consistent with a role for heterozygosity. Analysing the same data partitioned into a series of non-overlapping 2 Mb windows reveals a strong, non-linear correlation between the amount of heterozygosity lost “out of Africa” and the difference in substitution rate between Africans and non-Africans. Putative recent mutations, derived variants that occur only once among the 80 human chromosomes sampled, occur preferentially at the centre of 2 Kb windows that have elevated heterozygosity compared both with the same region in a closely related population and with an immediately adjacent region in the same population. More than half of all substitutions appear attributable to variation in heterozygosity. This observation provides strong support for HI with implications for many branches of evolutionary biology.     

OLFACTORY CILIA IN THE FROG

Olfactory epithelium from the frog was examined in the living state by light microscopy and in the fixed state by electron microscopy. Particular attention was paid to the layer of cilia and mucus which covers the surface of the epithelium. The olfactory cilia differed from typical cilia in that they (a) arose from bipolar neurons and had centrioles near their basal bodies, (b) were up to 200 microns in length, of which the greater part was a distal segment containing an atypical array of ciliary fibers, (c) were often immotile, (d) had their distal segments arranged in parallel rows near the surface of the mucus, and (e) had many vesicles along their shafts and had splits in the array of fibers in their distal segments. These specializations make the olfactory cilia similar to cilia found on other sensory cells and support the theory that they are the locus where electrical excitation in the olfactory organ is initiated by contact with odorous substances.     

Genomic Analysis of Natural Selection and Phenotypic Variation in High-Altitude Mongolians

Deedu (DU) Mongolians, who migrated from the Mongolian steppes to the Qinghai-Tibetan Plateau approximately 500 years ago, are challenged by environmental conditions similar to native Tibetan highlanders. Identification of adaptive genetic factors in this population could provide insight into coordinated physiological responses to this environment. Here we examine genomic and phenotypic variation in this unique population and present the first complete analysis of a Mongolian whole-genome sequence. High-density SNP array data demonstrate that DU Mongolians share genetic ancestry with other Mongolian as well as Tibetan populations, specifically in genomic regions related with adaptation to high altitude. Several selection candidate genes identified in DU Mongolians are shared with other Asian groups (e.g., EDAR), neighboring Tibetan populations (including high-altitude candidates EPAS1, PKLR, and CYP2E1), as well as genes previously hypothesized to be associated with metabolic adaptation (e.g., PPARG). Hemoglobin concentration, a trait associated with high-altitude adaptation in Tibetans, is at an intermediate level in DU Mongolians compared to Tibetans and Han Chinese at comparable altitude. Whole-genome sequence from a DU Mongolian (Tianjiao1) shows that about 2% of the genomic variants, including more than 300 protein-coding changes, are specific to this individual. Our analyses of DU Mongolians and the first Mongolian genome provide valuable insight into genetic adaptation to extreme environments.     

香果树组织培养过程中遗传变异的RAPD分析

用RAPD分子标记方法,从DNA水平上分析野生型香果树以及通过器官发生途径和体细胞胚胎发生途径得到的香果树再生植株以及体细胞胚胎发生过程中不同继代次数的培养物之间的遗传变异。筛选了100个随机引物,其中有75条随机引物能够扩增出条带,从中选取11个引物进行PCR扩增的结果显示：香果树体细胞胚胎无性系中有RAPD多态性位点,在胚性愈伤组织中也检测到少数RAPD变异位点。表明RAPD分子标记方法可以鉴定香果树组织培养过程中的遗传变异。     

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA

Non-coding genomic regions in complex eukaryotes, including intergenic areas, introns, and untranslated segments of exons, are profoundly non-random in their nucleotide composition and consist of a complex mosaic of sequence patterns. These patterns include so-called Mid-Range Inhomogeneity (MRI) regions -- sequences 30-10000 nucleotides in length that are enriched by a particular base or combination of bases (e.g. (G+T)-rich, purine-rich, etc.). MRI regions are associated with unusual (non-B-form) DNA structures that are often involved in regulation of gene expression, recombination, and other genetic processes (Fedorova & Fedorov 2010). The existence of a strong fixation bias within MRI regions against mutations that tend to reduce their sequence inhomogeneity additionally supports the functionality and importance of these genomic sequences (Prakash et al. 2009).Here we demonstrate a freely available Internet resource -- the Genomic MRI program package -- designed for computational analysis of genomic sequences in order to find and characterize various MRI patterns within them (Bechtel et al. 2008). This package also allows generation of randomized sequences with various properties and level of correspondence to the natural input DNA sequences. The main goal of this resource is to facilitate examination of vast regions of non-coding DNA that are still scarcely investigated and await thorough exploration and recognition.     

Post-zygotic Point Mutations Are an Underrecognized Source of De Novo Genomic Variation

De novo mutations are recognized both as an important source of genetic variation and as a prominent cause of sporadic disease in humans. Mutations identified as de novo are generally assumed to have occurred during gametogenesis and, consequently, to be present as germline events in an individual. Because Sanger sequencing does not provide the sensitivity to reliably distinguish somatic from germline mutations, the proportion of de novo mutations that occur somatically rather than in the germline remains largely unknown. To determine the contribution of post-zygotic events to de novo mutations, we analyzed a set of 107 de novo mutations in 50 parent-offspring trios. Using four different sequencing techniques, we found that 7 (6.5%) of these presumed germline de novo mutations were in fact present as mosaic mutations in the blood of the offspring and were therefore likely to have occurred post-zygotically. Furthermore, genome-wide analysis of “de novo” variants in the proband led to the identification of 4/4,081 variants that were also detectable in the blood of one of the parents, implying parental mosaicism as the origin of these variants. Thus, our results show that an important fraction of de novo mutations presumed to be germline in fact occurred either post-zygotically in the offspring or were inherited as a consequence of low-level mosaicism in one of the parents.