RAPD analysis of genome polymorphism in the family Lemnaceae

The multilocus RAPD analysis of intergeneric, inter-and intraspecific nuclear genome polymorphism was used for the first time to assess intergeneric, interspecific, and intraspecific polymorphism in Lemnaceae growing on the territory of Russia. The origin of the chosen accessions overlapped with the natural range of duckweeds in Russia. Seventy-five Lemnaceae accessions representing eight species (L. minor, L. gibba, L. turionifera, L. japonica, L. trisulca, L. aequinoctialis, S. polyrhiza, and L. punctata) from three genera (Lemna, Spirodela, and Landoltia), were analyzed. The highest variability levels were revealed in L. minor accessions (0.03–0.20). Species L. trisulca and S. polyrhiza were characterized by values of genetic distance 0.01–0.18 and 0.03–0.16, respectively. The lowest polymorphism levels were detected for L. turionifera (0.01–0.11). The dendrogram based on RAPD data showed that L. aequinoctialis was the most genetically distant species of the genus Lemna. Accessions of species L. turionifera and L. japonica, as well as L. minor and L. gibba, did not form separate species-specific subclusters; rather, they fell into clusters with L. japonica/L. turionifera and L. minor/L. gibba. Accessions of the genera Spirodela and Landoltia formed two separate clusters combined into one group.     

The detection of genome polymorphism in Stachys species using RAPD

Molecular genome analysis was for the first time carried out in the genus Stachys. RAPD analysis proved to be suitable for identifying the species-specific markers, studying the interspecific DNA polymorphism, and detecting the genetic changes that arise during in vitro culturing of Stachys sieboldii. In addition, RAPD was used for screening genetic variation in S. sieboldii regenerants obtained at various phytohormone concentrations. High cytokinin concentrations and multiple regeneration were shown to induce genetic changes detectable with RAPD patterns. High DNA polymorphism was demonstrated for two types of S. sieboldii callus cultures and for plants regenerated from a callus culture.     

RAPD analysis on the genome evolution of polyploids in Brassica

Polyploidy has played an important role in the evolution of higher plants.In order to understand how polyploid genomes evolve after their formation,the Brassica triangle was used to study genomic evolution after the formation of polyploids.Random amplifie     

芸薹属多倍体植物基因组进化的RAPD分析

多倍化是促进高等植物发生进化的重要力量。为了更清楚地了解多倍体在形成之后其基因组是如何进化的,利用38个随机引物对芸薹属Brassica L.禹氏三角（U’Triangle）中的多倍体物种及其祖先二倍体物种进行了研究。根据扩增出的273条带计算了遗传距离,并用UPGMA法进行了聚类分析。结果发现,二倍体物种B.campestris（AA）与B.oleracea（CC）的亲缘关系比与B.nigra（BB）的要近;异源多倍体B.napus（AACC）比起其二倍体祖先之一B.campestris（AA）与另一个     

金龟甲基因组DNA RAPD反应条件的优化

以华北大黑鳃金龟[Holotrichia oblita (Faldermann)]和矮臀鳃金龟(H.ernesti Reitter)为供试材料,对DNA模板、Mg2+、dNTPs浓度、淬火和循环内延伸时间及循环数进行优化.提出了金龟甲RAPD分析的最佳反应体系,即25 μL体系中含DNA模板1.2 ng·μL-1、Mg2+ 2. 5 mmol·L-1、dNTPs 0. 25 mmol·L-1;并确定最适淬火时间为40 s,循环内延伸时间为2 min;最佳循环数为40.     

Computational analysis of human genome polymorphism

While genome-era technologies focused on complete genome sequencing in various organisms, post-genome technologies aim at the understanding of the mechanisms of genetic information processing and elucidation of within-species variation. Single nucleotide polymorphisms (SNPs) are the most common source of genome variation in the human population. Nonsynonymous SNPs that occur in coding gene regions and result in amino acid substitutions are of particular interest. It is thought that such SNPs are responsible for phenotypic variation, quantitative traits, and the etiology of common diseases. PolyPhen is a computational tool for the prediction of putatively functional nonsynonymous SNPs by combining information of various types. The application areas of PolyPhen and similar methods include the genetics of complex diseases and congenital defects, the identification of functional mutations in model organisms, and evolutionary genetics.     

Bioinformatics analysis of SARS coronavirus genome polymorphism

Background  

We have compared 38 isolates of the SARS-CoV complete genome. The main goal was twofold: first, to analyze and compare nucleotide sequences and to identify positions of single nucleotide polymorphism (SNP), insertions and deletions, and second, to group them according to sequence similarity, eventually pointing to phylogeny of SARS-CoV isolates. The comparison is based on genome polymorphism such as insertions or deletions and the number and positions of SNPs.     

RAPD analysis of genome variability of planted ginseng,Panax ginseng

Genome variability of 23 ginseng plants (Panax ginseng) grown in culture in Primorskii Krai was studied by RAPD method. Eleven arbitrary chosen primers were used to analyze 138 loci of DNA samples, 17 of which appeared to be polymorphic. The OPD-11-1000 fragment was found to be a RAPD marker allowing plants to be differentiated according to their morphotype. Using five primers, it was demonstrated that the genetic polymorphism of the cultivated plants is lower than that in nature (7.6% and 10.6%, respectively). Dendrograms of genetic relatedness are in accord with genetic differences between individuals of plantedP. ginseng belonging to different morphotypes, and demonstrate close relatedness of one of the morphotypes to wild plants. This morphotype could be recommended for reintroduction into natural habitats.     

The mapping of the barley genome by RAPD analysis using double haploid strains

A map of the barley genome consisting of 107 loci was constructed using double haploid lines. 33 RAPD loci marks all barley chromosomes. The total length of the obtained map is 1047 centiMorgans (cM) with a 9.8 cM average distance between markers. 7 linkage groups was identified as certain chromosomes. The distribution of the markers was analyzed, comparison with other published maps was made. Some statistical considerations are presented. Alternative strategies of gene mapping are considered.     

肺形侧耳线粒体基因组多态性鉴定

线粒体是能量转化与ATP形成的重要场所,已有多种食用真菌的线粒体基因组被相继组装注释,但肺形侧耳的线粒体基因组鲜有报道。本研究对野生肺形侧耳X2菌株的线粒体基因组进行组装并注释,由野生菌株X2与主栽菌株JX线粒体大片段差异序列,构建分子标记来鉴别野生和主栽肺形侧耳菌株。结果显示X2的线粒体基因组为大小75 709bp的闭合环状结构,含有rRNA的大小亚基基因,25个负责携带氨基酸的tRNA基因以及14个常见蛋白编码基因,在cox1基因上含有9个内含子。内含子主要为IB型,包含LAGLIDADG_1 superfamily、GIY-YIG_Cterm superfamily保守结构域。位于菌株X2与JX内含子和基因间区上的大片段差异序列,是造成种内线粒体多态性的主要因素。根据两菌株的差异片段构建系统进化树的结果显示,内含子、rnl-trnX、trnD-atp6序列能够将两株野生菌株和其他主栽菌株区分开,可用于野生肺形侧耳种内鉴定,而且trnD-atp6效果最佳。     

Detection of point mutations in the chloroplast genome by single-stranded conformation polymorphism analysis

Single-stranded conformation polymorphism (SSCP) analysis was used to examine the mutations of the chloroplast 16S rRNA locus of streptomycin-resistant mutants in Nicotiana plumbaginifolia. DNA fragments of 121, 517, 968 and 1578 bp, each possessing a known point mutation, were generated by polymerase chain reaction (PCR). The resulting fragments were denatured and separated by nondenaturing polyacrylamide gel electrophoresis. Compared to the patterns of the wild-type DNA fragments, the bands of the single-stranded DNA fragments of 121 and 517 bp with base changes were shifted. However, no pattern variations were detected from the DNA fragments of 968 and 1578 bp generated from both wild-type and mutants.     

A family of repeated sequences in Drosophila genome with telomeric localization: properties and polymorphism

The previously cloned Drosophila genome fragment Dm665 (2.4 kb) hybridizing with telomers on polytene chromosomes is a representative of the family of repeats, a part of which being organized in tandem clusters. The repeats are not transcribed in cell culture, are species-specific and represented in 200-250 copies per haploid genome. In natural and laboratory Drosophila lines polymorphism has been revealed with regard to homology with Dm665 in the telomeres.     

A snapshot of viral evolution from genome analysis of the tectiviridae family

The origin, evolution and relationships of viruses are all fascinating topics. Current thinking in these areas is strongly influenced by the tailed double-stranded (ds) DNA bacteriophages. These viruses have mosaic genomes produced by genetic exchange and so new natural isolates are quite dissimilar to each other, and to laboratory strains. Consequently, they are not amenable to study by current tools for phylogenetic analysis. Less attention has been paid to the Tectiviridae family, which embraces icosahedral dsDNA bacterial viruses with an internal lipid membrane. It includes viruses, such as PRD1, that infect Gram-negative bacteria, as well as viruses like Bam35 with Gram-positive hosts. Although PRD1 and Bam35 have closely related virion morphology and genome organization, they have no detectable sequence similarity. There is strong evidence that the Bam35 coat protein has the "double-barrel trimer" arrangement of PRD1 that was first observed in adenovirus and is predicted to occur in other viruses with large facets. It is very likely that a single ancestral virus gave rise to this very large group of viruses. The unprecedented degree of conservation recently observed for two Bam35-like tectiviruses made it important to investigate those infecting Gram-negative bacteria. The DNA sequences for six PRD1-like isolates (PRD1, PR3, PR4, PR5, L17, PR772) have now been determined. Remarkably, these bacteriophages, isolated at distinctly different dates and global locations, have almost identical genomes. The discovery of almost invariant genomes for the two main Tectiviridae groups contrasts sharply with the situation in the tailed dsDNA bacteriophages. Notably, it permits a sequence analysis of the isolates revealing that the tectiviral proteins can be dissected into a slowly evolving group descended from the ancestor, the viral self, and a more rapidly changing group reflecting interactions with the host.     

Genetic polymorphism analysis of somatic embryo-derived plantlets of Cymbopogon flexuosus through RAPD assay

The genetic status of somatic embryo-derived plantlets of Cymbopogon flexuosus was examined by randomly amplified polymorphic DNA (RAPD) analysis. Auxins such as 2, 4-dichlorophenoxyacetic acid (2, 4-D) (1–4 mg/l) were used in Murashige and Skoog (MS) medium for induction of calli from rhizomatous explants of Cymbopogon flexuosus. Optimum calli were induced on MS medium supplemented with 2, 4-dichlorophenoxyacetic acid (2, 4-D) (3.5 mg/l) alone or in combination with N ⁶-benzyladenine (2 mg/l). Somatic embryogenesis was achieved from long term calli when cultured on MS medium containing 2, 4-dichlorophenoxyacetic acid (2, 4-D) (2 mg/l) along with N ⁶-benzyladenine (BA) (1–2 mg/l). Regeneration was achieved when freshly induced embryogenic calli were sub-cultured on MS medium supplemented with N ⁶-benzyladenine (3 mg/l) alone. Long-term cultured embryos showed profuse minute rooting on regeneration medium supplemented with N ⁶-benzyladenine (3 mg/l). Microshoots were rooted in the presence of indole-butyric acid (IBA) (2 mg/l). DNA samples from the mother plant and 18 randomly selected regenerated plants from a single callus were subjected to RAPD analysis with 6 arbitrary decamer primers for the selection of putative somaclones. A total of 64 band positions were scored, out of which 19 RAPD bands were polymorphic. From genetic similarity coefficient based on RAPD band data sharing, it was found that the majority of the clones were almost identical or more than 92% similar to the mother plant, except CL2 and CL9 (66%) which showed highest degree of genetic change with CL2 and CL9 showing presence of two non-parental bands each.     

Genetic relationships among Far Eastern species of the family Araliacea inferred by RAPD analysis

A molecular genetic study of Far Eastern species of the family Araliaceae by means of RAPD analysis was conducted. Using 21 primers we assessed variability at 595 loci. Based on matrices of genetic distances D, dendrograms of genetic relationships among eleven species of six genera of this family were constructed. Our results suggest that Acanthopanax sessiliflorus and Eleutherococcus senticosus belong to different genera, Aralia cordata and A. continentalis are different species, and A. elata and A. mandshurica probably cannot be regarded as distinct species. Genetic similarity of Far Eastern A. cordata and American A. hispida is shown.