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1.
基于DNA序列K-tuple分布的一种非序列比对分析   总被引:1,自引:0,他引:1  
沈娟  吴文武  解小莉  郭满才  袁志发 《遗传》2010,32(6):606-612
文章在基因组K-tuple分布的基础上, 给出了一种推测生物序列差异大小的非序列比对方法。该方法可用于衡量真实DNA序列和随机重排序列在K-tuple分布上的差异。将此方法用于构建含有26种胎盘哺乳动物线粒体全基因组的系统树时, 随着K的增大, 系统树的分类效果与生物学一致公认的结果愈加匹配。结果表明, 用此方法构建的系统进化树比用其他非序列比对分析方法构建的更加合理。  相似文献   

2.
拟南芥叶绿体DNA全序列微卫星分布规律的分析   总被引:5,自引:0,他引:5  
为进一步以拟南芥为模板,开发果树通用的叶绿体微卫星或称简单序列重复(chloroplast simple sequence repeat, cpSSR)引物,对拟南芥叶绿体DNA全序列cpSSR进行了统计分析.结果表明,拟南芥cpSSR以单碱基重复为主,占总数的78.6%,二碱基重复占总数的19%,三碱基重复占2.4%,三碱基以上重复为零.在单碱基重复中,又以A和T重复为主,占98.5%.二碱基重复全部为AT重复.单碱基重复中的纯粹重复41个,占总数的62.1%.间断重复数为23个,占总数的34.8%.复合重复数仅为2个.  相似文献   

3.
4.
肠道微生物与寄主具有复杂的、多方面的相互依存效应,这种依存效应所产生的共生关系或协同进化关系既可反映寄主间的系统演化关系,也可显示肠道微生物间的系统演化关系,共生关系或协同进化关系是由于寄主与肠道微生物两者之间存在着相互自然选择作用所形成的,在长期的进化历程中逐步发生的共生关系信息很可能被记录在DNA序列中。本文通过检测鲤鱼科8种鱼中9种肠道菌群的分布含量对这9种菌群进行分析,且利用从GenBank调取这9种肠道细菌菌属的43个种或亚种的16S DNA序列的构建NJ树和MP树,将这6个科9个属43个种或亚种分为革兰氏阴性和革兰氏阳性两大类群(一级分枝)。在这两类群中,又以科为单位分为6个亚类群(二级分枝),而肠杆菌科中则以属为单位分为4个小类群(三级分枝),此外球状菌与杆状菌也能截然分开。将16S DNA的NJ树隐去所有的种,以属为单位所得到的以分枝形式的无根树在拓扑结构上与菌群分布含量(寄主范围)所构建的无根树相近,但芽孢杆菌在两种无根树的位置中有较大的差异。如果提高检测水平,扩大所检测的寄主对象,这种差异有可能消除。 Abstract:There is a complex- and multi-effect for interdependent survival between intestinal- microorganisms and hosts.The symbiosis or coevolution that results from this effect for interdependent survival is used to reveal the phylogenies of hosts as well as intestinal microorganisms.The symbiosis or coevolution between intestinal microorganisms and hosts has been generated by interactive natural selection occurred between them.The symbiosis information that has been formed by interactive natural selection during a long evolutionary process must be recorded in DNA sequences.According to this point of view,we analyzed the phylogeny of 9 intestinal bacteria genera using their contents in intestines of 8 Cyrinidate species.At the same time,we fetched the 16S rRNA gene DNA sequences of 43 intestinal bacteria species being included in these nine genera of six intestinal families from GeneBank and constructed phylogenetic trees by NJ and MP methods.The NJ tree and MP tree have the same topologic configuration and are identical with the classical phylogenetic tree.Both the trees of 16S rRNA gene separated 43 bacteria species into gram-negative bacteria group and the gram-positive bacteria group,which are the first branches.Each of the first branches (groups) made again 6 subbranches (subgroups) where each subbranch is a family.Especially,the subbranch (subgroup) of enterobacteriaceace made again four small branches as genus taxon.This tree also shows that bacilliform bacterium is distinct from each other in the NJ and MP trees.After all species on the tree are merged,the topological configuration of the unrooted tree of 16S gene is closed to that of the host range unrooted tree.However,the position of bacillus is greatly changed on both the unrooted trees.The difference can be found if we increase the examination level and extend the hosts examed.  相似文献   

5.
赵庆新  谭远德 《遗传》2002,24(4):447-454
肠道微生物与寄主具有复杂的、多方面的相互依存效应,这种依存效应所产生的共生关系或协同进化关系既可反映寄主间的系统演化关系,也可显示肠道微生物间的系统演化关系,共生关系或协同进化关系是由于寄主与肠道微生物两者之间存在着相互自然选择作用所形成的,在长期的进化历程中逐步发生的共生关系信息很可能被记录在DNA序列中。本文通过检测鱼鲤鱼科8种鱼中9种肠道菌群的分布含量对这9种菌群进行分析,且利用从GenBank调取这9种肠道细菌菌属的43个种或亚种的16S DNA序列的构建NJ树和MP树,将这6个科9个属43个种或亚种分为革兰氏阴性和革兰氏阳性两大类群(一级分枝)。在这两类群中,又以科为单位分为6个亚类群(二级分枝),而肠杆菌科中则以属为单位分为4个小类群(三级分枝),此外球状菌与杆状菌也能截然分开。将16S DNA的NJ树隐去所有的种,以属为单位所得到的以分枝形式的无根树在拓扑结构上与菌群分布含量(寄主范围)所构建的无根树相近,但芽孢杆菌在两种无根树的位置中有较大的差异。如果提高检测水平,扩大所检测的寄主对象,这种差异有可能消除。  相似文献   

6.
1985年,Mullis等人发明了PCR技术,短短十余年间,这一技术得到迅速发展和应用,已由扩增已知基因发展到扩增未知基因。本文旨在介绍利用PCR技术扩增未知序列DNA片段的最新进展及这些技术在基因克隆研究中的应用。  相似文献   

7.
Rau M. E. 1979. The frequency distribution of Hymenolepis diminuta cysticercoids in natural, sympatric populations of Tenebrio molitor and T. obscurus. International Journal for Parasitology9: 85–87. Natural, sympatric populations of Tenebrio molitor and T. obscurus were examined for cysticercoids of Hymemlepis diminuta. The distribution of cysticeroids in both species and both sexes conformed to the negative binomial. Cysticeroids were more prevalent and the mean intensity of infection was higher in T. obscurus than in T. molitor. No differences in the intensity of infection were detected between the sexes. Larvae of both beetle species were always very lightly infected. The significance of these factors in the transmission of the infection to the rat definitive host is discussed.  相似文献   

8.
 Inter-simple sequence repeat (ISSR) amplification was used to analyze microsatellite motif frequency in the rice genome and to evaluate genetic diversity among rice cultivars. A total of 32 primers, containing different simple sequence repeat (SSR) motifs, were tested for amplification on a panel of 59 varieties, representative of the diversity of cultivated rice (Oryza sativa L.). The ISSR analysis provided insights into the organization, frequency and levels of polymorphism of different simple sequence repeats in rice. The more common dinucleotide motifs were more amenable to ISSR analysis than the more infrequent tri-, tetra- and penta-nucleotide motifs. The ISSR results suggested that within the dinucleotide class, the poly(GA) motif was more common than the poly(GT) motif and that the frequency and clustering of specific tri- and tetra-nucleotide simple sequence repeats was variable and motif-specific. Furthermore, trinucleotide ISSR markers were found to be less polymorphic than either dinucleotide or certain tetranucleotide ISSR markers, suggesting which motifs would be better targets for microsatellite marker development. The ISSR amplification pattern was used to group the rice genotypes by cluster analysis. These results were compared to surveys of the same varieties for amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP) and isozyme markers. The ISSR fingerprint could be used to differentiate the genotypes belonging to either Japonica or Indica sub species of cultivated rice and to dissect finer levels of diversity within each subspecies. A higher percentage of polymorphic bands was produced with the ISSR technique than the AFLP method, based on a similar PCR reaction. Therefore, ISSR amplification proved to be a valuable method for determining genetic variability among rice varieties and for rapidly identifying cultivars. This efficient genetic fingerprinting technique would be useful for characterizing the large numbers of rice accessions held in national and international germplasm centers. Received: 25 May 1998 / Accepted: 17 September 1998  相似文献   

9.
Summary Number and distribution of chiasmata were studied in the single pair of homologous rye chromosomes in 29 chromosomal F1 hybrids between the seven disomic wheat rye addition lines of Chinese Spring/ Imperial and five selected inbred genotypes of cultivated rye by using the differential Giemsa staining technique. The results indicate that the number and position of chiasmata is independent from the amount and position of C-heterochromatin. Genotype had an effect on chiasma number, whereas chiasma distribution within bivalents appeared to be determined by morphological features of chromosomes. Late replicating DNA in constitutive heterochromatin may delay the separation of half bivalents if chiasmata are formed between them and the centromere.Supported by Deutsche Forschungsgemeinschaft, Bonn  相似文献   

10.
玉米冠层内太阳直接辐射三维空间分布的模拟   总被引:22,自引:0,他引:22  
太阳直接辐射在植物冠层内的空间分布特征影响植物生理生态功能 ,是衡量植物群体结构是否合理的重要指标。利用田间实测的玉米冠层内植株各器官的三维空间坐标进行冠层结构分析 ,将冠层内的植株器官表面划分成小面元 ;根据几何光学中光的直线传播原理 ,利用面元沿太阳光线的平行投影和投影深度排序 (Z- buffer)算法计算冠层内面元受太阳光直接照射的情况 ,建立了太阳直接辐射在玉米冠层内三维空间分布的模拟模型。模型可计算出作物冠层内任选植株的器官表面或冠层内地面上的太阳直射光斑 (Sunflecks)分布 ,也可输出选定空间位置或范围上的太阳直接辐射的分布 ,同时可实现模拟结果的三维可视化。根据此模型的模拟结果可对太阳直接辐射在玉米冠层内的空间分布进行各种分析。利用玉米冠层内光斑的三维分布测定试验 ,在光合有效辐射 (PAR)波段对模型进行了检验。模型适用于任意三维结构可测并可进行面元化划分的植物群体或个体  相似文献   

11.
Summary Sequence data from regions of five vertebrate vitellogenin genes were used to examine the frequency, distribution, and mutability of the dinucleotide CpG, the preferred modification site for eukaryotic DNA methyltransferases. The observed level of the CpG dinucleotide in all five genes was markedly lower than that expected from the known mononucleotide frequencies. CpG suppression was greater in introns than in exons. CpG-containing codons were found to be avoided in the vitellogenin genes, but not completely despite the redundancy of the genetic code. Frequency and distribution patterns of this dinucleotide varied dramatically among these otherwise closely related genes. Dense clusters of CpG dinucleotides tended to appear in regions of either functional or structural interest (e.g., in the transposon-like Vi-element ofXenopus) and these clusters contained 5-methylcytosine (5 mC). 5 mC is known to undergo deamination to form thymidine, but the extent to which this transition occurs in the heavily methylated genomes of vertebrates and its contribution to CpG suppression are still unclear. Sequence comparison of the methylated vitellogenin gene regions identified CT and GA substitutions that were found to occur at relatively high frequencies. The predicted products of CpG deamination, TpG and CpA, were elevated. These findings are consistent with the view that CpG distribution and methylation are interdependent and that deamination of 5 mC plays an important role in promoting evolutionary change at the nucleotide sequence level.  相似文献   

12.
Targeted gene replacement via homologous recombination (HR) is a conventional approach for the analysis of gene function. However, this event is rare in Beauveria bassiana, which hampers efficient functional analysis in this widely used entomopathogenic fungus. To improve homologous recombination frequency in B. bassiana, we investigated the effect of the ratio of homologous sequence to non-homologous sequence (HS/NHS) in gene disruption cassette upon the HR frequency by two gene loci BbNtl and BbThi, using the herpes simplex virus thymidine kinase as a negative selectable marker against ectopic transformants. Our data revealed that an increase of the ratio of HS/NHS achieved by either extending homologous sequence or decreasing non-homologous sequence could improve HR frequency in B. bassiana. We determined empirically that (1) at least 700 bp of homology to both sides of a target gene was needed to get a reasonable number of disruptants, e.g., 6.7‰ to 13.3‰ in B. bassiana. (2) When the ratio of HS/NHS was above 0.8, an acceptable HR frequency could be achieved for gene replacement in B. bassiana, while when the ratio was below 0.3, few gene disrupted mutants were obtained.  相似文献   

13.
Bleomycin (BLM) is a cancer chemotherapeutic agent that cleaves cellular DNA at specific sequences. Using next-generation Illumina sequencing, the genome-wide sequence specificity of DNA cleavage by two BLM analogues, 6′-deoxy-BLM Z and zorbamycin (ZBM), was determined in human HeLa cells and compared with BLM. Over 200 million double-strand breaks were examined for each sample, and the 50,000 highest intensity cleavage sites were analysed. It was found that the DNA sequence specificity of the BLM analogues in human cells was different to BLM, especially at the cleavage site (position “0”) and the “+1” position. In human cells, the 6′-deoxy-BLM Z had a preference for 5′-GTGY*MC (where * is the cleavage site, Y is C or T, M is A or C); it was 5′-GTGY*MCA for ZBM; and 5′-GTGT*AC for BLM. With cellular DNA, the highest ranked tetranucleotides were 5′-TGC*C and 5′-TGT*A for 6′-deoxy-BLM Z; 5′-TGC*C, 5′-TGT*A and 5′-TGC*A for ZBM; and 5′-TGT*A for BLM. In purified human genomic DNA, the DNA sequence preference was 5′-TGT*A for 6′-deoxy-BLM, 5′-RTGY*AYR (where R is G or A) for ZBM, and 5′-TGT*A for BLM. Thus, the sequence specificity of the BLM analogue, 6′-deoxy-BLM Z, was similar to BLM in purified human DNA, while ZBM was different.  相似文献   

14.
The genomic organization and chromosomal distributions of two abundant tandemly repeated DNA sequences, dpTa1 and pSc119.2, were examined in six wild Hordeum taxa, representing the four basic genomes of the genus, by Southern and fluorescence in situ hybridization. The dpTa1 probe hybridized to between 30 and 60 sites on the chromosomes of all five diploid species studied, but hybridization patterns differed among the species. Hybridization of the pSc119.2 sequence to the chromosomes and Southern blots of digested DNA detected signals in Hordeum bulbosum, Hordeum chilense, Hordeum marinum and Hordeum murinum 4x, but not in Hordeum murinum 2x and Hordeum vulgare ssp. spontaneum. A maximum of one pSc119.2 signal was observed in the terminal or subterminal region of each chromosome arm in the species carrying this sequence. The species carrying the same I-genome differed in the presence (Hordeum bulbosum) or absence (Hordeum spontaneum) of pSc119.2. The presence of pSc119.2 in the tetraploid cytotype of Hordeum murinum, but its absence in the diploid cytotype, suggests that the tetraploid is not likely to be a simple autotetraploid of the diploid. Data about the inter- and intra-specific variation of the two independent repetitive DNA sequences give information about both the interrelationships of the species and the evolution of the repetitive sequences. Received: 17 March 1999 / Accepted: 16 June 1999  相似文献   

15.
南亚热带米老排人工林碳贮量及其分配特征   总被引:3,自引:0,他引:3  
刘恩  刘世荣 《生态学报》2012,32(16):5103-5109
米老排是我国南方速生用材树种,研究米老排(Mytilaria laosensis)人工林碳贮量与碳分配的规律,可为评价米老排人工林的固碳能力与发展人工林多目标经营提供科学依据。采用样地测定的方法,对南亚热带米老排人工林不同器官碳浓度、碳贮量及分配特征进行了研究。结果表明:不同器官碳浓度均值的变化范围为:51.73%—55.75%,各器官碳浓度大小为:新叶>新枝>老叶>树干>老枝>根桩>粗根>细根;凋落物碳浓度为未分解层>半分解层;0—100 cm土壤碳浓度随深度增加而降低,变化范围为0.62%—4.10%。20年生米老排人工林总碳贮量为331.61 t/hm2,乔木层,凋落物层和土壤层的碳贮量分别为154.07、2.74和174.80 t/hm2。年均总固碳量为14.77 t/hm2,折合CO2量为54.16 t,其中乔木层、凋落物层和土壤层所占比例分别为60.73%,6.16%和33.11%。  相似文献   

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