Associations between Nuclear Loci and Chloroplast DNA Genotypes in Wild Barley

Associations among alleles at nine nuclear loci and three chloroplast DNA (cpDNA) genotypes were assessed in a sample of 247 accessions of the wild barley, Hordeum vulgare ssp. spontaneum. Alleles at two of the nine nuclear loci are marked by length variations in the intergenic spacer region of ribosomal DNA (rDNA), and those of the other seven loci are well characterized allozymes. The three chloroplast DNA (cpDNA) genotypes are marked by restriction fragment length polymorphisms resulting from three polymorphic restriction sites detected by Southern blot hybridization. The analyses were performed by dividing the nine nuclear loci into a series of two-locus subsets and constructing log-linear models to characterize associations between the subsets of two nuclear loci and the cpDNA genotypes. Statistically significant associations were detected between six of the nine nuclear loci and the cpDNA genotypes, either individually as pairwise correlations, or through interaction with another nuclear locus to form three-variate complexes. Although the sample size of the present study was inadequate for statistical evaluation of higher order interactions, the results suggest the existence of interactions in which more than two nuclear loci are involved in associations with cpDNA genotypes. The observed cytonuclear associations appear to result from interplay among a number of evolutionary forces including a mating system of predominant selfing, differentiation among gene pools of local populations, and adaptation of barley genotypes to specific environmental conditions.     

Nucleotide Sequence Homology Exists between the Chloroplast and Nuclear Ribosomal DNAs of Euglena gracilis

The nuclear and chloroplast ribosomal DNAs from Euglena were shown to have specific regions of nucleotide sequence homology. The regions of homology were identified by hybridization of restriction endonuclease DNA fragments of cloned chloroplast and nuclear ribosomal DNAs to one another. The regions of homology between these two ribosomal DNAs were in that part of the genes that code for the 3′ end of the small rRNAs (16S and 19S) and near or at the DNA sequences coding for the 5S RNAs. The nucleotide sequence homology between these regions was estimated to be approximately 94% by the melting point depression of a hybrid formed between the two ribosomal DNAs.     

油菜叶绿体16SrRNA基因的一级结构分析

本文报道了油菜叶绿体16S rRNA基因的全顺序及其5′端上游的156bp和3′端下游的101bp的核苷酸顺序。油菜叶绿体16s rRNA基因长为1491bp,和烟草、玉米相比,同源程度分别为98.5％、96.1％。油菜叶绿体16S rRNA基因5′端上游及3′端下游的顺序能互补而形成一个较大的茎环结构,但与烟草相比,由于3′端下游顺序有79bp的缺失,因此,该结构中的茎部分大小仅为烟草的二分之一。     

Nucleotide Sequence Analysis of DNA

There are three major obstacles to the analysis of the nucleotide sequence in a DNA molecule starting from a known location in the DNA molecule. First, it is difficult to obtain large quantities of homogeneous DNA. Second, even the smallest DNA molecules contain several thousand nucleotides which make sequence analysis prohibitive. Third, there are no highly base-specific DNAases available for degrading DNA for sequence analysis. We have overcome some of these obstacles; first, by incorporating highly labelled deoxynucleotides into DNA in vitro, small amounts of material can be used for sequence analysis. Second, the nucleotide sequence of DNA molecules can now be determined from the 5′-terminal. Thus, two dodecanucleotide sequences corresponding to the two cohesive ends of λ DNA have been determined¹ and a nona-decanucleotide sequence corresponding to one cohesive end of phage 186 DNA has been completed². So far, our approach is limited to starting the analysis from the 5′-ends of a DNA molecule. A more general approach is being developed for starting the analysis from other selected parts of a DNA molecule with the use of specifically designed primers.     

Chloroplast DNA Diversity in Populations of Wild and Cultivated Barley

Chloroplast DNA (cpDNA) diversity was found within and among populations (245 accessions total) of wild barley, Hordeum vulgare L. ssp. spontaneum Koch from Israel and Iran. Three polymorphic restriction sites (HindIII, EcoRI, BclI) which define three distinct cpDNA lineages were detected. One lineage is common to populations in the Hule Valley and Kinneret of northern Israel, and in Iran. The second lineage is found predominantly in the Lower Jordan Valley and Negev. The distribution of the third lineage is scattered but widespread throughout Israel. Sixty two accessions of cultivated barleys, H. vulgare L., were found, with two exceptions, to belong to just one cpDNA lineage of wild barley, indicating that the cpDNA of cultivated barley is less variable than its wild ancestor. These results demonstrate the need for assessing intraspecific cpDNA variability prior to choosing single accessions for phylogenetic constructions at the species level and higher.     

Chloroplast DNA Sequence Homologies among Vascular Plants

The extent of sequence conservation in the chloroplast genome of higher plants has been investigated. Supercoiled chloroplast DNA, prepared from pea seedlings, was labeled in vitro and used as a probe in reassociation experiments with a high concentration of total DNAs extracted from several angiosperms, gymnosperms, and lower vascular plants. In each case the probe reassociation was accelerated, demonstrating that some chloroplast sequences have been highly conserved throughout the evolution of vascular plants. Only among the flowering plants were distinct levels of cross-reaction with the pea chloroplast probe evident; broad bean and barley exhibited the highest and lowest levels, respectively. With the hydroxylapatite assay these levels decreased with a decrease in probe fragment length (from 1,860 to 735 bases), indicating that many conserved sequences in the chloroplast genome are separated by divergent sequences on a rather fine scale. Despite differences observed in levels of homology with the hydroxylapatite assay, S1 nuclease analysis of heteroduplexes showed that outside of the pea family the extent of sequence relatedness between the probe and various heterologous DNAs is approximately the same: 30%. In our interpretation, the fundamental changes in the chloroplast genome during angiosperm evolution involved the rearrangement of this 30% with respect to the more rapidly changing sequences of the genome. These rearrangements may have been more extensive in dicotyledons than in monocotyledons. We have estimated the amount of conserved and divergent DNA interspersed between one another.     

The Effect of DNA Sequence Divergence on Sexual Isolation in Bacillus

We have investigated the relationship between sexual isolation and DNA sequence divergence in the transformation (at locus rpoB) of a naturally competent strain of Bacillus subtilis. Using both genomic DNA and a PCR-amplified segment of gene rpoB as donor, we found that the extent of sexual isolation at locus rpoB was closely predicted, over three orders of magnitude, as a log-linear function of sequence divergence at that locus. Because sexual isolation between a recipient and any potential donor may be determined as a general mathematical function of sequence divergence, transformation is perhaps the only sexual system, in either the prokaryotic or the eukaryotic world, in which sexual isolation can be predicted for a pair of species without having to perform the cross. These observations suggest the possibility of a general approach to the indirect prediction of sexual isolation in bacteria recombining principally by natural transformation.     

白腹锦鸡和红腹锦鸡的遗传分化

白腹锦鸡Chrysolophus amherstiae (Leadbeater)和红腹锦鸡Chrysolophus pictus (L.)是两个种还是两个亚种尚有争议。测定了白腹锦鸡C.amherstiae两个个体部分细胞色素b基因序列,得到完全相同的861bp的序列。与红腹锦鸡C.pictus的同源序列相比,在21个位点上出现变异,应用木村资生的双参数法算出两者的遗传距离为2.5％。根据鸡形目细胞色素b基因核苷酸替换的速率约为每百万年0.5％～ 0.7％,推断出两种锦鸡的分化时间至少为1.7百万年。从而在分子水平上支持白腹锦鸡(C.amherstiae)和红腹锦鸡(C.pictus)是两个独立种。 Abstract：It was disputed that Chrysolophus amherstiae (Leadbeater) and Chrysolophus pictus (L.) were two species or two subspecies.DNA sequences spanning 861 nucleotide bases of the mitochondrial cytochrome-b gene were reported in two C.amherstiae.21 sites were different compared with C.pictus's homologous sequences. Genetic distance between C.amherstiae and was 2.5％ based on the Kimura's two parameter's methods.The divergence time between C.amherstiae and C.pictus was at least 1.7My based on the substitution rate of nucleotide acid of cytothrome-b gene in Galliformes.We suggested that Chrysolophus amherstiae and Chrysolophus pictus are two distinct species.     

Studies with Chloroplast and Mitochondrial DNA: I. Evidence of Sequence Homology between Chloroplast and Nuclear DNA (Broad Bean) and between Mitochondrial and Nuclear DNA (Rat Liver)

A mixture of broad bean chloroplast and nuclear DNA or rat liver mitochondrial and nuclear DNA was taken through a heating and annealing cycle, and examined by CsCl density gradient centrifugation. The formation of intermediates between the two DNAs during joint annealing was used as a method of detecting sequence homology in different DNA samples. Homology was found between chloroplast and nuclear DNA from broad bean and between mitochondrial and nuclear DNA from rat liver. Since this method produces only qualitative data no implication for possible nucleocytoplasmic relationship can be assessed.     

Preparation of Chloroplast DNA from Barley and Lettuce and Comparison of Restriction Fragments

Chloroplast DNA from three barley cultivars and from one lettuce cultivar was prepared from chloroplasts isolated by Conventional differential centrifugation. Barley chloroplast DNA size was sensibly lower (130 kpb) than lettuce chloroplast DNA (150 kpb). Chloroplast DNAs from the three barley cultivars showed similar restriction fragment patterns after digestion with: BamHI, EcoRI or HindIII. The lettuce chloroplast DNA restriction pattern was very different from the barley chloroplast DNA restriction pattern.     

Mitochondrial DNA Sequence Divergence among Lycopersicon and Related Solanum Species

Sequence divergence among the mitochondrial (mt) DNA of nine Lycopersicon and two closely related Solanum species was estimated using the shared fragment method. A portion of each mt genome was highlighted by probing total DNA with a series of plasmid clones containing mt-specific DNA fragments from Lycopersicon pennellii. A total of 660 fragments were compared. As calculated by the shared fragment method, sequence divergence among the mtDNAs ranged from 0.4% for the L. esculentum-L. esculentum var. cerasiforme pair to 2.7% for the Solanum rickii-L. pimpinellifolium and L. cheesmanii-L. chilense pairs. The mtDNA divergence is higher than that reported for Lycopersicon chloroplast (cp) DNA, which indicates that the DNAs of the two plant organelles are evolving at different rates. The percentages of shared fragments were used to construct a phenogram that illustrates the present-day relationships of the mtDNAs. The mtDNA-derived phenogram places L. hirsutum closer to L. esculentum than taxonomic and cpDNA comparisons. Further, the recent assignment of L. pennellii to the genus Lycopersicon is supported by the mtDNA analysis.     

The Appearance of a Different DNA Sequence May Decrease Nucleotide Diversity

Nucleotide diversity may be decreased when a different DNA sequence type appears in a population. This undesirable property in a genetic diversity index is demonstrated by mathematical examples. The possibility of this phenomenon in natural populations is briefly discussed. Received: 21 June 1999 / Accepted: 27 July 1999     

龙葵叶绿体的阿特拉津抗性基因psbA的核苷酸序列及有关分析

对克隆在psb135质粒上的来自龙葵阿特拉津抗性生物型的psbA基因进行DNA序列分析,测得长为1384个核苷酸的全序列,包括该基因的全部编码区和5′上游顺序。该基因的核苷酸序列与另一个独立来源的龙葵阿特拉津抗性基因的核苷酸序列完全相同,在由核苷酸推导的氨基酸序列的基础上,比较了分别由龙葵抗阿特拉津和对阿特拉津敏感的psbA基因编码的32kD蛋白质的二级结构,并对其可能的含意进行了讨论。     

大鼠高重复顺序DNA的核苷酸顺序分析及其与灵长类类α-DNA顺序的比较

 啮齿目动物高重复顺序DNA的结构特征,虽已有人进行过分析,并提出大鼠DNA中有酶切位点分布独特的高重复顺序,也有人认为在Sprague-Dawlay大鼠中有类似于α-DNA大小的高重复顺序,并命名为α型(α-type),是否大鼠中也含有类α顺序,并没有人讨论过。我们对Wistar大鼠高重复顺序DNA进行了分离、纯化、分子克隆及核苷酸序列分析,测定了全序列为370bp,它也是具有酶切点分布独特的高重复顺序,但与前者存在着18％的差异性。我们对此顺序与灵长类类α-DNA进行了比较分析,发现二者在几方面都不存在相似之处,如此序列G-C含量占全部碱基组成的37.3％,而类α顺序的G-C含量约在40％以上,一些酶切位点也与类α-DNA完全不相同,另外在此序列的相应位置上也不具有灵长类类α-DNA的三个“冷点区”等等,由此得出大鼠这一高重复顺序并非类α顺序,而类α顺序只是灵长类动物所特有的。     

The EMBL Nucleotide Sequence Database

The EMBL Nucleotide Sequence Database (aka EMBL-Bank; http://www.ebi.ac.uk/embl/) incorporates, organises and distributes nucleotide sequences from all available public sources. EMBL-Bank is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis. Major contributors to the EMBL database are individual scientists and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, email and World Wide Web interfaces. EBI’s Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many other specialized databases. For sequence similarity searching, a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk.     

拟南芥叶绿体DNA全序列微卫星分布规律的分析

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.     

Sequence Homology between Chloroplast DNAs from Several Higher Plants

An estimate has been made of the amount of sequence homology present in the chloroplast DNA (ctDNA) of several higher plants by the technique of DNA-DNA hybridization. Approximately 85% of tomato, 60% of spinach, 45% of kale, and 15% of barley ctDNA sequences were found to hybridize with tobacco ctDNA under conditions in which maximum hybridization in homologous reactions reached 85%. All heteroduplexes contained significant amounts of sequence mismatch as indicated by a 3 to 9 C decrease in melting temperature as compared to homoduplex.     

玉米基因组的简单重复序列遗传研究进展

前言在真核生物基因组中重复序列占有很大比重,它的绝大部分存在于诸如间隔序列和调控序列非编码序列中,但它也分布在有些结构基因的序列中,它多为轻度重复序列。植物的基因组重复序列一般占80%左右,基因组较大其重复序列所占比重较大,如玉米基因组(ｈａｐｌｏｉｄｇｅｎｏｍｅ)大约有3×109,其中几乎80%以上是重复序列[12]。重复序列对维持染色体的空间结构、基因的表达、遗传重组都具有重要作用。重复序列单...