Base sequence studies of 300 nucleotide renatured repeated human DNA clones

A band of 300 nucleotide long duplex DNA is released by treating renatured repeated human DNA with the single strand-specific endonuclease S₁. Since many of the interspersed repeated sequences in human DNA are 300 nucleotides long, this band should be enriched in such repeats. We have determined the nucleotide sequences of 15 clones constructed from these 300 nucleotide S₁-resistant repeats. Ten of these cloned sequences are members of the Alu family of interspersed repeats. These ten sequences share a recognizable consensus sequence from which individual clones have an average divergence of 12.8%. The 300 nucleotide Alu family consensus sequence has a dimeric structure and was evidently formed from a head to tail duplication of an ancestral monomeric sequence. Three of the remaining clones are variations on a simple pentanucleotide sequence previously reported for human satellite III DNA. Two of the 15 clones have distinct and complex sequences and may represent other families of interspersed repeated sequences.     

Genome nucleotide composition shapes variation in simple sequence repeats

Simple sequence repeats (SSRs) or microsatellites are a common component of genomes but vary greatly across species in their abundance. We tested the hypothesis that this variation is due in part to AT/GC content of genomes, with genomes biased toward either high AT or high CG generating more short random repeats that are long enough to enhance expansion through slippage during replication. To test this hypothesis, we identified repeats with perfect tandem iterations of 1-6 bp from 25 protists with complete or near-complete genome sequences. As expected, the density and the frequency are highly related to genome AT content, with excellent fits to quadratic regressions with minima near a 50% AT content and rising toward both extremes. Within species, the same trends hold, except the limited variation in AT content within each species places each mainly on the descending (GC rich), middle, or ascending (AT rich) part of the curve. The base usages of repeat motifs are also significantly correlated with genome nucleotide compositions: Percentages of AT-rich motifs rise with the increase of genome AT content but vice versa for GC-rich subgroups. Amino acid homopolymer repeats also show the expected quadratic relationship, with higher abundance in species with AT content biased in either direction. Our results show that genome nucleotide composition explains up to half of the variance in the abundance and motif constitution of SSRs.     

Genome size and endonuclear DNA replication in spiders

Although genome sizes (C-values) are now available for 115 arachnid species (Gregory and Shorthouse [2003] J Hered 94:285-290), the extent of genome amplification (endonuclear DNA replication or polyploidization) accompanying tissue differentiation in this diverse and abundant class of invertebrates remains unknown. To explore this aspect of arachnid development, samples of hemolymph and other tissues were taken from wild-caught specimens as air-dried smears, stained with the Feulgen reaction for DNA, and assayed using both scanning and image analysis densitometry. Cells from midgut diverticula and Malpighian tubules of Argiope and Lycosa (=Pardosa) often showed giant nuclei with 50-100 pg of DNA per nucleus, reflecting at least four cycles of endonuclear DNA replication when compared to the DNA content of hemocytes or sperm from the same specimen. Nuclei with markedly elevated DNA levels also appeared, but far less frequently, in tissue samples from several other arachnid species (Antrodiaetus, Hypochilus, Latrodectus, Liphistus and Loxosceles), but revealed no correlation with differences in somatic cell (2C) genome sizes. Our data show that several DNA classes of polysomatic nuclei regularly arise during tissue differentiation in some species of spiders and may provide an interesting model system for further study of patterns of tissue-specific variation in DNA endoreduplication during development.     

Genome size and A-T rich DNA in selachians

The nuclear DNA content of 23 selachian species (10 Batoidea, 11 Galeomorphii, and 2 Squalomorphii) was histophotometrically studied. Their genome sizes range from 7.5 pg/N in Raja fillae (Batoidea) to 34.1 pg/N in Oxynotus centrina (Squalomorphii).Results show slight differences in the pattern of quantitative variations between the superorders Batoidea and Galeomorphii; Squalomorphii preserve their peculiar wide interspecific variability at the intrafamilial level, with values sited between 13.1 and 34.1 pg/N.In 21 species also the DNA base composition was determined by means of DAPI. The study shows that in the species examined the DAPI positive fraction varies from a minimum of 27.7% in Oxynotus centrina, which possesses the largest genome size among all the Selachians studied, to a maximum of 72.5% in Carcharhinus limbatus. As a whole the data show an inverse correlation between the DNA content and the DAPI positive fraction, a condition common to all cold-blooded vertebrates.The low percentage of DAPI positive DNA found in Oxynotus centrina could be attributable to a lower stainability by the fluorochrome caused by a higher chromatin condensation in the erythrocytes.The validity of the DAPI method was verified by comparison with the biochemical assay according to the thermal denaturation method in 6 selachian species.     

DNA interaction and nucleotide sequence cleavage of copper-streptonigrin

The copper-accelerated DNA binding and cleavage of streptonigrin have been investigated by 1H-NMR, ESR spectrometry and nucleotide sequence analysis. In the DNA breakage by the streptonigrin-Cu(II)-NADPH system, the somewhat preferred cleavage sites were several cytosine bases adjacent to purine bases such as GCGG(5'----3'), ACGC(5'----3') and GGCG(5'----3') sequences. The proton chemical shifts for the streptonigrin-Cu(I)-poly(dA-dT) complex demonstrated the interaction between the pyridine ring of the drug and the purine bases of the nucleic acid. Indeed, the temperature profile of adenine H-2 proton clearly showed the Tm to shift from 70 degrees C in the binary streptonigrin-poly(dA-dT) system to 75 degrees C in the ternary streptonigrin-Cu(I)-poly(dA-dT) system. The interaction of the streptonigrin-Cu(II) complex with DNA also induced the apparent change of ESR parameters. The tricyclic phenanthidium ring system including the copper chelate ring appears to significantly contribute to the present DNA interaction and cleavage of copper-streptonigrin.     

高等植物DNA重复序列的主要类型和特点

高等植物核基因组的一个显著特征是其内含有大量的ＤＮＡ重复序列,因此它们在核基因组结构和功能研究中居于举足轻重的地位。一些ＤＮＡ重复序列已日趋广泛地作为分子民用于构建遗传图谱、鉴别品种、研究进化和分离目标基因等。主要介绍高等植物几类重要ＤＮＡ重复序列,如卫星ＤＮＡ、微卫星ＤＮＡ、核糖体ＲＮＡ基因、端粒重复序列和转座子等的若干特点和用途。     

A conserved tandemly repeated DNA sequence inCruciferae

Several HindIII monomer units of a tandemly repeated nuclear DNA sequence ofBrassica campestris andBrassica juncea (Cruciferae) have been cloned and sequenced. The monomer units, of 177 bp length, are AT-rich and share 88% homology between themselves and more than 65% homology with similar repeats of otherCruciferae likeBrassica oleracea, Sinapis alba andRaphanus sativus. Thus unlike the rapid divergence of tandemly repeated satellite DNA in other organisms, this DNA element is highly conserved thus indicating its importance.     

Chromosomal mapping and nucleotide sequence of a human DNA autonomously replicating sequence

A 1.1-kb human DNA fragment (ARSH1) capable of functioning as a putative origin of replication in yeast cells has been characterized both by in situ hybridization to human metaphase chromosomes and by DNA sequencing. Our hybridization studies show a preferential localization of ARSH1 in chromosome regions 1p34-36 and 2q34-37. DNA sequence analysis indicates that in addition to the consensus sequence required for ARS function in yeast cells, nuclear matrix-associated DNA motifs are also present in the 1.1-kb fragment. These results suggest that ARSH1 sequences may serve as points of anchorage to the nuclear matrix for chromosomes 1 and 2.     

Genome size reduction can trigger rapid phenotypic evolution in invasive plants

Background and Aims

The study of rapid evolution in invasive species has highlighted the fundamental role played by founder events, emergence of genetic novelties through recombination and rapid response to new selective pressures. However, whether rapid adaptation of introduced species can be driven by punctual changes in genome organization has received little attention. In plants, variation in genome size, i.e. variation in the amount of DNA per monoploid set of chromosomes through loss or gain of repeated DNA sequences, is known to influence a number of physiological, phenological and life-history features. The present study investigated whether change in genome size has contributed to the evolution of greater potential of vegetative growth in invasive populations of an introduced grass.

Methods

The study was based on the recent demonstration that invasive genotypes of reed canarygrass (Phalaris arundinacea) occurring in North America have emerged from recombination between introduced European strains. The genome sizes of more than 200 invasive and native genotypes were measured and their genome size was related to their phenotypic traits measured in a common glasshouse environment. Population genetics data were used to infer phylogeographical relationships between study populations, and the evolutionary history of genome size within the study species was inferred.

Key Results

Invasive genotypes had a smaller genome than European native genotypes from which they are derived. This smaller genome size had phenotypic effects that increased the species'' invasive potential, including a higher early growth rate, due to a negative relationship between genome size and rate of stem elongation. Based on inferred phylogeographical relationships of invasive and native populations, evolutionary models were consistent with a scenario of genome reduction by natural selection during the invasion process, rather than a scenario of stochastic change.

Conclusions

Punctual reduction in genome size could cause rapid changes in key phenotypic traits that enhance invasive ability. Although the generality of genome size variation leading to phenotypic evolution and the specific genomic mechanisms involved are not known, change in genome size may constitute an important but previously under-appreciated mechanism of rapid evolutionary change that may promote evolutionary novelties over short time scales.Key words: Biological invasion, evolutionary models, genome size, Phalaris arundinacea, quantile regression, relative growth rate, rapid evolution     

Sequence analysis of Vicia faba highly repeated DNA: the BamHI repeated sequence families

Cleavage of Vicia faba nuclear DNA with the restriction endonuclease BamHI yielded discrete size classes of 250, 850, 900, 990, 1 150, 1 500 and 1 750 bp of highly repetitive DNA. Each of these sequence families comprised about 3% of the total genomic DNA. Some sequence members from each sequence family were cloned in pBR322 and their primary structures determined. Computer analyses of nucleotide sequences suggested the existence of about 60 bp sequence periodicity within the repeating unit of the 990 bp sequence family, though the extent of homology among the surmised shorter subrepeat units was very low. With other BamHI sequence families, however, the data did not show any clear internal sequence periodicity. The repeat units of the 850 bp and 1 750 bp sequence families contained nucleotide sequences homologous to the 250 bp family sequence. No sequence relationship between or among other sequence families was observed. There was 13–25% sequence variation among 6 cloned members of the 250 bp family and probably also among those of other BamHI repeat families. DNA sequences homologous to these V. faba BamHI repeat families were detected in Pisum sativum DNA by Southern blot hybridization. Furthermore, very weak cross-hybridization was observed with plant DNAs from Phaseolus vulgaris, Triticum aestivum, Cucumis sativus and Trillium kamtschaticum.     

Genome deterioration: loss of repeated sequences and accumulation of junk DNA

A global survey of microbial genomes reveals a correlation between genome size, repeat content and lifestyle. Free-living bacteria have large genomes with a high content of repeated sequences and self-propagating DNA, such as transposons and bacteriophages. In contrast, obligate intracellular bacteria have small genomes with a low content of repeated sequences and no or few genetic parasites. In extreme cases, such as in the 650kb-genomes of aphid endosymbionts of the genus Buchnera all repeated sequences above 200bp have been eliminated. We speculate that the initial downsizing of the genomes of obligate symbionts and parasites occurred by homologous recombination at repeated genes, leading to the loss of large blocks of DNA as well as to the consumption of repeated sequences. Further sequence elimination in these small genomes seems primarily to result from the accumulation of short deletions within genic sequences. This process may lead to temporary increases in the genomic content of pseudogenes and junk DNA. We discuss causes and long-term consequences of extreme genome size reductions in obligate intracellular bacteria.     

Preliminary characterization of the repeated DNA sequence from Vicia sativa

We have identified a family of interspersed repeated sequences present in about 40,000 copies in the genomes of Vicia sativa and its near relative Vicia faba. The element vif is at least 6 kb in length, and members of the repeat family display a degree of heterogeneity in restriction pattern. Homologous elements in V. faba are much more heterogeneous than their V. sativa counterparts; however, analysis of five different V. faba lines revealed substantially the same patterns, suggesting that this family was reamplified prior to the divergence of the lines studied.     

Limited permutations of the nucleotide sequence in bacteriophage T1 DNA

In the mature DNA molecules of bacteriophage T1 three different nucleotide sequence arrangements are found, differing from each other by circular permutations through 6% or 12% of the total length. Using a short region of non-homology between T1⁺ and T1Ds DNAs as a sequence marker, we have measured the positions of this marker with respect to the ends of the individual component strands in T1⁺: T1Ds heteroduplexes. The frequency distribution shows three peaks, at 37%, 43% and 49% of the total length, measured from the free end in molecules, one of whose ends is identified by being bound to the phage ghost. Since the distance between peaks is equal to the length of the terminally repeated segment of nucleotide sequence in T1DNA (6.1% of the molecular length), this finding suggests that T1 DNA is matured by the headful mode, commencing from a particular initiation site within the nucleotide sequence and proceeding with the maturation of only three consecutive headfuls (or sometimes two, and rarely four). The relative frequency of occurrence at the three principal positions, approximately 0.4:0.4:0.2, respectively, suggests that the maturation initiation site lies at the ghost-bound end in the permutation identified with the 37% position of the Ds non-homology.