Rapidly varying DNA sequences in flax

1986 ◽  
Vol 28 (2) ◽  
pp. 252-259 ◽  
Author(s):  
C. A. Cullis ◽  
W. Cleary
Keyword(s):  
Dna Sequences ◽  
Copy Number ◽  
Repetitive Sequences ◽  
Repeated Sequences ◽  
Dna Variation ◽  
Environmental Induction ◽  
Wild Progenitors ◽  
Flax Variety ◽  
Flax Genome ◽  
Tandem Arrays

The highly repetitive sequences of the flax genome have been characterized. This has been done using a series of cloned probes that represent most, if not all, of the highly repetitive families in the flax genome. All of them are arranged as tandem arrays. The organization and copy number of these sequences has been compared in a number of lines including those lines (termed genotrophs) derived from the flax variety 'Stormont Cirrus' by the environmental induction of heritable changes, two other flax and linseed cultivars, and some of the supposed wild progenitors of flax. It was found that all except the light satellite differed in copy number between some of the lines. A particular subset of the 5S genes was shown to be preferentially affected when changes occurred. The extent of the variation between genotrophs was similar to that between different varieties or between flax and its supposed progenitor.Key words: flax, DNA variation, repeated sequences.

Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 431-441 ◽  
Author(s):  
Evgueni V Ananiev ◽  
M Isabel Vales ◽  
Ronald L Phillips ◽  
Howard W Rines
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Avena Sativa ◽  
Genomic Dna ◽  
Repetitive Sequences ◽  
Repeated Sequences ◽  
C Genome ◽  
Copy Dna

DNA gel-blot and in situ hybridization with genome-specific repeated sequences have proven to be valuable tools in analyzing genome structure and relationships in species with complex allopolyploid genomes such as hexaploid oat (Avena sativa L., 2n = 6x = 42; AACCDD genome). In this report, we describe a systematic approach for isolating genome-, chromosome-, and region-specific repeated and low-copy DNA sequences from oat that can presumably be applied to any complex genome species. Genome-specific DNA sequences were first identified in a random set of A. sativa genomic DNA cosmid clones by gel-blot hybridization using labeled genomic DNA from different Avena species. Because no repetitive sequences were identified that could distinguish between the A and D gneomes, sequences specific to these two genomes are refereed to as A/D genome specific. A/D or C genome specific DNA subfragments were used as screening probes to identify additional genome-specific cosmid clones in the A. sativa genomic library. We identified clustered and dispersed repetitive DNA elements for the A/D and C genomes that could be used as cytogenetic markers for discrimination of the various oat chromosomes. Some analyzed cosmids appeared to be composed entirely of genome-specific elements, whereas others represented regions with genome- and non-specific repeated sequences with interspersed low-copy DNA sequences. Thus, genome-specific hybridization analysis of restriction digests of random and selected A. sativa cosmids also provides insight into the sequence organization of the oat genome.Key words: oat, cosmid library, in situ hybridization.

Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA

Genome ◽  
1994 ◽  
Vol 37 (4) ◽  
pp. 565-576 ◽  
Author(s):  
Jeffrey L. Bennetzen ◽  
Kathrin Schrick ◽  
Patricia S. Springer ◽  
Willis E. Brown ◽  
Phillip SanMiguel
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Copy Number ◽  
Repetitive Sequences ◽  
Restriction Enzymes ◽  
Single Copy ◽  
Chromosomal Dna ◽  
Coding Regions ◽  
Highly Repetitive Dna ◽  
Copy Dna

We have characterized the copy number, organization, and genomic modification of DNA sequences within and flanking several maize genes. We found that highly repetitive DNA sequences were tightly linked to most of these genes. The highly repetitive sequences were not found within the coding regions but could be found within 6 kb either 3′ or 5′ to the structural genes. These highly repetitive regions were each composed of unique combinations of different short repetitive sequences. Highly repetitive DNA blocks were not interrupted by any detected single copy DNA. The 13 classes of highly repetitive DNA identified were found to vary little between diverse Zea isolates. The level of DNA methylation in and near these genes was determined by scoring the digestibility of 63 recognition/cleavage sites with restriction enzymes that were sensitive to 5-methylation of cytosines in the sequences 5′-CG-3′ and 5′-CNG-3′. All but four of these sites were digestible in chromosomal DNA. The four undigested sites were localized to extragenic DNA within or near highly repetitive DNA, while the other 59 sites were in low copy number DNAs. Pulsed field gel analysis indicated that the majority of cytosine modified tracts range from 20 to 200 kb in size. Single copy sequences hybridized to the unmodified domains, while highly repetitive sequences hybridized to the modified regions. Middle repetitive sequences were found in both domains.Key words: genome organization, interspersed repetitive DNA, DNA modification.

Genomic organization, evolution, and structural peculiarities of highly repetitive DNA of Hordeum vulgare

Genome ◽  
1990 ◽  
Vol 33 (3) ◽  
pp. 441-449 ◽  
Author(s):  
A. V. Vershinin ◽  
E. A. Salina ◽  
V. V. Solovyov ◽  
L. L. Timofeyeva
Keyword(s):  
Hordeum Vulgare ◽  
Dna Sequences ◽  
Genome Organization ◽  
Copy Number ◽  
Repetitive Sequences ◽  
Repeated Dna ◽  
Repeated Dna Sequences ◽  
Highly Repeated Dna ◽  
Structural Peculiarities ◽  
Hordeum Jubatum

A fraction of highly repeated DNA sequences of Hordeum vulgare has been investigated by cloning 19 separate highly repetitive sequences in the plasmid pBR327. Characteristics studied included genus specificity of isolated sequences, their prevalence, and genome organization. Sequences (pHv7161, pHv7191, pHv7179) have been identified that are the most widespread in the H. vulgare genome and have a complicated arrangement. A tandemly arranged sequence, pHv7141, was also identified. The primary structure of a 999 bp long, BamHI fragment of one of the most widespread sequences, pHv7161, as well as the adjacent pHv7302 and pHv7245 sequences was determined. The fragment abounds in inverted repeats, of which two are flanked by direct repeats, and contains short subrepeats, A, B, and C, and a great variety of potential protein-binding sites. A comparison is drawn between the content and genome organization of highly repeated DNA sequences of H. vulgare and those of the wild barley species Hordeum bulbosum, Hordeum jubatum, Hordeum geniculatum, Hordeum brevisubulatum, Hordeum turkestanicum, and Hordeum murinum. According to the above characters (close copy number and genome organization similarity of highly repetitive sequences) the species under discussion have been classified into four groups. This division is in good agreement with other data on interspecific crossing in Hordeum and on chromosome pairing in hybrid meiosis.Key words: Hordeum, highly repeated DNA sequences, copy number.

Micronuclear DNA sequences from Tetrahymena do not confer mitotic stability on ARS plasmids in Saccharomyces

Genome ◽  
1988 ◽  
Vol 30 (5) ◽  
pp. 690-696 ◽  
Author(s):  
Wendy H. Horsfall ◽  
Ronald E. Pearlman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Sequences ◽  
Copy Number ◽  
Tetrahymena Thermophila ◽  
Assay System ◽  
Mitotic Stability ◽  
Yeast Saccharomyces Cerevisiae ◽  
Genomic Libraries ◽  
Ade2 Gene

Genomic libraries containing micronuclear DNA sequences from Tetrahymena thermophila have been constructed in a vector containing ARS1, SUP11, and ura3 sequences from the yeast Saccharomyces cerevisiae. When transformed into a strain of S. cerevisiae carrying a suppressible ochre mutation in the ade2 gene, viable transformants are obtained only if the transforming plasmid is maintained at a copy number of one or two per cell. Mitotic segregation of the plasmid is easily assessed in a colour assay of transformants. Using this assay system, we showed that micronuclear DNA from Tetrahymena does not contain sequences that confer mitotic stability on yeast ARS-containing plasmids; i.e., sequences that function analogously to yeast centromere sequences. One transformant was analyzed that carries Tetrahymena sequences that maintain the copy number of the ARS plasmid at one or two per cell. However, these sequences do not confer mitotic stability on the transformants and they confer a phenotype in this assay similar to that of the REP3 gene of the yeast 2 μm plasmid.Key words: mitotic stability, centromere, Tetrahymena, Saccharomyces.

Clusters of interspersed repeated DNA sequences in the rice genome (Oryza)

Genome ◽  
1993 ◽  
Vol 36 (5) ◽  
pp. 944-953 ◽  
Author(s):  
Xinping Zhao ◽  
Gary Kochert
Keyword(s):  
Dna Sequences ◽  
Blot Hybridization ◽  
Rice Genome ◽  
Repeated Sequence ◽  
Repeated Sequences ◽  
Repeated Dna ◽  
Rice Varieties ◽  
Slot Blot Hybridization ◽  
Repeated Dna Sequence ◽  
Genus Oryza

We have characterized a repeated DNA sequence (RTL 122) from rice (Oryza sauva L.) with respect to its organization in the rice genome and its distribution among rice and other plants. The results indicate that the RTL 122 sequence is interspersed in the rice genome and limited to the genus Oryza. It is highly polymorphic and can be used to fingerprint rice varieties. A structure was observed in which several repeated sequences were clustered in DNA regions of 15–20 kb. We characterized three bacteriophage lambda clones that contained the RTL 122 sequence. Southern analysis using probes derived from restriction fragments of the three lambda clones indicated that all fragments except one are interspersed repeated sequences and belong to different repeated sequence families. Subsequent slot blot hybridization showed that most of them are only present within the genus Oryza. Some of the Oryza-specific, physically linked sequences show the same phylogenetic distribution, which suggests that these sequences might have evolved in a coordinate fashion. On the other hand, some of the repeated sequences have a different distribution even though they are physically adjacent in the genome. We speculate that such blocks of interspersed repeated sequences may serve as hotspots for rapid changes in the rice genome.Key words: rice, Oryza, repeated sequences, DNA fingerprinting, coordinated evolution.

scholarly journals The M26 Hotspot of Schizosaccharomyces pombe Stimulates Meiotic Ectopic Recombination and Chromosomal Rearrangements

Genetics ◽  
1998 ◽  
Vol 149 (3) ◽  
pp. 1191-1204 ◽  
Author(s):  
Jeffrey B Virgin ◽  
Jeffrey P Bailey
Keyword(s):  
Homologous Recombination ◽  
Schizosaccharomyces Pombe ◽  
Dna Sequences ◽  
Chromosomal Rearrangements ◽  
Low Frequency ◽  
Repeated Sequences ◽  
Crossing Over ◽  
Ectopic Recombination ◽  
Recombination Hotspots ◽  
Integration Sites

Abstract Homologous recombination is increased during meiosis between DNA sequences at the same chromosomal position (allelic recombination) and at different chromosomal positions (ectopic recombination). Recombination hotspots are important elements in controlling meiotic allelic recombination. We have used artificially dispersed copies of the ade6 gene in Schizosaccharomyces pombe to study hotspot activity in meiotic ectopic recombination. Ectopic recombination was reduced 10–1000-fold relative to allelic recombination, and was similar to the low frequency of ectopic recombination between naturally repeated sequences in S. pombe. The M26 hotspot was active in ectopic recombination in some, but not all, integration sites, with the same pattern of activity and inactivity in ectopic and allelic recombination. Crossing over in ectopic recombination, resulting in chromosomal rearrangements, was associated with 35–60% of recombination events and was stimulated 12-fold by M26. These results suggest overlap in the mechanisms of ectopic and allelic recombination and indicate that hotspots can stimulate chromosomal rearrangements.

Distribution, expression and germ line transmission of exogenous DNA sequences following microinjection into Xenopus laevis eggs

Development ◽  
1987 ◽  
Vol 99 (1) ◽  
pp. 15-23
Author(s):  
L.D. Etkin ◽  
B. Pearman
Keyword(s):  
Xenopus Laevis ◽  
Dna Sequences ◽  
Copy Number ◽  
Germ Line ◽  
Gene Promoter ◽  
Early Gene ◽  
Mosaic Pattern ◽  
Exogenous Dna ◽  
Gene Coding ◽  
Germ Line Transmission

We analysed the fate, expression and germ line transmission of exogenous DNA which was microinjected into fertilized eggs of Xenopus laevis. DNA was injected into fertilized eggs within 1 h following fertilization. The injected DNA was dispersed around the site of injection and became localized to cleavage nuclei by stage 6. Injected DNA persisted in the tissues of 6- to 8-month-old frogs and exhibited a mosaic pattern of distribution with regard to the presence or absence and copy number between different tissues. We detected the exogenous DNA sequences in 60% of injected frogs. Restriction digestion analysis of this DNA suggested that it is not rearranged and was organized as head-to-tail multimers. The copy number varied from 2 to 30 copies/cell in various tissues of the same frog. Plasmid pSV2CAT which contains the prokaryotic gene coding for chloramphenicol acetyl transferase (CAT) enzyme linked to the SV40 early gene promoter was expressed in 50% of the animals containing the gene. The pattern of expression, however, varied between different animals and could not be correlated with copy number. We also showed that the exogenous DNA sequences were transmitted through the male germ line and that each offspring contained the gene integrated into a different region of the genome.

Variable copy number DNA sequences in rice

1987 ◽  
Vol 210 (3) ◽  
pp. 373-380 ◽  
Author(s):  
Shoshi Kikuchi ◽  
Fumio Takaiwa ◽  
Kiyoharu Oono
Keyword(s):  
Dna Sequences ◽  
Copy Number

scholarly journals A method for mapping germ line sequences in Tetrahymena thermophila using the polymerase chain reaction.

Genetics ◽  
1994 ◽  
Vol 137 (1) ◽  
pp. 95-106 ◽  
Author(s):  
D Cassidy-Hanley ◽  
M C Yao ◽  
P J Bruns
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Tetrahymena Thermophila ◽  
Germ Line ◽  
Repetitive Sequences ◽  
Mapping Technique ◽  
Ciliated Protozoan ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Template Dna

Abstract A method for mapping DNA sequences to specific germinal chromosomes in the ciliated protozoan Tetrahymena thermophila has been developed. This mapping technique (PCR mapping) utilizes the polymerase chain reaction and template DNA derived from nullisomic strains to directly assign micronuclear DNA sequences to specific micronuclear chromosomes. Using this technique, a number of unique sequences and short repetitive sequences flanked by unique sequences have been mapped to four of the five germinal chromosomes.

scholarly journals Optimization of Droplet Digital Polymerase Chain Reaction (Ddpcr) For Dna Copy Number Variation Analysis of Cnv Esv27061 in Young Adults with Higher Blood Pressure

2017 ◽  
Vol 16 (1) ◽  
Author(s):  
Siti Radziah Shaik Alaudeen ◽  
Aszrin Abdullah ◽  
Azarisman Shah Mohd Shah ◽  
Norlelawati Abdul Talib
Keyword(s):  
Blood Pressure ◽  
Young Adults ◽  
Copy Number Variation ◽  
High Blood Pressure ◽  
Dna Sequences ◽  
Copy Number ◽  
Healthy Controls ◽  
Cross Sectional ◽  
Dna Concentration ◽  
Number Variation

Introduction: Copy number variation (CNV) caused by changes in DNA sequences of 1000 or more bases is implicated with susceptibility to common diseases. A study on CNV esv27061 among hypertensive Australian adults reported association with high blood pressure (BP). In Malaysia, no study on CNV among hypertensive young adults is available. Thus, this investigation aimed to assess the CNV esv27061 of young Malaysian adults with high blood pressure using optimized ddPCR. Materials and method: Ten samples each from hypertensive and healthy controls were randomly selected from samples collected for an on-going comparative cross-sectional research project among young adults living in Kuantan. The DNAs were purified using Maxwell RSC Buffy Coat DNA Kit and the concentration was measured using SimpliNano spectrophotometer. Subsequently, restriction digestion of DNAs by EcoRV was performed prior to ddPCR. The products were later subjected to droplet generation (QX100 Droplet Generator), PCR amplification and finally CNV was read by QX100 Droplet reader. Unfortunately, the above method did not yield any result. Thus, an alternative method in which purified DNA concentration was determined by QuantiFluor ONE dsDNA System (Quantus fluorometer). The DNAs (60 ng) and Alu1 were added in master mix during ddPCR and CNV esv27061 analysis was performed as stated above. Results: Optimization of method in this study showed that the detection of CNV esv27061 was possible by the use of more sensitive measurement of DNA concentration, Alu1 restriction enzyme instead of EcoRV and digestion in ddPCR reaction method rather than prior digestion. The finalized protocol run on selected hypertensive and healthy controls has shown to be reproducible and easily interpretable discrimination of gene's copy numbers. Conclusion: This optimized protocol for CNV esv27061 analysis proved useful in identifying CNV and will allow a reproducible assay evaluation and the application of this method to a bigger sample size.

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