DNA sequence organization in the common Pacific starfish Pisaster ochraceous

1978 ◽  
Vol 56 (11) ◽  
pp. 1048-1054 ◽  
Author(s):  
Michael J. Smith ◽  
Robin Boal
Keyword(s):  
Dna Sequences ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Sea Star ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Reassociation Kinetics ◽  
Short Period ◽  
The Common ◽  
Copy Dna

The sequence arrangement of the genomic DNA from the common sea star Pisaster ochraceous has been examined. Reassociation kinetics at DNA fragment lengths of 300 base pairs (bp) indicate the presence of at least three repetitive components in this DNA. The majority of these repetitive sequences are reiterated over the range from 10 to 100's. Approximately one-third of the nucleotides are found in repetitive sequences. Analysis of the reassociation kinetics of 3000-bp DNA fragments demonstrates the interspersion of repetitive and unique DNA sequences. The hyperchromicity of 3000-bp fragments reassociated to low Cot values (the product of moles of nucleotide per litre and time in seconds), and the size distribution of S1 nuclease resistant DNA duplex in these reassociation products, indicate a short-period interspersion pattern in the starfish genome. Repetitive segments (400 ± 100 bp) are interspersed with longer unique DNA sequences. At a fragment length of 3000 bp the major fraction of the single-copy DNA is found in such an arrangement. In addition to short repetitive segments a substantial portion of the repetitive DNA nucleotides are found in segments excluded by Sepharose CL-2B (≥ 2000 bp). As much as one-quarter of the repetitive sequence nucleotides can be assigned to long segments.

DNA sequence organization in the starfish Dermasterias imbricata

1980 ◽  
Vol 58 (4) ◽  
pp. 352-360 ◽  
Author(s):  
Michael J. Smith ◽  
A. Lui ◽  
K. K. Gibson ◽  
J. K. Etzkorn
Keyword(s):  
Genomic Dna ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Sequence Organization ◽  
A Genome ◽  
Short Period ◽  
Nuclease Digestion ◽  
Kinetics Of

The sequence arrangement in the genomic DNA of the starfish Dermasterias imbricata has been examined. Analyses of kinetics of reassociation in solution at DNA lengths of 400, 3100, and 6200 base pairs (bp) demonstrate the interspersion of repetitive and unique DNA. At a fragment length of 400 bp, 45% of the DNA reacts at a rate appropriate for single-copy sequences in a genome of this size (0.54 pg). Interspersion of repetitive sequences is also demonstrated by the reduced hyperchromicity of 3100- or 6200-bp fragments reacted to Cot 10, where only repetitive sequences have formed duplex. S1 nuclease digestion of 3100-bp fragments reassociated to Cot 10 shows that both short (~ 230 bp) and long (≥ 2600 bp) repetitive sequences are present in this DNA. These data demonstrate a short period interspersion pattern in Dermasterias.

scholarly journals Microdissection of and microcloning from the short arm of human chromosome 2.

1986 ◽  
Vol 6 (11) ◽  
pp. 3826-3830 ◽  
Author(s):  
G P Bates ◽  
B J Wainwright ◽  
R Williamson ◽  
S D Brown
Keyword(s):  
Human Chromosome ◽  
Dna Sequences ◽  
Chromosomal Location ◽  
Genetic Diseases ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Chromosome 2 ◽  
Insert Size ◽  
Base Pairs ◽  
The Mean

A bank of cloned DNA sequences from the distal half of the short arm of human chromosome 2 was generated by using microdissection and microcloning techniques. DNA was purified from 106 chromosomal fragments, manually dissected from peripheral lymphocytes in metaphase, and cloned into the EcoRI site of lambda gt10. A total of 257 putative recombinants were recovered, of which 41% were found to contain human inserts. The mean insert size was 380 base pairs (median size, 83 base pairs), and fewer than 10% of the clones contained highly repetitive sequences. All single-copy sequences examined were shown to map to the short arm of chromosome 2 by using hybrid panels. This technique provides a rapid method of isolating probes specific to a human subchromosomal region to generate linked markers to genetic diseases for which the chromosomal location is known.

Sequence organization and developmental expression of an interspersed, repetitive element and associated single-copy DNA sequences in Dictyostelium discoideum

1985 ◽  
Vol 5 (8) ◽  
pp. 2123-2130
Author(s):  
A R Kimmel ◽  
R A Firtel
Keyword(s):  
Dna Sequences ◽  
Transcription Initiation ◽  
Sequence Data ◽  
Single Copy ◽  
Developmental Expression ◽  
Cdna Clones ◽  
Base Pairs ◽  
Sequence Element ◽  
Copy Dna ◽  
Single Copy Dna

We have examined the genomic organization and developmental expression pattern of a short, transcribed, interspersed repeat element and its associated single-copy sequences. We have previously shown that 1% of the polyadenylated [poly(A)+] RNA from vegetative cells contains sequences that hybridize to this repeat. The complementary RNA is heterogeneous in size, and 90% of its mass hybridizes to single-copy DNA. In this study, we examined a series of genomic DNAs and cDNAs derived from poly(A)+ RNAs which are complementary to the repeat. Comparisons of sequence data from various genomic and cDNA clones indicated that (AAC)n X (GTT)n is the common sequence element. The tandem repeat occurred in approximately 100 short segments (approximately 35 to 150 base pairs) per haploid genome interspersed with single-copy DNA. Probes from regions adjacent to this element hybridized to unique restriction fragments on DNA blots and unique poly(A)+ RNA species on RNA blots. The (AAC)n X (GTT)n sequence was asymmetrically transcribed with only (AAC)n sequences represented in RNA. The repeat was localized within the transcribed regions of several genes and 70 base pairs 5' to the transcription initiation site of another gene. Individual (AAC)n-containing RNAs exhibited a developmental pattern of expression suggestive of the coordinate expression of many AAC gene family members.

scholarly journals Sequence organization and developmental expression of an interspersed, repetitive element and associated single-copy DNA sequences in Dictyostelium discoideum.

1985 ◽  
Vol 5 (8) ◽  
pp. 2123-2130 ◽  
Author(s):  
A R Kimmel ◽  
R A Firtel
Keyword(s):  
Dna Sequences ◽  
Transcription Initiation ◽  
Sequence Data ◽  
Single Copy ◽  
Developmental Expression ◽  
Cdna Clones ◽  
Base Pairs ◽  
Sequence Element ◽  
Copy Dna ◽  
Single Copy Dna

We have examined the genomic organization and developmental expression pattern of a short, transcribed, interspersed repeat element and its associated single-copy sequences. We have previously shown that 1% of the polyadenylated [poly(A)+] RNA from vegetative cells contains sequences that hybridize to this repeat. The complementary RNA is heterogeneous in size, and 90% of its mass hybridizes to single-copy DNA. In this study, we examined a series of genomic DNAs and cDNAs derived from poly(A)+ RNAs which are complementary to the repeat. Comparisons of sequence data from various genomic and cDNA clones indicated that (AAC)n X (GTT)n is the common sequence element. The tandem repeat occurred in approximately 100 short segments (approximately 35 to 150 base pairs) per haploid genome interspersed with single-copy DNA. Probes from regions adjacent to this element hybridized to unique restriction fragments on DNA blots and unique poly(A)+ RNA species on RNA blots. The (AAC)n X (GTT)n sequence was asymmetrically transcribed with only (AAC)n sequences represented in RNA. The repeat was localized within the transcribed regions of several genes and 70 base pairs 5' to the transcription initiation site of another gene. Individual (AAC)n-containing RNAs exhibited a developmental pattern of expression suggestive of the coordinate expression of many AAC gene family members.

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.

Microdissection of and microcloning from the short arm of human chromosome 2

1986 ◽  
Vol 6 (11) ◽  
pp. 3826-3830
Author(s):  
G P Bates ◽  
B J Wainwright ◽  
R Williamson ◽  
S D Brown
Keyword(s):  
Human Chromosome ◽  
Dna Sequences ◽  
Chromosomal Location ◽  
Genetic Diseases ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Chromosome 2 ◽  
Insert Size ◽  
Base Pairs ◽  
The Mean

A bank of cloned DNA sequences from the distal half of the short arm of human chromosome 2 was generated by using microdissection and microcloning techniques. DNA was purified from 106 chromosomal fragments, manually dissected from peripheral lymphocytes in metaphase, and cloned into the EcoRI site of lambda gt10. A total of 257 putative recombinants were recovered, of which 41% were found to contain human inserts. The mean insert size was 380 base pairs (median size, 83 base pairs), and fewer than 10% of the clones contained highly repetitive sequences. All single-copy sequences examined were shown to map to the short arm of chromosome 2 by using hybrid panels. This technique provides a rapid method of isolating probes specific to a human subchromosomal region to generate linked markers to genetic diseases for which the chromosomal location is known.

scholarly journals High frequency repeat-induced point mutation (RIP) is not associated with efficient recombination in Neurospora.

Genetics ◽  
1994 ◽  
Vol 138 (4) ◽  
pp. 1093-1103 ◽  
Author(s):  
J T Irelan ◽  
A T Hagemann ◽  
E U Selker
Keyword(s):  
Point Mutation ◽  
Dna Sequences ◽  
High Frequency ◽  
Recombination Frequency ◽  
Single Copy ◽  
Sexual Cycle ◽  
Base Pairs ◽  
Copy Gene ◽  
The Relationship ◽  
Repeat Induced Point Mutation

Abstract Duplicated DNA sequences in Neurospora crassa are efficiently detected and mutated during the sexual cycle by a process named repeat-induced point mutation (RIP). Linked, direct duplications have previously been shown to undergo both RIP and deletion at high frequency during premeiosis, suggesting a relationship between RIP and homologous recombination. We have investigated the relationship between RIP and recombination for an unlinked duplication and for both inverted and direct, linked duplications. RIP occurred at high frequency (42-100%) with all three types of duplications used in this study, yet recombination was infrequent. For both inverted and direct, linked duplications, recombination was observed, but at frequencies one to two orders of magnitude lower than RIP. For the unlinked duplication, no recombinants were seen in 900 progeny, indicating, at most, a recombination frequency nearly three orders of magnitude lower than the frequency of RIP. In a direct duplication, RIP and recombination were correlated, suggesting that these two processes are mechanistically associated or that one process provokes the other. Mutations due to RIP have previously been shown to occur outside the boundary of a linked, direct duplication, indicating that RIP might be able to inactivate genes located in single-copy sequences adjacent to a duplicated sequence. In this study, a single-copy gene located between elements of linked duplications was inactivated at moderate frequencies (12-14%). Sequence analysis demonstrated that RIP mutations had spread into these single-copy sequences at least 930 base pairs from the boundary of the duplication, and Southern analysis indicated that mutations had occurred at least 4 kilobases from the duplication boundary.

scholarly journals A systematic comparison of eight new plastome sequences from Ipomoea L

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6563
Author(s):  
Jianying Sun ◽  
Xiaofeng Dong ◽  
Qinghe Cao ◽  
Tao Xu ◽  
Mingku Zhu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Next Generation Sequencing ◽  
Chloroplast Genome ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Next Generation ◽  
Variable Regions ◽  
Chloroplast Genomes ◽  
Generation Sequencing

Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato’s close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,910 bp each) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57–89 pairs of repetitive sequences and 39–64 simple sequence repeats were found. By conducting a sliding window analysis, we found six relatively high variable regions (ndhA intron, ndhH-ndhF, ndhF-rpl32, rpl32-trnL, rps16-trnQ, and ndhF) in the Ipomoea genus, eight (trnG, rpl32-trnL, ndhA intron, ndhF-rpl32, ndhH-ndhF, ccsA-ndhD, trnG-trnR, and pasA-ycf3) in the Batatas group, and eight (ndhA intron, petN-psbM, rpl32-trnL, trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ, and trnG) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies. Conclusions The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced Ipomoea species. Our comparative analysis included a broad range of Ipomoea chloroplast genomes, providing valuable information for Ipomoea species identification and enhancing the understanding of Ipomoea genetic resources.

Electron microscopy of Achlya deoxyribonucleic acid sequence organization

1981 ◽  
Vol 1 (2) ◽  
pp. 136-143
Author(s):  
M Pellegrini ◽  
W E Timberlake ◽  
R B Goldberg
Keyword(s):  
Dna Sequences ◽  
Deoxyribonucleic Acid ◽  
Microscopic Analysis ◽  
Single Copy ◽  
Electron Microscopic ◽  
Sequence Organization ◽  
Double Stranded Dna ◽  
Copy Dna ◽  
Gene 32 ◽  
Single Copy Dna

Electron microscopic analysis of reassociated deoxyribonucleic acid (DNA) from the aquatic fungus Achlya bisexualis revealed details of the sequence arrangement of the inverted repeats and both the highly and moderately repetitive sequence clusters. We used the gene 32 protein-ethidium bromide technique for visualizing the DNA molecules, a procedure which provides excellent contrast between single- and double-stranded DNA regions. Long (greater than 6-kilobase) DNA fragments were isolated after reannealing to two different repetitive C0t values, and the renatured structures were then visualized in an electron microscope. Our results showed that the inverted repeat sequences were short (0.5 kilobase, number-average) and separated by nonhomologous DNA of various lengths. These pairs of sequences were not clustered within the genome. Both highly repetitive and moderately repetitive DNA sequences were organized as tandem arrays of precisely paired, regularly repeating units. No permuted clusters of repeating sequences were observed, nor was there evidence of interspersion of repetitive with single-copy DNA sequences in the Achlya genome.

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