Neutral mutations and repetitive DNA

1987 ◽  
Vol 7 (7) ◽  
pp. 599-606 ◽  
Author(s):  
William F. Loomis ◽  
Michael E. Gilpin
Keyword(s):  
Dna Sequence ◽  
Computer Simulations ◽  
Repetitive Dna ◽  
Repetitive Sequences ◽  
Multigene Families ◽  
Neutral Mutations ◽  
Evolution Of Genomes

We have previously shown that computer simulations of processes that generate selectively advantageous changes together with random duplications and deletions give rise to genomes with many different genes embedded in a large amount of dispensable DNA sequence. We now explore the consequences of neutral changes on the evolution of genomes. We follow the consequences of sequence divergences that are neutral when they occur in dispensable sequences or extra copies of genes present in multigene families. We find that when divergence occurs at about the same frequency as duplication/deletion events, genomes carry repetitive sequences in proportion to their size. Inspection of the genomes as they evolved showed that multigene families were generated by relatively recent duplications of single genes and so would be expected to be highly homogeneous.

scholarly journals A MODEL OF DUPLICATIVE TRANSPOSITION AND GENE CONVERSION FOR REPETITIVE DNA FAMILIES

Genetics ◽  
1985 ◽  
Vol 110 (3) ◽  
pp. 513-524
Author(s):  
Tomoko Ohta
Keyword(s):  
Gene Conversion ◽  
Repetitive Dna ◽  
Repetitive Sequences ◽  
Diploid Cell ◽  
Multigene Families ◽  
Numerical Studies

ABSTRACT A model of duplicative transposition and gene conversion for the evolution of repetitive DNA families was studied. In this model, transposition and conversion (both unbiased) are assumed to occur both within and between the genomes in a diploid cell, and any degree of linkage intensity is incorporated. The transition equations for allelic and nonallelic identity coefficients have been formulated by using the previous results. The results are widely applicable to many repetitive sequences, from dispersed families like transposons to tightly linked multigene families. It has been shown through extensive numerical studies on equilibrium properties that duplicative transposition and gene conversion have very similar effects on nonallelic identity coefficients, but that allelism and allelic identity are greatly influenced by the relative rates of occurrence of the two processes.

Molecular characterization of a tandem repeat, Afa family, and its distribution among Triticeae

Genome ◽  
1995 ◽  
Vol 38 (3) ◽  
pp. 479-486 ◽  
Author(s):  
Kiyotaka Nagaki ◽  
Hisashi Tsujimoto ◽  
Kazuhiro Isono ◽  
Tetsuo Sasakuma
Keyword(s):  
Dna Sequence ◽  
Repetitive Dna ◽  
Repetitive Sequences ◽  
Diploid Species ◽  
Restriction Enzymes ◽  
D Genome ◽  
Triticeae Species ◽  
Repetitive Dna Sequence ◽  
Aegilops Squarrosa ◽  
Digestion Pattern

We have characterized a so-called D genome specific repetitive DNA sequence (pAs1) of Aegilops squarrosa L. (2n = 14, genome DD) with respect to its DNA sequence and its distribution among Triticeae species. The clone consisted of three units of a repetitive DNA sequence of 336 or 337 base pairs, and was AT rich (65.2%). DNA analyses revealed the presence of the pAs1-like sequences in other genomes of Triticeae species, although the repetition was greatly (as much as 100-fold) variable among the genomes. The repetitive sequences from 10 diploid species were amplified using PCR with specific primers, and the sequential variability was analyzed by the digestion pattern obtained with five restriction enzymes. Since the AfaI site was the most conservatively present in the unit of the repetitive sequences, we named them "Afa family." The analysis clearly displayed the variation of the repetitive sequences regardless of the uniformity of the size of the amplified product. These results indicated that plural amplification events of these repetitive sequences happened independently in the genome evolution of Triticeae.Key words: Triticeae, Aegilops squarrosa, repetitive DNA sequence, CAPS analysis, Afa family.

scholarly journals Mismatch induced speciation in Salmonella : model and data

2006 ◽  
Vol 361 (1475) ◽  
pp. 2045-2053 ◽  
Author(s):  
Daniel Falush ◽  
Mia Torpdahl ◽  
Xavier Didelot ◽  
Donald F Conrad ◽  
Daniel J Wilson ◽  
...  
Keyword(s):  
New Species ◽  
Natural Selection ◽  
Dna Sequence ◽  
Computer Simulations ◽  
De Novo ◽  
Sequence Data ◽  
Biological Species ◽  
Species Boundaries ◽  
Population Subdivision ◽  
Geographical Population

In bacteria, DNA sequence mismatches act as a barrier to recombination between distantly related organisms and can potentially promote the cohesion of species. We have performed computer simulations which show that the homology dependence of recombination can cause de novo speciation in a neutrally evolving population once a critical population size has been exceeded. Our model can explain the patterns of divergence and genetic exchange observed in the genus Salmonella , without invoking either natural selection or geographical population subdivision. If this model was validated, based on extensive sequence data, it would imply that the named subspecies of Salmonella enterica correspond to good biological species, making species boundaries objective. However, multilocus sequence typing data, analysed using several conventional tools, provide a misleading impression of relationships within S. enterica subspecies enterica and do not provide the resolution to establish whether new species are presently being formed.

scholarly journals Structures and stability of simple DNA repeats from bacteria

2020 ◽  
Vol 477 (2) ◽  
pp. 325-339 ◽  
Author(s):  
Vaclav Brazda ◽  
Miroslav Fojta ◽  
Richard P. Bowater
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Genetic Instability ◽  
Repetitive Sequences ◽  
Biological Significance ◽  
Human Diseases ◽  
Repetitive Dna Sequences ◽  
Dna Repeats ◽  
Diverse Range ◽  
Dna Structures

DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.

scholarly journals Characterisation of a novel repetitive DNA sequence fromMycobacterium bovis

1992 ◽  
Vol 96 (2-3) ◽  
pp. 179-185 ◽  
Author(s):  
T.J. Doran ◽  
A.L.M. Hodgson ◽  
J.K. Davies ◽  
A.J. Radford
Keyword(s):  
Dna Sequence ◽  
Repetitive Dna ◽  
Repetitive Dna Sequence

scholarly journals C-Ag+−C based repetitive DNA sequence

2020 ◽  
Vol 1679 ◽  
pp. 022049
Author(s):  
M A Popova ◽  
V I Rolich ◽  
R R Ramazanov ◽  
N A Kasyanenko ◽  
P A Sokolov
Keyword(s):  
Dna Sequence ◽  
Repetitive Dna ◽  
Repetitive Dna Sequence

scholarly journals Functional role of a highly repetitive DNA sequence in anchorage of the mouse genome

1988 ◽  
Vol 16 (17) ◽  
pp. 8351-8360 ◽  
Author(s):  
Beatrice Neuer-Nitsche ◽  
Xiang Lu ◽  
Dieter Werner
Keyword(s):  
Dna Sequence ◽  
Repetitive Dna ◽  
Functional Role ◽  
Mouse Genome ◽  
Repetitive Dna Sequence ◽  
Highly Repetitive Dna

Cloning and characterization of repetitive DNA sequences from genomes of Oryza minuta and Oryza australiensis

Genome ◽  
1991 ◽  
Vol 34 (5) ◽  
pp. 790-798 ◽  
Author(s):  
H. Aswidinnoor ◽  
R. J. Nelson ◽  
J. F. Dallas ◽  
C. L. McIntyre ◽  
H. Leung ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Repetitive Sequences ◽  
Rice Genome ◽  
Repetitive Dna Sequences ◽  
Cross Hybridization ◽  
Oryza Minuta ◽  
Wild Rice Species ◽  
Oryza Australiensis

The value of genome-specific repetitive DNA sequences for use as molecular markers in studying genome differentiation was investigated. Five repetitive DNA sequences from wild species of rice were cloned. Four of the clones, pOm1, pOm4, pOmA536, and pOmPB10, were isolated from Oryza minuta accession 101141 (BBCC genomes), and one clone, pOa237, was isolated from Oryza australiensis accession 100882 (EE genome). Southern blot hybridization to different rice genomes showed strong hybridization of all five clones to O. minuta genomic DNA and no cross hybridization to genomic DNA from Oryza sativa (AA genome). The pOm1 and pOmA536 sequences showed cross hybridization only to all of the wild rice species containing the C genome. However, the pOm4, pOmPB10, and pOa237 sequences showed cross hybridization to O. australiensis genomic DNA in addition to showing hybridization to the O. minuta genomic DNA.Key words: rice, genome-specific repetitive sequences, Oryza.

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