Repetitive DNA sequences from polyploid Elymus trachycaulus and the diploid progenitor species: detection and genomic affinity of Elymus chromatin added to wheat

A set of four repetitive DNA clones, pEt1, pEt2, pCb1, and pCb3, were isolated from SH-genome polyploid Elymus trachycaulus and H-genome diploid Critesion bogdanii. The clone Et1 represents a tandemly arranged telomeric sequence. Et2 represents tandem repeats interspersed along the entire length of individual chromosomes. The Cb1 sequence was more evenly dispersed. The Et1 clone shared homology with a 350 base pair family of rye sequences. The Cb3 sequence was evenly distributed in S- and H-genome species. All the repetitive DNA sequences were excellent markers for the specific detection and genomic affinity of Elymus chromatin added to wheat. All clones showed intragenomic variation in copy number and chromosomal location. Based on the analysis of this variation, we conclude that E. trachycaulus most probably originated from putative diploid H- and S-genome species resembling Critesion californicum and Pseudoroegneria spicata, respectively.Key words: wheatgrass, wheat–Elymus hybrid, addition lines, polyploidy, restriction fragment length polymorphism.

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Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene

Genes ◽

10.3390/genes10121014 ◽

2019 ◽

Vol 10 (12) ◽

pp. 1014 ◽

Cited By ~ 1

Author(s):

Ana Paço ◽

Renata Freitas ◽

Ana Vieira-da-Silva

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Tandem Repeats ◽

Evolutionary Relationship ◽

Repetitive Dna Sequences ◽

Dna Remodeling ◽

Eukaryotic Genomes ◽

Similar Organization ◽

Dispersed Repeats

Eukaryotic genomes are rich in repetitive DNA sequences grouped in two classes regarding their genomic organization: tandem repeats and dispersed repeats. In tandem repeats, copies of a short DNA sequence are positioned one after another within the genome, while in dispersed repeats, these copies are randomly distributed. In this review we provide evidence that both tandem and dispersed repeats can have a similar organization, which leads us to suggest an update to their classification based on the sequence features, concretely regarding the presence or absence of retrotransposons/transposon specific domains. In addition, we analyze several studies that show that a repetitive element can be remodeled into repetitive non-coding or coding sequences, suggesting (1) an evolutionary relationship among DNA sequences, and (2) that the evolution of the genomes involved frequent repetitive sequence reshuffling, a process that we have designated as a “DNA remodeling mechanism”. The alternative classification of the repetitive DNA sequences here proposed will provide a novel theoretical framework that recognizes the importance of DNA remodeling for the evolution and plasticity of eukaryotic genomes.

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Repetitive DNA variation and pivotal–differential evolution of wild wheats

Genome ◽

10.1139/g93-003 ◽

1993 ◽

Vol 36 (1) ◽

pp. 14-20 ◽

Cited By ~ 13

Author(s):

L. E. Talbert ◽

G. Kimber ◽

G. M. Magyar ◽

C. B. Buchanan

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Sympatric Species ◽

Repetitive Dna Sequences ◽

Large Set ◽

Polyploid Species ◽

Genome Species ◽

Dna Variation ◽

Cytogenetic Evidence ◽

M Genome

Several polyploid species in the genus Triticum contain a U genome derived from the diploid T. umbellulatum. In these species, the U genome is considered to be unmodified from the diploid based on chromosome pairing analysis, and it is referred to as pivotal. The additional genome(s) are considered to be modified, and they are thus referred to as differential genomes. The M genome derived from the diploid T. comosum is found in many U genome polyploids. In this study, we cloned three repetitive DNA sequences found primarily in the U genome and two repetitive DNA sequences found primarily in the M genome. We used these to monitor variation for these sequences in a large set of species containing U and M genomes. Investigation of sympatric and allopatric accessions of polyploid species did not show repetitive DNA similarities among sympatric species. This result does not support the idea that the polyploid species are continually exchanging genetic information through introgression. However, it is also possible that repetitive DNA is not a suitable means of addressing the question of introgression. The U genomes of both diploid and polyploid U genome species were similar regarding hybridization patterns observed with U genome probes. Much more variation was found both among diploid T. comosum accessions and polyploids containing M genomes. The observed variation supports the cytogenetic evidence that the M genome is more variable than the U genome. It also raises the possibility that the differential nature of the M genome may be due to variation within the diploid T. comosum, as well as among polyploid M genome species and accessions.Key words: wheat, molecular, evolution, introgression.

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Cloning and characterization of the majority of repetitive DNA in cotton (Gossypium L.)

Genome ◽

10.1139/g95-156 ◽

1995 ◽

Vol 38 (6) ◽

pp. 1177-1188 ◽

Cited By ~ 15

Author(s):

Xinping Zhao ◽

Rod A. Wing ◽

Andrew H. Paterson

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Tandem Repeats ◽

Repetitive Sequences ◽

Repetitive Dna Sequences ◽

Tetraploid Cotton ◽

Cotton Genome ◽

Cotton Species ◽

Dna Elements ◽

Repetitive Dna Elements

Repetitive DNA elements representing 60–70% of the total repetitive DNA in tetraploid cotton (Gossypium barbadense L.) and comprising 30–36% of the tetraploid cotton genome were isolated from a genomic library of DNA digested with a mixture of four blunt-end cutting restriction enzymes. A total of 313 clones putatively containing nuclear repetitive sequences were classified into 103 families, based on cross hybridization and Southern blot analysis. The 103 families were characterized in terms of genome organization, methylation pattern, abundance, and DNA variation. As in many other eukaryotic genomes, interspersed repetitive elements are the most abundant class of repetitive DNA in the cotton genome. Paucity of tandem repeat families with high copy numbers (>104) may be a unique feature of the cotton genome as compared with other higher plant genomes. Interspersed repeats tend to be methylated, while tandem repeats seem to be largely unmethylated in the cotton genome. Minimal variation in repertoire and overall copy number of repetitive DNA elements among different tetraploid cotton species is consistent with the hypothesis of a relatively recent origin of tetraploid cottons.Key words: genome analysis, genome evolution, tandemly repetitive DNA sequences, interspersed repetitive DNA sequences, polyploid.

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The R173 family of rye-specific repetitive DNA sequences: a structural analysis

Genome ◽

10.1139/g91-015 ◽

1991 ◽

Vol 34 (1) ◽

pp. 88-95 ◽

Cited By ~ 25

Author(s):

Peter M. Rogowsky ◽

Susanne Manning ◽

Jin-Yuan Liu ◽

Peter Langridge

Keyword(s):

Restriction Fragment Length Polymorphism ◽

Repetitive Dna ◽

Length Polymorphism ◽

Dna Sequences ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Chromosome 1 ◽

Repetitive Dna Sequences ◽

Flanking Regions ◽

Restriction Fragment Length

In contrast to all other characterised families, repetitive DNA sequences of the rye-specific R173 family occur generally as a monomer and have an unusually long repeat unit. A genomic library was generated from a wheat line with three copies of the short arm of chromosome 1 of rye, 1RS. Seventy-seven λ clones, representing independent members of the family, were isolated by hybridization to pAW173. They share a common region of approximately 3.5 kbp, which is free of large internal repeats and therefore constitutes the basic unit of the dispersed R173 family. The analysis of flanking regions showed that individual members of the R173 family are generally not found in the vicinity of other characterised families of repetitive DNA. The flanking regions of four selected λ clones were different from each other and comprised both repetitive and low-copy sequences. A restriction fragment length polymorphism probe, mapping to the short arm of chromosome 1, was obtained by subcloning of flanking regions of the R173 family.Key words: repetitive DNA sequences, wheat, rye, restriction fragment length polymorphism marker.

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