Distribution of repetitive DNAs and the hybrid origin of the red vizcacha rat (Octodontidae)

Genome ◽  
2012 ◽  
Vol 55 (2) ◽  
pp. 105-117 ◽  
Author(s):  
E.Y. Suárez-Villota ◽  
R.A. Vargas ◽  
C.L. Marchant ◽  
J.E. Torres ◽  
N. Köhler ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Repetitive Sequences ◽  
Diploid Species ◽  
Hybrid Origin ◽  
Comparative Genomic ◽  
Telomeric Dna ◽  
Meiotic Chromosomes ◽  
Yellow Orange ◽  
Orange Fluorescence

Great genome size (GS) variations described in desert-specialist octodontid rodents include diploid species ( Octomys mimax and Octodontomys gliroides ) and putative tetraploid species ( Tympanoctomys barrerae and Pipanacoctomys aureus ). Because of its high DNA content, elevated chromosome number, and gigas effect, the genome of T. barrerae is claimed to have resulted from tetraploidy. Alternatively, the origin of its GS has been attributed to the accumulation of repetitive sequences. To better characterize the extent and origin of these repetitive DNA, self-genomic in situ hybridization (self-GISH), whole-comparative genomic hybridization (W-CGH), and conventional GISH were conducted in mitotic and meiotic chromosomes. Self-GISH on T. barrerae mitotic plates together with comparative self-GISH (using its closest relatives) discriminate a pericentromeric and a telomeric DNA fraction. As most of the repetitive sequences are pericentromeric, it seems that the large GS of T. barrerae is not due to highly repeated sequences accumulated along chromosomes arms. W-CGH using red-labeled P. aureus DNA and green-labeled O. mimax DNA simultaneously on chromosomes of T. barrerae revealed a yellow–orange fluorescence over a repetitive fraction of the karyotype. However, distinctive red-only fluorescent signals were also detected at some centromeres and telomeres, indicating closer homology with the DNA sequences of P. aureus. Conventional GISH using an excess of blocking DNA from either P. aureus or O. mimax labeled only a fraction of the T. barrerae genome, indicating its double genome composition. These data point to a hybrid nature of the T. barrerae karyotype, suggesting a hybridization event in the origin of this species.

Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome

Genome ◽  
2011 ◽  
Vol 54 (9) ◽  
pp. 710-717 ◽  
Author(s):  
B. Kolano ◽  
B.W. Gardunia ◽  
M. Michalska ◽  
A. Bonifacio ◽  
D. Fairbanks ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Chenopodium Quinoa ◽  
5S Rdna ◽  
Rrna Gene ◽  
Fish Analysis ◽  
Rdna Loci

The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18–24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18–24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12–13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12–13P was very similar to GISH results, suggesting that the 12–13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

scholarly journals Cloning and preliminary verification of telomere-associated sequences in upland cotton

2020 ◽  
Vol 14 (2) ◽  
pp. 183-195
Author(s):  
Yuling Liu ◽  
Zhen Liu ◽  
Yangyang Wei ◽  
Yanjun Wang ◽  
Jiaran Shuang ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Gossypium Hirsutum ◽  
Dna Sequences ◽  
Upland Cotton ◽  
Repetitive Sequences ◽  
Associated Sequences ◽  
End Sequences ◽  
Important Evidence ◽  
Single Primer

Telomeres are structures enriched in repetitive sequences at the end of chromosomes. In this study, using the telomere primer AA(CCCTAAA)3CCC for the single primer PCR, two DNA sequences were obtained from Gossypium hirsutum (Linnaeus, 1753) accession (acc.) TM-1. Sequence analysis showed that the two obtained sequences were all rich in A/T base, which was consistent with the characteristic of the telomere-associated sequence (TAS). They were designated as GhTAS1 and GhTAS2 respectively. GhTAS1 is 489 bp long, with 57.6% of A/T, and GhTAS2 is 539 bp long, with 63.9% of A/T. Fluorescence in situ hybridization results showed that both of the cloned TASs were located at the ends of the partial chromosomes of G. hirsutum, with the strong signals, which further confirmed that GhTAS1 and GhTAS2 were telomere-associated sequences including highly tandemly repetitive sequences. Results of blast against the assembled genome of G. hirsutum showed that GhTAS sequences may be missed on some assembled chromosomes. The results provide important evidence for the evaluation of the integrity of assembled chromosome end sequences, and will also contribute to the further perfection of the draft genomes of cotton.

A molecular analysis of the origin of the Crepis capillaris B chromosome

1994 ◽  
Vol 107 (3) ◽  
pp. 703-708 ◽  
Author(s):  
M. Jamilena ◽  
C. Ruiz Rejon ◽  
M. Ruiz Rejon
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
B Chromosome ◽  
Dna Probes ◽  
Telomeric Repeats ◽  
Crepis Capillaris ◽  
Telomeric Sequences ◽  
Hybridization Data

The origin of the B chromosome of Crepis capillaris has been studied by using in situ hybridization with different DNA probes. Genomic in situ hybridization (GISH) with DNA from plants with and without Bs as probes indicates that the B chromosome has many DNA sequences in common with A chromosomes, showing no region rich in B-specific sequences. Six additional DNA probes were used to test the possible origin of this B from the standard NOR chromosome (chromosome 3). In the short arm of the NOR chromosome, we detected not only 18 S + 25 S rDNA, but also 5 S rDNA and a specific repetitive sequence from the NOR chromosome (pCcH32); in the heterochromatic bands of the long arm, we found two different repetitive sequences (pCcE9 and pCcD29). In the B chromosome, however, only the 18 S + 25 S rDNA and the telomeric sequences from Arabidopsis thaliana were observed. Our in situ hybridization data with telomeric repeats indicate that the two telomeres of the B are larger than those of the A chromosomes, confirming the isochromosomal nature of this B. Hybridizations of 18 S + 25 S rDNA and telomeric repeats to blots of DNA from plants with and without Bs reveal a high homology between A and B 18 S + 25 S rDNA genes, but some sequence dissimilarities between A and B telomeres. Taken as a whole, these data indicate that the entire B of C. capillaris, although possibly having originated from the standard genome, did not derive directly from the NOR chromosome.

Amplification of DNA sequences in wheat and its relatives: the Dgas44 and R350 families of repetitive sequences

Genome ◽  
1994 ◽  
Vol 37 (2) ◽  
pp. 320-327 ◽  
Author(s):  
D. McNeil ◽  
E. S. Lagudah ◽  
U. Hohmann ◽  
R. Appels
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Tetraploid Wheat ◽  
Genomic Clone ◽  
Sequence Family ◽  
Chain Reaction ◽  
D Genome ◽  
Polymerase Chain

The sequence of a Triticum tauschii genomic clone representing a family of D-genome amplified DNA sequences, designated Dgas44, is reported. The Dgas44 sequence occurs on all chromosomes of the D genome of wheat, Triticum aestivum, and in situ hybridization revealed it to be evenly dispersed on all seven chromosome pairs. An internal HindIII fragment of Dgas44, designated Dgas44-3, defines the highly amplified region that is specific to the D genome. The polymerase chain reaction was used to amplify a 236-bp fragment within Dgas44-3 from chromosomes 1D, 2D, 3D, 4D, 5D, and 7D, and identical copies of this region of the Dgas44-3 sequence were found among the isolates from each of the chromosomes. The Dgas44-3 sequence population from specific chromosomes differed on average by 0.22% from the original Dgas44 sequence. The Dgas44 sequence was found to differentiate between the D genome present in T. aestivum, T. tauschii, hexaploid T. crassum, T. cylindricum, T. ventricosum, in which the sequence was present in a highly amplified form and T. juvenale, T. syriacum, and tetraploid T. crassum where the sequence family was difficult to detect. Another class of amplified sequences previously considered to be rye "specific." R350, was isolated from tetraploid wheat and its dispersed distribution on chromosomes was similar to the Dgas44 family in T. tauschii. In contrast with the Dgas44 sequence family, genome specificity for the remnant R350 sequence family was not evident since it was present on all wheat chromosomes.Key words: D genome, sequence amplification, in situ hybridization.

Molecular characterization and chromosome location of repeated DNA sequences in Hordeum species and in the amphiploid tritordeum (×Tritordeum Ascherson et Graebner)

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 850-857 ◽  
Author(s):  
Esther Ferrer ◽  
Yolanda Loarce ◽  
Gregorio Hueros
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Diploid Species ◽  
Repeated Sequences ◽  
Hordeum Chilense ◽  
Repeated Dna ◽  
Repeated Dna Sequences ◽  
In Situ Experiments ◽  
Basic Genome

Genomic DNA from 19 species and subspecies representing the four basic genomes (H, I, X, and Y) of Hordeum was restricted with HaeIII and hybridized with two repeated DNA sequences of Hordeum chilense. The potential use of repeated sequences in ascertaining genomic affinities within the genus Hordeum was studied by comparing restriction fragment patterns. The study demonstrated the following: (i) species that shared a basic genome showed more similar hybridization fragment patterns than species with different genomes, whether with pHchl or pHch3; (ii) hybridization with pHchl revealed the presence of certain fragments limited to the species with a H genome; and (iii) the alloploid nature of species like H. jubatum was confirmed. The chromosomal distribution of the two repeated sequences was studied in species representing each basic genome and in the amphiploid tritordeum using fluorescent in situ hybridization. No interspecific differences were found between the diploid species. In situ experiments indicated the alloploid nature of H. depressum. Both sequences allow H. chilense chromatin to be distinguished from wheat chromosomes in tritordeum.Key words: repeated DNA sequences; in situ hybridization, Hordeum, tritordeum.

The Use of Primed in situ Synthesis (PRINS) to Analyze Nucleolar Organizer Regions (NORs) and Telomeric DNA Sequences in the Domestic Chicken Genome

2013 ◽  
Vol 61 (3) ◽  
pp. 149-153
Author(s):  
Monika Bugno-Poniewierska ◽  
Leszek Potocki ◽  
Beata Błądek ◽  
Klaudia Pawlina ◽  
Maciej Wnuk ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Chicken Genome ◽  
Nucleolar Organizer ◽  
In Situ Synthesis ◽  
Domestic Chicken ◽  
Nucleolar Organizer Regions ◽  
Telomeric Dna

Isolation, characterization, and analysis of Leymus-specific DNA sequences

Genome ◽  
2003 ◽  
Vol 46 (4) ◽  
pp. 673-682 ◽  
Author(s):  
Sigridur Klara Bödvarsdóttir ◽  
Kesara Anamthawat-Jónsson
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Southern Hybridization ◽  
Genetic Relatedness ◽  
Repetitive Sequences ◽  
Nucleolar Organiser Regions ◽  
Basic Genome ◽  
Specific Sequences ◽  
Leymus Mollis

Genomic Southern hybridization using labeled total genomic DNA of Leymus mollis as probe showed intense hybridization signals on all restriction enzyme digested DNA from five species of Leymus Hochst., and four species of Psathyrostachys Nevski. Experiments using the same L. mollis probe, but with unlabeled blocking DNA from Psathyrostachys, showed no hybridization at all. These two genera evidently had the same genomic content. Southern hybridization without blocking allowed identification of DNA fragments abundant in Leymus and Psathyrostachys. Fragments potentially specific to Leymus were cloned. Five repetitive DNA clones from L. mollis and L. arenarius were characterized: pLmIs1, pLmIs44, pLmIs51, pLmIs53, and pLaIs56. These clones hybridized to both Leymus and Psathyrostachys on Southern blots — no clone hybridized to only one of these genera. Both Southern blot and fluorescence in situ hybridization (FISH) experiments showed that all the clones contained dispersed repetitive sequences. They painted all and whole chromosomes uniformly except at centromeres, telomeres, and nucleolar organiser regions. Three of these clones, i.e., pLmIs1, pLmIs44, and pLmIs53, were essentially specific to Leymus and Psathyrostachys — little or no hybridization was detected in other genera such as Triticum, Hordeum, Thinopyrum, or Elymus. Sequence analysis further revealed that the clones were part of retroelements. In particular, the clone pLmIs44 produced hybridization profiles suitable for analysis of genetic relatedness among species. The present study shows that Leymus and Psathyrostachys share the same basic genome, Ns, and therefore provides strong evidence for combining these two genera.Key words: Triticeae, Leymus, Psathyrostachys, genome-specific sequences, retrotransposons.

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