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.

Molecular characterization and chromosomal distribution of species-specific repetitive DNA sequences from Beta corolliflora, a wild relative of sugar beet

Genome ◽  
2000 ◽  
Vol 43 (6) ◽  
pp. 1073-1080 ◽  
Author(s):  
D Gao ◽  
T Schmidt ◽  
C Jung
Keyword(s):  
Sugar Beet ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Southern Hybridization ◽  
Repetitive Dna Sequences ◽  
Wild Relative ◽  
Chromosomal Distribution ◽  
Species Specific ◽  
Specific Sequences

Repetitive DNA sequences have been isolated from a Sau3AI plasmid library of tetraploid Beta corolliflora (2n = 4x = 36), a wild relative of sugar beet (B. vulgaris). The library was screened by differential hybridization with genomic DNA of B. corolliflora and B. vulgaris. When used as probes for Southern hybridization of genomic DNA, six clones were determined to represent highly repetitive DNA families present only in the B. corolliflora genome. Five other sequences were highly repetitive in B. corolliflora and low or single copy in B. vulgaris. The insert size varied between 43 bp and 448 bp. Two sequences pBC1279 and pBC1944 displayed strong homology to a previously cloned satellite DNA from B. nana. With one exception, sequences are tandemly arranged as revealed by a typical ladder pattern after genomic Southern hybridization. The chromosomal distribution of five probes was determined by fluorescence in situ hybridization (FISH) of mitotic metaphases from B. corolliflora and a triploid hybrid between B. vulgaris and B. corolliflora. Three sequences were spread along all chromosome arms of B. corolliflora while one sequence was present on only six chromosomes. The chromosome-specific sequence pBC216 was found in close vicinity to the 5S rDNA located on B. corolliflora chromosome IV. This set of species-specific sequences has the potential to be used as probes for the identification of monosomic alien addition lines and for marker-assisted gene transfer from wild beet to cultivated beet.Key words: Beta vulgaris, FISH, repetitive DNA, species-specific 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.

Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 769-777 ◽  
Author(s):  
Melanie Mehes-Smith ◽  
Paul Michael ◽  
Kabwe Nkongolo
Keyword(s):  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Pinus Monticola ◽  
The Family ◽  
Species Specific ◽  
Rapd And Issr ◽  
Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

scholarly journals Retention of relict satellite DNA sequences in Anemone (Ranunculaceae)

2013 ◽  
Vol 72 (1) ◽  
pp. 1-133 ◽  
Author(s):  
Višnja Besendorfer ◽  
Jelena Mlinarec
Keyword(s):  
Dna Sequences ◽  
Southern Hybridization ◽  
Repeat Unit ◽  
Similar Species ◽  
Genomic Component ◽  
Library Hypothesis ◽  
Species Specific ◽  
Eukaryotic Organisms ◽  
Fish Signal

Abstract Satellite DNAis a genomic component present in virtually all eukaryotic organisms. The turnover of highly repetitive satellite DNAis an important element in genome organization and evolution in plants. Here we study the presence, physical distribution and abundance of the satellite DNAfamily AhTR1 in Anemone. Twenty-two Anemone accessions were analyzed by PCR to assess the presence of AhTR1, while fluorescence in situ hybridization and Southern hybridization were used to determine the abundance and genomic distribution of AhTR1. The AhTR1 repeat unit was PCR-amplified only in eight phylogenetically related European Anemone taxa of the Anemone section. FISH signal with AhTR1 probe was visible only in A. hortensis and A. pavonina, showing localization of AhTR1 in the regions of interstitial heterochromatin in both species. The absence of a FISH signal in the six other taxa as well as weak signal after Southern hybridization suggest that in these species AhTR1 family appears as relict sequences. Thus, the data presented here support the »library hypothesis« for AhTR1 satellite evolution in Anemone. Similar species-specific satellite DNAprofiles in A. hortensis and A. pavonina support the treatment of A. hortensis and A. pavonina as one species, i.e. A. hortensis s.l.

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.

Molecular cytogenetic analysis of durum wheat × tritordeum hybrids

Genome ◽  
1997 ◽  
Vol 40 (3) ◽  
pp. 362-369 ◽  
Author(s):  
J. Lima-Brito ◽  
H. Guedes-Pinto ◽  
G. E. Harrison ◽  
J. S. Heslop-Harrison
Keyword(s):  
In Situ Hybridization ◽  
Plant Breeding ◽  
Durum Wheat ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Tandem Repeats ◽  
Nuclear Architecture ◽  
Molecular Cytogenetics ◽  
Hordeum Chilense

Southern and in situ hybridization were used to examine the chromosome constitution, genomic relationships, repetitive DNA sequences, and nuclear architecture in durum wheat × tritordeum hybrids (2n = 5x = 35), where tritordeum is the fertile amphiploid (2n = 6x = 42) between Hordeum chilense and durum wheat. Using in situ hybridization, H. chilense total genomic DNA hybridized strongly to the H. chilense chromosomes and weakly to the wheat chromosomes, which showed some strongly labelled bands. pHcKB6, a cloned repetitive sequence isolated from H. chilense, enabled the unequivocal identification of each H. chilense chromosome at metaphase. Analysis of chromosome disposition in prophase nuclei, using the same probes, showed that the chromosomes of H. chilense origin were in individual domains with only limited intermixing with chromosomes of wheat origin. Six major sites of 18S–26S rDNA genes were detected on the chromosomes of the hybrids. Hybridization to Southern transfers of restriction enzyme digests using genomic DNA showed some variants of tandem repeats, perhaps owing to methylation. Both techniques gave complementary information, extending that available from phenotypic, chromosome morphology, or isozyme analysis, and perhaps are useful for following chromosomes or chromosome segments during further crossing of the lines in plant breeding programs.Key words: In situ hybridization, molecular cytogenetics, plant breeding, Hordeum chilense, Southern hybridization, durum wheat, hybrids.

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.

Detection of maize DNA sequences amplified in wheat

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 946-950 ◽  
Author(s):  
Juan Zhang ◽  
Bernd Friebe ◽  
Bikram S. Gill
Keyword(s):  
Triticum Aestivum ◽  
Zea Mays ◽  
In Situ Hybridization ◽  
Dna Sequences ◽  
Hexaploid Wheat ◽  
Chinese Spring ◽  
Genomic Dna ◽  
Genomic In Situ Hybridization ◽  
Metaphase Chromosomes

Genomic in situ hybridization to somatic metaphase chromosomes of hexaploid wheat cv. Chinese Spring using biotinylated maize genomic DNA as a probe revealed the existence of amplified maize DNA sequences in five pairs of chromosomes. The in situ hybridization sites were located on chromosomes 1A, 7A, 2B, 3B, and 7B. One pair of in situ hybridization sites was also observed in hexaploid oat. The locations and sizes of in situ hybridization sites varied among progenitor species.Key words: Triticum aestivum, Zea mays, shared DNA sequences, genomic in situ hybridization.

MOLECULAR CLONING OF α-AMYLASE GENES FROM DROSOPHILA MELANOGASTER. I. CLONE ISOLATION BY USE OF A MOUSE PROBE

Genetics ◽  
1985 ◽  
Vol 110 (2) ◽  
pp. 299-312
Author(s):  
Robert M Gemmill ◽  
Jack N Levy ◽  
Winifred W Doane
Keyword(s):  
Drosophila Melanogaster ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Cdna Sequence ◽  
Lambda Phage ◽  
Hybridization Probe ◽  
Class A ◽  
Class B ◽  
Small Set

ABSTRACT A cloned ä-amylase cDNA sequence from the mouse is homologous to a small set of DNA sequences from Drosophila melanogaster under appropriate conditions of hybridization. A number of recombinant lambda phage that carry homologous Drosophila genomic DNA sequences were isolated using the mouse clone as a hybridization probe. Putative amylase clones hybridized in situ to one or the other of two distinct sites in polytene chromosome 2R and were assigned to one of two classes, A and B. Clone λDm32, representing class A, hybridizes within chromosome section 53CD. Clone λDm65 of class B hybridizes within section 54A1-B1. Clone λDm65 is homologous to a 1450- to 1500-nucleotide RNA species, which is sufficiently long to code for α-amylase. No RNA homologous to λDm32 was detected. We suggest that the class B clone, λDm65, contains the functional Amy structural gene(s) and that class A clones contain an amylase pseudogene.

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.

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