Tandem repeat DNA localizing on the proximal DAPI bands of chromosomes in Larix, Pinaceae

Genome ◽  
2002 ◽  
Vol 45 (4) ◽  
pp. 777-783 ◽  
Author(s):  
Masahiro Hizume ◽  
Fukashi Shibata ◽  
Ayako Matsumoto ◽  
Yukie Maruyama ◽  
Eiji Hayashi ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Genomic Dna ◽  
Repeat Unit ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Repeat Sequence ◽  
Proximal Region

Repetitive DNA was cloned from HindIII-digested genomic DNA of Larix leptolepis. The repetitive DNA was about 170 bp long, had an AT content of 67%, and was organized tandemly in the genome. Using fluorescence in situ hybridization and subsequent DAPI banding, the repetitive DNA was localized in DAPI bands at the proximal region of one arm of chromosomes in L. leptolepis and Larix chinensis. Southern blot hybridization to genomic DNA of seven species and five varieties probed with cloned repetitive DNA showed that the repetitive DNA family was present in a tandem organization in genomes of all Larix taxa examined. In addition to the 170-bp sequence, a 220-bp sequence belonging to the same DNA family was also present in 10 taxa. The 220-bp repeat unit was a partial duplication of the 170-bp repeat unit. The 220-bp repeat unit was more abundant in L. chinensis and Larix potaninii var. macrocarpa than in other taxa. The repetitive DNA composed 2.0–3.4% of the genome in most taxa and 0.3 and 0.5% of the genome in L. chinensis and L. potaninii var. macrocarpa, respectively. The unique distribution of the 220-bp repeat unit in Larix indicates the close relationship of these two species. In the family Pinaceae, the LPD (Larix proximal DAPI band specific repeat sequence family) family sequence is widely distributed, but their amount is very small except in the genus Larix. The abundant LPD family in Larix will occur after its speciation.Key words: AT-rich tandem repetitive DNA, fluorescence in situ hybridization, Larix, proximal DAPI band.

Molecular analyses of a repetitive DNA sequence in wheat (Triticum aestivum L.)

Genome ◽  
2000 ◽  
Vol 43 (3) ◽  
pp. 556-563 ◽  
Author(s):  
P P Ueng ◽  
A Hang ◽  
H Tsang ◽  
J M Vega ◽  
L Wang ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
In Situ Hybridization ◽  
Long Terminal Repeat ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Sequence ◽  
Genomic Dna ◽  
Repeat Unit ◽  
Terminal Repeat ◽  
Genomic Clones

A repetitive sequence designated WE35 was isolated from wheat genomic DNA. This sequence consists of a 320-bp repeat unit and represents approximately 0.002% of the total wheat DNA. It is unidirectionally distributed either continuously or discretely in the genome. Ladder-like banding patterns were observed in Southern blots when the wheat genomic DNA was restricted with endonuclease enzymes EcoRI, HincII, NciI, and NdeI, which is characteristic for tandemly organized sequences. Two DNA fragments in p451 were frequently associated with the WE35 repetitive unit in a majority of λ wheat genomic clones. A 475-bp fragment homologous to the 5'-end long terminal repeat (LTR) of cereal retroelements was also found in some λ wheat genomic clones containing the repetitive unit. Physical mapping by fluorescence in situ hybridization (FISH) indicated that one pair of wheat chromosomes could be specifically detected with the WE35 positive probe p551. WE35 can be considered a chromosome-specific repetitive sequence. This repetitive unit could be used as a molecular marker for genetic, phylogenetic, and evolutionary studies in the tribe Triticeae.Key words: repetitive sequence, genomic DNA, Triticum aestivum, fluorescence in situ hybridization, long terminal repeat.

C-banding and fluorescence in situ hybridization studies of the wheat–alien hybrid 'Agrotana'

Genome ◽  
1994 ◽  
Vol 37 (3) ◽  
pp. 477-481 ◽  
Author(s):  
Jie Xu ◽  
R. L. Conner ◽  
A. Laroche
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Genomic Dna ◽  
Chromosome Engineering ◽  
C Banding ◽  
Chinese Spring Wheat ◽  
Mother Cells ◽  
Alien Chromatin ◽  
Chromosome Segments

'Agrotana', a wheat-alien hybrid (2n = 56), is a potential source of resistance to common root rot, stem rust, wheat streak mosaic virus, and the wheat curl mite. However, the origin of 'Agrotana', reported to be durum wheat × Agropyron trichophorum (pubescent wheatgrass), is uncertain. The objective of this investigation was to determine the chromosome constitution of 'Agrotana' using C-banding and fluorescence in situ hybridization techniques. The F1 hybrid of 'Agrotana' × 'Chinese Spring' wheat showed 7 I + 21 II in 14.9% of the pollen mother cells, evidence of the presence of the A, B, and D genomes in 'Agrotana'. The hybrid had 16 heavily C-banded chromosomes, namely 4A, and 1-7B of wheat, and a translocation that probably involved wheat chromosomes 2A and 2D. In situ hybridization using biotinylated genomic DNA of Ag. trichophorum cv. Greenleaf blocked with CS DNA failed to identify the alien chromosomes in 'Agrotana', indicating that the alien chromosomes were not likely derived from pubescent wheatgrass. In situ hybridization using labelled wheat genomic DNA blocked with 'Agrotana' DNA revealed that 'Agrotana' had 40 wheat, 14 alien, and 2 (a pair) wheat–alien translocated chromosomes. There was no homology between wheat and the alien chromosomes or chromosome segments involved in the wheat–alien recombinant. Two of the seven pairs of alien chromosomes were homoeologous to each other. The ability to identify alien chromatin in wheat using labelled wheat DNA instead of labelled alien DNA will be particularly useful in chromosome engineering of wheat germplasms having alien chromatin of unknown origin.Key words: wheat–alien hybrid, C-banding, fluorescence in situ hybridization, labelled wheat DNA as probe.

Fluorescence in situ hybridization on plant extended chromatin DNA fibers for single-copy and repetitive DNA sequences

2011 ◽  
Vol 30 (9) ◽  
pp. 1779-1786 ◽  
Author(s):  
Kun Yang ◽  
Hecui Zhang ◽  
Richard Converse ◽  
Yong Wang ◽  
Xiaoying Rong ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Single Copy ◽  
Repetitive Dna Sequences

A rapid procedure for the isolation of C0t-1 DNA from plants

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 138-142 ◽  
Author(s):  
Michael S. Zwick ◽  
Robert E. Hanson ◽  
M. Nurul Islam-Faridi ◽  
David M. Stelly ◽  
Rod A. Wing ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Copy Number ◽  
Genomic Dna ◽  
Mammalian Species ◽  
Repetitive Dnas ◽  
Rapid Procedure ◽  
Dna Elements ◽  
Repetitive Dna Elements

In situ hybridization (ISH) for the detection of single- or low-copy sequences, particularly large DNA fragments cloned into YAC or BAC vectors, generally requires the suppression or "blocking" of highly-repetitive DNAs. C0t-1 DNA is enriched for repetitive DNA elements, high or moderate in copy number, and can therefore be used more effectively than total genomic DNA to prehybridize and competitively hybridize repetitive elements that would otherwise cause nonspecific hybridization. C0t-1 DNAs from several mammalian species are commercially available, however, none is currently available for plants to the best of our knowledge. We have developed a simple 1-day procedure to generate C0t-1 DNA without the use of specialized equipment.Key words: C0t-1 DNA, in situ hybridization, BACs, plants.

scholarly journals Comparison Between Integrated Genomic DNA/RNA Profiling and Fluorescence In Situ Hybridization in the Detection of MYC, BCL-2, and BCL-6 Gene Rearrangements in Large B-Cell Lymphomas

2019 ◽  
Vol 153 (3) ◽  
pp. 353-359 ◽  
Author(s):  
Daniel P Cassidy ◽  
Jennifer R Chapman ◽  
Rafael Lopez ◽  
Kyle White ◽  
Yao-Shan Fan ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
B Cell ◽  
Fluorescence In Situ Hybridization ◽  
Genomic Dna ◽  
Standard Of Care ◽  
Gene Rearrangements ◽  
B Cell Lymphomas ◽  
Rna Profiling ◽  
Large B Cell

Abstract Objectives To compare fluorescence in situ hybridization (FISH) and a commercially available sequencing assay for comprehensive genomic profiling (CGP) to determine the best approach to identify gene rearrangements (GRs) in large B-cell lymphomas (LBCLs). Methods Comparison of standard-of-care FISH assays (including a two-probe approach for MYC; break-apart and fusion probes) and an integrated genomic DNA/RNA sequencing CGP approach on a set of 69 consecutive LBCL cases. Results CGP detected GRs, including those involving MYC (1), BCL-2 (3), and BCL-6 (3), not detected by FISH. FISH detected non–IgH-MYC (4) and BCL-6 (2) GRs that were not detected by CGP. In four instances, standalone CGP or FISH testing would have missed a double-hit lymphoma. Conclusions CGP was superior to FISH in the detection of IgH-MYC rearrangements but was inferior for the detection of non–IgH-MYC rearrangements. Our study demonstrates the rationale for development of a customized approach to identify GRs in LBCLs.

Variation in highly repetitive DNA composition of heterochromatin in rye studied by fluorescence in situ hybridization

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1061-1069 ◽  
Author(s):  
A. Cuadrado ◽  
N. Jouve ◽  
C. Ceoloni
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
5S Rdna ◽  
Individual Identification ◽  
Highly Repetitive Dna ◽  
The Individual

The molecular characterization of heterochromatin in six lines of rye has been performed using fluorescence in situ hybridization (FISH). The highly repetitive rye DNA sequences pSc 119.2, pSc74, and pSc34, and the probes pTa71 and pSc794 containing the 25S–5.8S–18S rDNA (NOR) and the 5S rDNA multigene families, respectively, were used. This allowed the individual identification of all seven rye chromosomes and most chromosome arms in all lines. All varieties showed similar but not identical patterns. A standard in situ hybridization map was constructed following the nomenclature system recommended for C-bands. All FISH sites observed appeared to correspond well with C-band locations, but not all C-banding sites coincided with hybridization sites of the repetitive DNA probes used. Quantitative and qualitative differences between different varieties were found for in situ hybridization response at corresponding sites. Variation between plants and even between homologous chromosomes of the same plant was found in open-pollinated lines. In inbred lines, the in situ pattern of the homologues was practically identical and no variation between plants was detected. The observed quantitative and qualitative differences are consistent with a corresponding variation for C-bands detected both within and between cultivars.Key words: fluorescence in situ hybridization, repetitive DNA, rye, Secale cereale, polymorphism.

Genome discrimination by in situ hybridization in Icelandic species of Elymus and Elytrigia (Poaceae: Triticeae)

Genome ◽  
2001 ◽  
Vol 44 (2) ◽  
pp. 275-283 ◽  
Author(s):  
Marian Ørgaard ◽  
Kesara Anamthawat-Jónsson
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Genomic Dna ◽  
Genomic In Situ Hybridization ◽  
Pseudoroegneria Spicata ◽  
Genome Constitution ◽  
Elytrigia Repens ◽  
Elymus Caninus ◽  
Elymus Species

The genome constitution of Icelandic Elymus caninus, E. alaskanus, and Elytrigia repens was examined by fluorescence in situ hybridization using genomic DNA and selected cloned sequences as probes. Genomic in situ hybridization (GISH) of Hordeum brachyantherum ssp. californicum (diploid, H genome) probe confirmed the presence of an H genome in the two tetraploid Elymus species and identified its presence in the hexaploid Elytrigia repens. The H chromosomes were painted uniformly except for some chromosomes of Elytrigia repens which showed extended unlabelled pericentromeric and subterminal regions. A mixture of genomic DNA from H. marinum ssp. marinum (diploid,Xa genome) and H. murinum ssp. leporinum (tetraploid,Xu genome) did not hybridize to chromosomes of the Elymus species or Elytrigia repens, confirming that these genomes were different from the H genome. The St genomic probe from Pseudoroegneria spicata (diploid) did not discriminate between the genomes of the Elymus species, whereas it produced dispersed and spotty hybridization signals most likely on the two St genomes of Elytrigia repens. Chromosomes of the two genera Elymus and Elytrigia showed different patterns of hybridization with clones pTa71 and pAes41, while clones pTa1 and pSc119.2 hybridized only to Elytrigia chromosomes. Based on FISH with these genomic and cloned probes, the two Elymus species are genomically similar, but they are evidently different from Elytrigia repens. Therefore the genomes of Icelandic Elymus caninus and E. alaskanus remain as StH, whereas the genomes of Elytrigia repens are proposed as XXH.Key words: Elymus, Elytrigia, H genome, St genome, in situ hybridization.

Detection of barley chromatin added to wheat by genomic in situ hybridization

Genome ◽  
1991 ◽  
Vol 34 (3) ◽  
pp. 448-452 ◽  
Author(s):  
Y. Mukai ◽  
B. S. Gill
Keyword(s):  
In Situ Hybridization ◽  
Genomic Dna ◽  
Repeat Sequence ◽  
Genomic Clone ◽  
Genomic In Situ Hybridization ◽  
Addition Lines ◽  
Interphase Nuclei ◽  
Nucleolar Organizing Region ◽  
Chromosome Domains

A technique for in situ hybridization is reported that can be used to detect barley chromatin in wheat background using total genomic DNA as a probe. A 1:2 ratio of biotin-labeled genomic DNA of barley to blocking (unlabeled, sheared) DNA of wheat was sufficient to reveal brownish labeled barley chromosome domains against bluish background of unlabeled wheat chromatin in metaphase, prophase, and interphase nuclei of wheat-barley addition lines. Using this procedure, the behavior of specific barley chromosomes was analyzed in interphase and prophase cells. In prophase cells, the 6H chromosome was always associated with a nucleolus. A genomic clone of α-amylase gene (gRAmy56) that contains a barley-specific dispersed repeat sequence was also used to detect barley chromosomes in a wheat background.Key words: Hordeum vulgare, Triticum aestivum, genomic in situ hybridization, biotin, nucleolar organizing region.

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