Molecular cytogenetic analysis of supernumerary heterochromatic segments in Rumex acetosa

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 391-397 ◽  
Author(s):  
Fukashi Shibata ◽  
Masahiro Hizume ◽  
Yuzo Kuroki
Keyword(s):  
In Situ Hybridization ◽  
Copy Number ◽  
Tandem Repeats ◽  
Mitotic Chromosomes ◽  
Dioecious Plant ◽  
Rumex Acetosa ◽  
Interphase Nuclei ◽  
Heterochromatic Segment ◽  
Molecular Cytogenetic

The dioecious plant Rumex acetosa shows intraspecific karyotype variation, caused by supernumerary heterochromatic segments or DAPI (4',6-diamidino-2 phenylindole)-bands at the ends of the short arms of three pairs of autosomes. A DNA sequence (RAE730) specific to the supernumerary heterochromatic segments was cloned and sequenced. RAE730 was about 730 bp and AT-rich (71% AT-content). Using fluorescence in situ hybridization (FISH), RAE730 was localized in the supernumerary DAPI-positive heterochromatic segments on several mitotic chromosomes and chromocenters in interphase nuclei, but not in the DAPI-bands of Y or B chromosomes. RAE730 was tandemly arranged in the genome, and the copy number varied between plants from 40 000 to 304 000 copies per 2C, corresponding to the relative amount of supernumerary heterochromatic segments per genome. These results indicate that the karyotype variation caused by the supernumerary heterochromatic segment was generated by amplification or reduction of the tandem repeats of RAE730. Key words: Rumex acetosa, repetitive sequence, supernumerary heterochromatic segment, intraspecific karyotype variation, DAPI-band.

Alterations in subtelomeric tandem repeats during early stages of allopolyploidy in wheat

Genome ◽  
2004 ◽  
Vol 47 (5) ◽  
pp. 860-867 ◽  
Author(s):  
E A Salina ◽  
O M Numerova ◽  
H Ozkan ◽  
M Feldman
Keyword(s):  
In Situ Hybridization ◽  
Copy Number ◽  
First Generation ◽  
Tandem Repeats ◽  
Southern Hybridization ◽  
Homoeologous Pairing ◽  
Genomic Changes ◽  
Intergenomic Recombination ◽  
Copy Numbers

The genomic content of the subtelomeric repeated sequences Spelt1 and Spelt52 was studied by dot, Southern, and in situ hybridization in 11 newly synthesized amphiploids of Aegilops and Triticum, and data were compared with the parental plants. Spelt1 had reduced copy numbers in the first generation of three synthetic amphiploids, but two others did not change; Spelt52 was amplified in nine amphiploids and did not change in two. In the second allopolyploid generation, Spelt1 copy number did not change, whereas there was amplification of Spelt52 in some allopolyploids and decreases in others. Neither allopolyploidy level nor the direction of the cross affected the patterns of change in the newly synthesized amphiploids. Changes did not result from intergenomic recombination because similar alterations were noticed in allopolyploids with and without Ph1, a gene that suppresses homoeologous pairing. No differences in Spelt1 and Spelt52 tandem organization were found by Southern hybridization. The significance of these data are discussed in relation to the establishment of newly formed allopolyploids.Key words: Aegilops, genomic changes, polyploidy, subtelomeric tandem repeats, Triticum, wheat.

Detection of retinoblastoma gene copy number in metaphase chromosomes and interphase nuclei by fluorescence in situ hybridization

1992 ◽  
Vol 60 (3-4) ◽  
pp. 190-193 ◽  
Author(s):  
A. Kallioniemi ◽  
O.-P. Kallioniemi ◽  
F.M. Waldman ◽  
L.-C. Chen ◽  
L.-C. Yu ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Retinoblastoma Gene ◽  
Metaphase Chromosomes ◽  
Interphase Nuclei

scholarly journals Fundamentally different repetitive element composition of sex chromosomes in Rumex acetosa

2020 ◽  
Vol 127 (1) ◽  
pp. 33-47
Author(s):  
Wojciech Jesionek ◽  
Markéta Bodláková ◽  
Zdeněk Kubát ◽  
Radim Čegan ◽  
Boris Vyskot ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
X Chromosome ◽  
Sex Chromosomes ◽  
Tandem Repeats ◽  
Sex Chromosome ◽  
Rumex Acetosa ◽  
Dioecious Species ◽  
Y Chromosomes

Abstract Background and Aims Dioecious species with well-established sex chromosomes are rare in the plant kingdom. Most sex chromosomes increase in size but no comprehensive analysis of the kind of sequences that drive this expansion has been presented. Here we analyse sex chromosome structure in common sorrel (Rumex acetosa), a dioecious plant with XY1Y2 sex determination, and we provide the first chromosome-specific repeatome analysis for a plant species possessing sex chromosomes. Methods We flow-sorted and separately sequenced sex chromosomes and autosomes in R. acetosa using the two-dimensional fluorescence in situ hybridization in suspension (FISHIS) method and Illumina sequencing. We identified and quantified individual repeats using RepeatExplorer, Tandem Repeat Finder and the Tandem Repeats Analysis Program. We employed fluorescence in situ hybridization (FISH) to analyse the chromosomal localization of satellites and transposons. Key Results We identified a number of novel satellites, which have, in a fashion similar to previously known satellites, significantly expanded on the Y chromosome but not as much on the X or on autosomes. Additionally, the size increase of Y chromosomes is caused by non-long terminal repeat (LTR) and LTR retrotransposons, while only the latter contribute to the enlargement of the X chromosome. However, the X chromosome is populated by different LTR retrotransposon lineages than those on Y chromosomes. Conclusions The X and Y chromosomes have significantly diverged in terms of repeat composition. The lack of recombination probably contributed to the expansion of diverse satellites and microsatellites and faster fixation of newly inserted transposable elements (TEs) on the Y chromosomes. In addition, the X and Y chromosomes, despite similar total counts of TEs, differ significantly in the representation of individual TE lineages, which indicates that transposons proliferate preferentially in either the paternal or the maternal lineage.

scholarly journals An Approach for Quantitative Assessment of Fluorescence In Situ Hybridization (FISH) Signals for Applied Human Molecular Cytogenetics

2005 ◽  
Vol 53 (3) ◽  
pp. 401-408 ◽  
Author(s):  
Ivan Y. Iourov ◽  
Ilia V. Soloviev ◽  
Svetlana G. Vorsanova ◽  
Viktor V. Monakhov ◽  
Yuri B. Yurov
Keyword(s):  
In Situ Hybridization ◽  
Quantitative Assessment ◽  
Dna Probes ◽  
Interphase Nuclei ◽  
Homologous Chromosomes ◽  
Molecular Cytogenetic ◽  
Cytogenetic Studies ◽  
Chromosomal Heteromorphism ◽  
Somatic Pairing

A number of applied molecular cytogenetic studies require the quantitative assessment of fluorescence in situ hybridization (FISH) signals (for example, interphase FISH analysis of aneuploidy by chromosome enumeration DNA probes; analysis of somatic pairing of homologous chromosomes in interphase nuclei; identification of chromosomal heteromorphism after FISH with satellite DNA probes for differentiation of parental origin of homologous chromosome, etc.). We have performed a pilot study to develop a simple technique for quantitative assessment of FISH signals by means of the digital capturing of microscopic images and the intensity measuring of hybridization signals using Scion Image software, commonly used for quantification of electrophoresis gels. We have tested this approach by quantitative analysis of FISH signals after application of chromosome-specific DNA probes for aneuploidy scoring in interphase nuclei in cells of different human tissues. This approach allowed us to exclude or confirm a low-level mosaic form of aneuploidy by quantification of FISH signals (for example, discrimination of pseudo-monosomy and artifact signals due to over-position of hybridization signals). Quantification of FISH signals was also used for analysis of somatic pairing of homologous chromosomes in nuclei of postmortem brain tissues after FISH with “classical” satellite DNA probes for chromosomes 1, 9, and 16. This approach has shown a relatively high efficiency for the quantitative registration of chromosomal heteromorphism due to variations of centromeric alphoid DNA in homologous parental chromosomes. We propose this approach to be efficient and to be considered as a useful tool in addition to visual FISH signal analysis for applied molecular cytogenetic studies.

scholarly journals Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Liuyang Fu ◽  
Qian Wang ◽  
Lina Li ◽  
Tao Lang ◽  
Junjia Guo ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Physical Mapping ◽  
Tandem Repeats ◽  
Genetic Research ◽  
Diploid Species ◽  
Reference Sequence ◽  
A Genome ◽  
Genome Map ◽  
Chromosomal Variants

Abstract Background Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge. Results A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligo probes were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3 and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1 and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of the peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of the chromosomes. Conclusions The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions.

In Situ Hybridization of Plant Meiotic and Mitotic Chromosomes: Differences in Signal Detection

1992 ◽  
Vol 67 (5) ◽  
pp. 265-267 ◽  
Author(s):  
Melody S. Clark ◽  
John S. Parker
Keyword(s):  
In Situ Hybridization ◽  
Signal Detection ◽  
Mitotic Chromosomes

Diagnosis of aneuploidy by in situ hybridization: Analysis of interphase nuclei

1991 ◽  
Vol 112 (4) ◽  
pp. 1480-1483 ◽  
Author(s):  
S. G. Vorsanova ◽  
Yu. B. Yurov ◽  
G. V. Deryagin ◽  
I. V. Solov'ev ◽  
G. A. Bytenskaya
Keyword(s):  
In Situ Hybridization ◽  
Hybridization Analysis ◽  
Interphase Nuclei

A Centromeric Tandem Repeat Family Originating From a Part of Ty3/gypsy-Retroelement in Wheat and Its Relatives

Genetics ◽  
2003 ◽  
Vol 164 (2) ◽  
pp. 665-672 ◽  
Author(s):  
Zhi-Jun Cheng ◽  
Minoru Murata
Keyword(s):  
In Situ Hybridization ◽  
Tandem Repeats ◽  
Diploid Species ◽  
Upstream Region ◽  
Aegilops Speltoides ◽  
Repeat Family ◽  
B Genome ◽  
Intervening Sequences ◽  
Wild Diploid Species

AbstractFrom a wild diploid species that is a relative of wheat, Aegilops speltoides, a 301-bp repeat containing 16 copies of a CAA microsatellite was isolated. Southern blot and fluorescence in situ hybridization revealed that ∼250 bp of the sequence is tandemly arrayed at the centromere regions of A- and B-genome chromosomes of common wheat and rye chromosomes. Although the DNA sequence of this 250-bp repeat showed no notable homology in the databases, the flanking or intervening sequences between the repeats showed high homologies (>82%) to two separate sequences of the gag gene and its upstream region in cereba, a Ty3/gypsy-like retroelement of Hordeum vulgare. Since the amino acid sequence deduced from the 250 bp with seven CAAs showed some similarity (∼53%) to that of the gag gene, we concluded that the 250-bp repeats had also originated from the cereba-like retroelements in diploid wheat such as Ae. speltoides and had formed tandem arrays, whereas the 300-bp repeats were dispersed as a part of cereba-like retroelements. This suggests that some tandem repeats localized at the centromeric regions of cereals and other plant species originated from parts of retrotransposons.

Abstract LB190: DNAscopeTM: A novel chromogenic in-situ hybridization technology for high-resolution detection of DNA copy number and structural variations

2021 ◽  
Author(s):  
Li-Chong Wang ◽  
Farzaneh Tondnevis ◽  
Courtney Todorov ◽  
Jayson Gaspar ◽  
Aparna Sahajan ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
High Resolution ◽  
Copy Number ◽  
Structural Variations ◽  
Dna Copy Number ◽  
Chromogenic In Situ Hybridization
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