The molecular characterization of the genome of Muraena helena L. I. Isolation and hybridization of two MboI-restricted DNA fractions

Genome ◽  
1995 ◽  
Vol 38 (4) ◽  
pp. 809-813 ◽  
Author(s):  
G. Pichiri ◽  
M. Nieddu ◽  
R. Mezzanotte ◽  
P. P. Coni ◽  
S. Salvadori ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Electrophoretic Pattern ◽  
Nucleolar Organizer ◽  
Fish Chromosomes ◽  
Highly Repetitive Dna ◽  
Total Dna

To investigate the genome of the anguilliform fish Muraena helena at the molecular level we characterized total DNA by agarose gel electrophoresis after cleavage with AluI, HaeIII, MboI, and DdeI restriction endonucleases. Subsequently, we isolated the DNA from two specific electrophoretic fractions to be used as probes for Southern and in situ hybridization experiments. One such fraction showed an electrophoretic pattern typical of highly repetitive DNA localized in the centromeres of many chromosomes. The other fraction was shown to be located in the nucleolar organizer region, partially coincident with 45S rDNA, and to be composed of highly repetitive sequences.Key words: fish chromosomes, rDNA, highly repetitive DNA.

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.

scholarly journals First chromosome analysis of Thai pufferfish Pao cochinchinensis (Steindachner, 1866)

2020 ◽  
Vol 21 (9) ◽  
Author(s):  
MANACHAYA PISSAPARN ◽  
SUMALEE PHIMPHAN ◽  
PATCHARAPORN CHAIYASAN ◽  
ALONGKLOD TANOAMTONG ◽  
THOMAS LIEHR ◽  
...  
Keyword(s):  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Molecular Cytogenetics ◽  
Nucleolar Organizer ◽  
Chromosome Analysis ◽  
Chromosomal Evolution ◽  
Giemsa Staining ◽  
Heteromorphic Sex Chromosomes ◽  
Almost All

Abstract. Pissaparn M, Phimphan S, Chaiyasan P, Tanoamtong A, Liehr T, Suwannapoom C, Reungsing M, Supiwong W. 2020. First chromosome analysis of Thai pufferfish Pao cochinchinensis (Steindachner, 1866). Biodiversitas 21: 4309-4316. Here first analysis of chromosomes and nucleolar organizer region (NOR) pattern in pufferfish Pao cochinchinensis (Steindachner, 1866) was undertaken. Chromosomal preparations were obtained from kidney of P. cochinchinensis from Chi River basin in Thailand. Chromosomal characteristics were analyzed by Giemsa staining, Ag-NOR banding as well as fluorescence in situ hybridization (FISH) using microsatellites d(CA)15 and d(CGG)10 probes. P. cochinchinensis had 2n = 40 with the fundamental number (NF) 74, both in male and female. The karyotype exhibited 12 metacentric (m), 10 submetacentric (sm), 12 acrocentric (a) and 6 telocentric (t) chromosomes. No differentiated heteromorphic sex chromosomes were observed. NORs were located on short arms adjacent to telomere of the metacentric chromosome pair 4, which coincide with signals of d(CGG)10 probe. FISH with d(CGG)10 sequences were also displayed at the telomeres of most other chromosomes, whereas d(CA)15 repeats highly accumulated throughout almost all entire chromosomes except for centromeric regions. The results of conventional Giemsa staining presented the differentiation even the same genus. The localization of NORs on one pair of chromosomes only is a common characteristic found in many fish groups as well as other vertebrates. Mapping of two distinct microsatellites demonstrated the remarkable chromosomal diversification that characterizes evolution in the genus Pao. Both, conventional and molecular cytogenetics are excellent tools to study, and better understand chromosomal evolution, as well as to uncover biodiversity among fishes.

Molecular cloning and characterization of an unusually large intergenic spacer from the Nor-B2 locus of hexaploid wheat

Genome ◽  
1996 ◽  
Vol 39 (2) ◽  
pp. 288-292 ◽  
Author(s):  
R. K. Sardana ◽  
R. B. Flavell
Keyword(s):  
Key Words ◽  
Ribosomal Dna ◽  
Hexaploid Wheat ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Intergenic Spacer ◽  
Nucleolar Organizer ◽  
Spacer Length ◽  
Spacer Length Variants

An allelic rDNA variant from the Nor-B2 locus of 'Bezostaya' wheat that forms an especially active nucleolus was cloned and characterized. It carries an unusually large intergenic spacer compared with rDNA units in most other wheat genotypes. The additional intergenic length is in the array of 135-bp A repeats and not in other internal repeats. These A repeats have sequences nearly identical to other A repeats described for other alleles. It is suggested therefore that the more active Nor-B2 locus of 'Bezostaya' may be due to the constituent rDNA units possessing a larger array of A repeats. Key words : ribosomal DNA, nucleolar organizer region, A and B repeats, allelic, spacer length variants.

scholarly journals In situ fluorescent visualization of nucleolar organizer region-associated proteins with a thiol reagent.

1993 ◽  
Vol 41 (9) ◽  
pp. 1413-1417 ◽  
Author(s):  
G Méhes ◽  
E Kálmán ◽  
L Pajor
Keyword(s):  
Silver Staining ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
Nucleolar Organizer Regions ◽  
Thiol Reagent ◽  
Sh Group ◽  
Associated Proteins ◽  
Rnase Digestion

Nucleolar organizer regions (NORs) are nucleolus-forming rDNA loops associated with argyrophil proteins, the amount of which varies according to the proliferative state of the cell. It has been presumed that the nucleolar protein-related thiol groups may have a role in selective silver staining. We investigated the nuclear thiol distribution with a fluorescent thiol reagent, coumarinyl-phenyl-maleimide (CPM) in human K-562 myeloblast cultures and found that SH group-related fluorescence was brightest in the area of nucleoli, which became highly selective after RNAse digestion. A remarkable co-localization of AgNOR silver reaction and CPM fluorescence was observed, although occupation of the SH groups by CPM did not prevent the silver staining. We applied the stain to dual-parameter flow cytometry in combination with DNA content measurements, which provide further information on nucleolar function and changes in experimental and pathological specimens.

scholarly journals Repetitive DNA sequences in Crocus vernus Hill (Iridaceae): The genomic organization and distribution of dispersed elements in the genus Crocus and its allies

Genome ◽  
2000 ◽  
Vol 43 (5) ◽  
pp. 902-909 ◽  
Author(s):  
S Frello ◽  
J S Heslop-Harrison
Keyword(s):  
In Situ Hybridization ◽  
Sequence Analysis ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Southern Hybridization ◽  
Genomic Organization ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Taxonomic Structure

Eight clones of repetitive DNA were isolated from Crocus vernus Hill. The genomic organization of the clones was analyzed by in situ hybridization to C. vernus and Southern hybridization to a range of Crocus and other species. Seven clones were used for in situ hybridization. Sequence analysis showed that all eight clones were nonhomologous, and thus represented eight different sequence-families. In situ hybridization showed that six were dispersed in high copy numbers on all chromosomes of the C. vernus genome, whereas one was localized proximal to the secondary constriction, at the NOR (nucleolar organizer region) and was not further analyzed, as it was considered part of the 18S-25S rDNA repeat. Except for short palindromes, none of the sequences showed notable internal structures. Clone pCvKB4 showed homology to the reverse transcriptase gene of Ty1-copia-like retrotransposons; the others showed no homology to known sequences. When used as probes for Southern hybridization, four showed a ladder of 3-4 bands superimposed by irregular patterns, indicating organization in short tandem arrays. Each clone had a unique distribution among Crocus species (12-16 species analyzed with each clone) and six species of Iridaceae, Liliaceae, and Amaryllidaceae; all seven investigated sequences were Iridaceae specific and four were Crocus specific. The species distribution of these seven clones showed notable discrepancies with the taxonomic subdivision of the genus at the subgenus, section, and series levels. The results suggest that the phylogeny and taxonomic structure of the genus Crocus might need reconsideration. The analysis of repetitive DNA as a major and rapidly evolving part of the genome could contribute to the study of species relationships and evolution.Key words: phylogeny, evolution, in situ hybridization, sequence analysis, dispersed elements.

Genomic relationships between maize and its wild relatives

Genome ◽  
1999 ◽  
Vol 42 (6) ◽  
pp. 1201-1207 ◽  
Author(s):  
C Takahashi ◽  
J A Marshall ◽  
M D Bennett ◽  
I J Leitch
Keyword(s):  
Genomic Dna ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Diploid Species ◽  
Nucleolar Organizer ◽  
Wild Relatives ◽  
Tripsacum Dactyloides ◽  
Genomic Relationships ◽  
Genome Donors

Recent molecular studies confirm the long-held theory that maize is a tetraploid, but the identity of the ancestral diploid species remains an enigma. The various hypotheses were investigated using genomic in situ hybridization (GISH). Total genomic DNA from 10 wild relatives of maize were used as probes onto maize chromosomes to see if this could identify the ancestral genome donors in maize. While none of the taxa hybridized to a subset of chromosomes, genomic DNA from Zea mays ssp. mexicana, Z. mays ssp. parviglumis, Z. diploperennis, Tripsacum dactyloides and Coix lacryma-jobi all showed a similar hybridization pattern consisting of a dispersed signal over all maize chromosomes. Moreover, the first four species also showed highly localized subtelomeric signal on the long arms of maize chromosomes 5, 6 ,7, and 8. In contrast, three Sorghum species tested (S. bicolor, S. halapense, and S. versicolor) only showed hybridization at the nucleolar organizer region. In light of recent data on retrotransposon occurrence in maize, the results may provide insights into the timing of speciation of Zea, Tripsacum, and Coix. Data obtained from the tetraploid Z. perennis strongly supported its taxonomic separation from the diploid Z. diploperennis.Key words: Zea, GISH, evolution, Tripsacum, Sorghum.

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