Relationships among Nicotiana species revealed by the 5S rDNA spacer sequence and fluorescence in situ hybridization

To investigate phylogenetic relationships in Nicotiana, the intergenic spacer sequences of 5S rDNA were analyzed in species with 2n=18, 20 or 24, and amphidiploid species with 2n=48. The chromosomal localization of the 5S rDNA was determined by fluorescence in situ hybridization (FISH). In species with 2n=24 and their descendants, a major 5S rDNA-specific PCR fragment of 400–650 bp was obtained. The amphidiploid species contained similar length of 5S rDNA units derived from putative diploid progenitors. Among the five clones from each representative PCR fragment, some nucleotide exchanges and length heterogeneity were observed. The latter was due to variation in the spacer region, such as differences in the length of poly A and/or poly T tracts as well as insertions/deletions. Interspecific comparisons of each 5S rDNA sequence demonstrated that the spacer sequence could be divided into three regions. Excluding gaps from the aligned spacer sequences of 5S rDNA, phylogenetic trees were constructed. Each phylogenetic tree showed an almost identical topology even if different algorithms were applied. The chromosomal locations of the 5S rDNA in each species correlated with the phylogenetic topology. The phylogenetic trees were generally in agreement with the current classification. Received: 15 January 2001 / Accepted: 15 February 2001     

Physical mapping of 5S and 18S-26S ribosomal RNA gene families inAllium victorialis var.platyphyllum

A physical map of the 5S and 18S–26S rRNA genes was determined using bi-color fluorescencein situ hybridization technique inA. victorialis var.platyphyllum. 5S rRNA genes were positioned in the intercalary regions of the short arms in homologous chromosomes 6. Two major loci of the 18S-26S rRNA genes were detected in the secondary constrictions flanking with a pair of satellite and terminal region of short arm in chromosome 4. And two additional minor loci were heterotype, representing one signal on the terminal region of the short arm in one homolog of chromsome 2, and other on one homolog of chromosome 6 with linked 5S rRNA loci. In addition chromomycin A₃ (CMA,) fluorescent banding method was used to identify the relation between Nucleolus Organizer Region (NOR) sites and CMA, positive heterochromatin sites. In homologous chromosome 4 showing 18S–26S rDNA hybridization signals revealed also distinct CMA, positive band.     

Evolution of 5S rDNA units and their chromosomal localization in Allium cepa and Allium schoenoprasum revealed by microdissection and FISH

Allium cepa and Allium schoenoprasum each possess 5S rDNA units of two different sizes. The evolution of the two repeat units and their chromosomal localization were investigated. A. cepa has 5S rDNA loci in the proximal and distal regions of the short arm of chromosome 7. When the proximal and distal segments of the short arm of chromosome 7 were microdissected separately, and used as templates for PCR, the short and long 5S rDNA fragments were amplified predominantly from the proximal and distal segments, respectively. The nucleotide sequence of the long 5S rDNA unit resulted from partial duplication of a non-transcribed spacer (NTS) and the insertion of a unique sequence. FISH using a probe consisting of the unique sequence demonstrated that the long unit was distally localized. In A. cepa, the long 5S rDNA unit is only present distally and the short unit is predominantly located proximally on the short arm of chromosome 7. In A. schoenoprasum, the NTSs of the two different-sized 5S rDNAs had quite different sequences. The two 5S rDNA loci were localized very close together in the interstitial region of chromosome 6. FISH, using long and short 5S rDNA unit probes with a competitor of a 120-bp sequence of the 5S rRNA gene, indicated that the long 5S rDNA unit was localized proximally and the short unit distally. Although the NTSs of the 5S rDNA of A. cepa and A. schoenoprasum had quite different nucleotide sequences, the long 5S rDNA units of A. cepa and A. schoenoprasum share a common 75-bp sequence. This sequence might act in the formation of the long 5S rDNA unit in Allium species.     

Direct and sensitive fluorescence in situ hybridization of 45S rDNA on tomato chromosomes.

We describe a direct and sensitive fluorescence in situ hybridization protocol for plant chromosomes. We labelled 45S rDNA with fluorescein-12-dUTP and hybridized to somatic chromosomes of four tomato genotypes. This technique does not require posthybridization immunocytochemical amplifications. The improved signal sensitivity with this technique allowed identification of new rDNA loci on three pairs of chromosomes, in addition to the previously known locus on chromosome 2. We discuss favorable features of direct fluorescence in situ hybridization for chromosomes fixed on a slide and chromosomes or cells in suspension.     

Analysis of somaclonal variation through tissue culture and chromosomal localization of rDNA sites by fluorescent in situ hybridization in wild Allium tuberosum and a regenerated variant

The effects of basal media and growth regulators on callus initiation and shoot regeneration have been investigated in wild Allium tuberosum (2n = 4x = 32). Callus initiation was greatest from flower bud explants cultured on MS medium supplemented with 2,4-D and BA at 1 mg l⁻¹ each. Maximum number of shoots was obtained from callus grown on MS medium supplemented with NAA and BA at 0.2 and 2 mg l⁻¹, respectively. The chromosome analysis of regenerants derived from callus revealed variation in ploidy, such as 2n = 28, 29, 30, 31, 33 as well as normal tetraploid. During the culture period for two generations, one aneuploid regenerant with 2n = 30 (named At30) showed better viability and growth than tetraploid plants and other aneuploid variants. In a karyotypic analysis of At30, the chromosomal positions of 5S and 18S-5.8S-26S rDNA were physically mapped by fluorescent in situ hybridization and compared to chromosomes of wild type A. tuberosum. Both wild type A. tuberosum and At30 exhibited two sets of 5S rDNA sites, one on the proximal position of the short arm of chromosome 3, and the other on the intercalary region on the long arm of chromosome 6. There was one 18S-5.8S-26S rDNA site in the secondary constriction including flanking short chromosomal segments of satellite and terminal regions on the short arm of chromosome 8 in wild type A. tuberosum. However, At30 showed only three labelled chromosome 8 indicating that this was one of the lost chromosomes of At30. This revised version was published online in June 2006 with corrections to the Cover Date.     

Cytogenetic study in Corydoras britskii (Siluriformes: Callichthyidae), using different chromosomal banding and fluorescence hybridization in situ with rDNA probes

Cytogenetic analyses were performed on Corydoras britskii from the Miranda River basin, an important river located in the Pantanal, Mato Grosso do Sul State, Brazil. The karyotype of this species comprises 90 chromosomes and a karyotype formula of 4m + 10 sm + 22 st + 54a. The nucleolus organizer regions were detected by impregnation with silver nitrate and FISH with an 18S rDNA probe on the short arm of three acrocentric chromosomes. The constitutive heterochromatin is distributed in pericentromeric and interstitial positions, and also associated with the NORs. The HinfI restriction endonuclease was used and showed homology with practically all types of heterochromatin observed in C. britskii, except for two interstitial heterochromatic blocks present in a subtelocentric pair. The fluorochrome staining evidenced six chromosomes with chromomycin-positive signals indicating that both the heterochromatin interspersed with NORs and some heterochromatic blocks were rich in GC base pairs. FISH using a 5S rDNA probe revealed the presence of these regions in only one subtelocentric pair in the interstitial position. The obtained data substantiate the karyotype diversity of the genus Corydoras and provide novel information about the composition of heterochromatin and location of 5S and 18S rDNA sites.     

Microbial community of a volcanic mudspring in the Philippines as revealed by 16S rDNA sequence analysis and fluorescence in situ hybridization

Mt. Makiling Mudspring in Laguna, Philippines is a thermophilic, acidophilic environment that previously has been shown to harbor novel microorganisms. We assessed the microbial community that exists at this volcanic mudspring using 16S rRNA-based approaches. DNA was extracted from solfataric soils and sediments taken from Mudspring. The 16S rDNA was PCR amplified using universal (519F-1392R) and archaeal-specific (23FPL-1391R) primer pairs, cloned, and sequenced. Phylogenetic analysis of the cloned 16S rDNA showed that eleven clones clustered with, and therefore related to Sulfolobus tokodaii 7 and two clones clustered with S. solfataricu, S. shibatae and S. islandicus. Three clone sequences were related to those found in thermophilic chalcopyrite (CuFeS₂), a copper sulfuric ore from bioleaching reactors. One clone had low similarity (95% identity) with uncultured archaeon clone KOZ184. Fluorescence in situ hybridization (FISH) analysis revealed that about 71% of the microbial community present in the Mudspring belong to domain Archaea of which 63% were Crenarchaeota and 8% were Euryarchaeota. Seventeen percent (17%) of the population consisted of bacteria as indicated by the positive hybridization with the BACT338 probe, and the remaining 12% are unidentified. This study is the first attempt to use molecular techniques in any environment in the Philippines.     

A populational survey of 45S rDNA polymorphism in the Jefferson salamander Ambystoma jeffersonianum revealed by fluorescence in situ hybridization （FISH）

The chromosomal localization of 45S ribosomal RNA genes in Ambystoma jeffersonianum was determined by fluorescence in situ hybridization with 18S rDNA fragment as a probe (FISH-rDNA). Our results revealed the presence of rDNA polymorphism among A.jeffersonianum populations in terms of number, location and FISH signal intensity on the chromosomes. Nine rDNA cytotypes were found in ten geographically isolated populations and most of them contained derivative rDNA sites. Our preliminary study provides strong indication of karyotypic diversification of A.jeffersonianum that is demonstrated by intraspecific variation of 45S rDNA cytotypes. rDNA cytotype polymorphism has been described in many other caudate amphibians. We predict that habitat isolation, low dispersal ability and decline of effective population size could facilitate the fixation and accumulation of variable rDNA cytotypes during their chromosome evolution [Current Zoology 55(2):145-149,2009].     

Chromosome analysis by fluorescence in situ hybridization of callus-derived regenerants in Allium cyaneum R.

Investigations were performed to confirm the optimal in vitro culture condition for callus induction and plant regeneration, to observe if somoclonal variation occurs among regenerated plants at the ploidy level and to analyse the chromosomal location of 5S and 18S-26S rRNA gene families using fluorescence in situ hybridization in callus-derived plants of Allium cyaneum. High-est callus initiation was achieved with bulb explants cultured on MS medium supplemented with 2,4-D and BAP at 1 mg l^–1 each. A total of 195 plants was obtained when using MS medium supplemented with 1 mg l^–1 NAA and 5 mg l^–1 BAP; about 92% were diploid having 2n=16; 8% showed a variation in ploidy level. Using digoxigenin-labelled 5S rRNA and biotin-labelled 18S-26S rRNA gene probes, we compared the fluorescence in situ hybridization patterns of autotetraploid plants with the A. cyaneum wild type. The 5S rRNA gene sites were detected on the interstitial region in the short arm of chromosome 4 and on the interstitial region in both arms of chromosome 7. The 18S-26S rRNA gene sites were detected on the terminal region of the short arm, including the satellite of chromosome 5, as well as on a part of chromosome B. The chromosomal location of both rRNA genes in regenerated autotetraploid plants corresponded to those of the wild species. Received: 20 March 1998 / Revision received: 15 June 1998 / Accepted: 8 July 1998     

Preliminary karyotype and chromosomal localization of ribosomal DNA sites in white spruce using fluorescence in situ hybridization.

We have localized the major ribosomal DNA (rDNA) loci on metaphase chromosomes and in interphase nuclei of white spruce (2n = 24) by fluorescence in situ hybridization. Hybridization sites of the biotin-labelled rDNA probe were detected using antibody-fluorochrome conjugates and a confocal laser scanning microscope. White spruce has at least 12, and possibly as many as 14, rDNA sites, 1 site present on each of seven separate chromosome pairs. This is one of the highest numbers of rDNA loci yet reported among plant species. The position of the rDNA loci together with secondary constriction patterns permit, for the first time, all homologous pairs of white spruce chromosomes to be distinguished. We discuss the application of molecular cytogenetics in studies relating to the organization and evolution of DNA sequences within conifer genomes.     

The use of double fluorescence in situ hybridization to physically map the positions of 5S rDNA genes in relation to the chromosomal location of 18S-5.8S-26S rDNA and a C genome specific DNA sequence in the genus Avena.

A physical map of the locations of the 5S rDNA genes and their relative positions with respect to 18S-5.8S-26S rDNA genes and a C genome specific repetitive DNA sequence was produced for the chromosomes of diploid, tetraploid, and hexaploid oat species using in situ hybridization. The A genome diploid species showed two pairs of rDNA loci and two pairs of 5S loci located on both arms of one pair of satellited chromosomes. The C genome diploid species showed two major pairs and one minor pair of rDNA loci. One pair of subtelocentric chromosomes carried rDNA and 5S loci physically separated on the long arm. The tetraploid species (AACC genomes) arising from these diploid ancestors showed two pairs of rDNA loci and three pairs of 5S loci. Two pairs of rDNA loci and 2 pairs of 5S loci were arranged as in the A genome diploid species. The third pair of 5S loci was located on one pair of A-C translocated chromosomes using simultaneous in situ hybridization with 5S rDNA genes and a C genome specific repetitive DNA sequence. The hexaploid species (AACCDD genomes) showed three pairs of rDNA loci and six pairs of 5S loci. One pair of 5S loci was located on each of two pairs of C-A/D translocated chromosomes. Comparative studies of the physical arrangement of rDNA and 5S loci in polyploid oats and the putative A and C genome progenitor species suggests that A genome diploid species could be the donor of both A and D genomes of polyploid oats. Key words : oats, 5S rDNA genes, 18S-5.8S-26S rDNA genes, C genome specific repetitive DNA sequence, in situ hybridization, genome evolution.     

Incidence of chromosomal mosaicism in human embryos at different developmental stages analyzed by fluorescence in situ hybridization

Chromosomal mosaicism has been reported in in vitro-cultured embryos at early cleavage stages, as well as in morulae and blastocysts. We have assessed the incidence and pattern of mosaicism during in vitro development of human embryos from early-cleavage stages to morula and blastocyst. Fifty spare embryos were fixed for fluorescence in situ hybridization (FISH) analysis for chromosomes X, Y, 13, 18, and 21 on days 2 or 3 (4- to 10-cell stage) (n = 16), on day 4 (morula stage) (n = 14), on day 5 (pre-expanded blastocyst) (n = 5), and the expanded blastocyst stages (n = 15). Blocked embryos (no cleavage observed within the last 24 hr) were not included. A total of 2367 cells were analyzed. Four early-cleavage stage embryos were found uniformly diploid; all of the others were mosaic for the chromosomes analyzed (mean diploid nuclei 48.3% +/- 28.7). All of the embryos at more advanced developmental stages, except one fully normal morula, had mosaic chromosome constitutions, with an increase in the percentage of diploid cells in morulae, pre-expanded, and expanded blastocysts, respectively (mean diploid nuclei 78.6% +/- 11.7, 66.0% +/- 20.8, 79.6% +/- 12.8), in comparison with earlier stages. Hypotheses about the origin of mosaicism and embryo regulation mechanisms will be discussed.     

Quantitative analysis of chromosomal localization of two human cloned satellite DNA III sequences by in situ hybridization

Chromosomal location of two cloned human satellite DNA III sequences pPD9 and pPD18 has been studied in 30 individuals by in situ hybridization. Pericentromeric localization of the DNA subsets studied was found in practically all chromosomes of the set. The majority of label was observed over the pericentromeric region of chromosome 9 (38.3% for pPD18 clone and 26.2% for pPD9), the short arm of chromosome 15 (17.2% - the pPD9 clone and 10.6% - the pPD18 clone) and the distal part of the long arm of Y chromosome (19.6% - the pPD9 clone and 15.4% - the pPD18 clone). Besides significant interchromosomal differences, moderately pronounced interindividual differences were also detected in the number of grains over the regular sites of the chromosomal location. Pretreatment of slides with DA/DAPI induced differences in the results of quantitative analysis is described.     

Mapping of rDNA on the chromosomes of Eleusine species by fluorescence in situ hybridization

Mapping of rDNA sites on the chromosomes of four diploid and two tetraploid species of Eleusine has provided valuable information on genome relationship between the species. Presence of 18S-5.8S-26S rDNA on the largest pair of the chromosomes, location of 5S rDNA at four sites on two pairs of chromosomes and presence of 18S-5.8S-26S and 5S rDNA at same location on one pair of chromosomes have clearly differentiated E. multiflora from rest of the species of Eleusine. The two tetraploid species, E. coracana and E. africana have the same number of 18S-5.8S-26S and 5S rDNA sites and located at similar position on the chromosomes. Diploid species, E. indica, E. floccifolia and E. tristachya have the same 18S-5.8S-26S sites and location on the chromosomes which also resembled with the two pairs of 18S-5.8S-26S rDNA locations in tetraploid species, E. coracana and E. africana. The 5S rDNA sites on chromosomes of E. indica and E. floccifolia were also comparable to the 5S rDNA sites of E. africana and E. coracana. The similarity of the rDNA sites and their location on chromosomes in the three diploid and two polyploid species also supports the view that genome donors to tetraploid species may be from these diploid species.     

Tentative chromosomal localization of the bovine major histocompatibility complex by in situ hybridization

Summary. A genetic region, most likely the major histocompatibility complex, was assigned to bands q13–23 of cattle chromosome 23 by in situ hybridization using a cloned DNA sequence of a class I gene of the pig major histocompatibility complex.     

Tentative chromosomal localization of the bovine major histocompatibility complex by in situ hybridization

A genetic region, most likely the major histocompatibility complex, was assigned to bands q13-23 of cattle chromosome 23 by in situ hybridization using a cloned DNA sequence of a class I gene of the pig major histocompatibility complex.     

Rapid prenatal diagnosis of chromosomal aneuploidies by fluorescence in situ hybridization: clinical experience with 4,500 specimens.

Detection of chromosome aneuploidies in uncultured amniocytes is possible using fluorescence in situ hybridization (FISH). We herein describe the results of the first clinical program which utilized FISH for the rapid detection of chromosome aneuploidies in uncultured amniocytes. FISH was performed on physician request, as an adjunct to cytogenetics in 4,500 patients. Region-specific DNA probes to chromosomes 13, 18, 21, X, and Y were used to determine ploidy by analysis of signal number in hybridized nuclei. A sample was considered to be euploid when all autosomal probes generated two hybridization signals and when a normal sex chromosome pattern was observed in greater than or equal to 80% of hybridized nuclei. A sample was considered to be aneuploid when greater than or equal to 70% of hybridized nuclei displayed the same abnormal hybridization pattern for a specific probe. Of the attempted analyses, 90.2% met these criteria and were reported as informative to referring physicians within 2 d of receipt. Based on these reporting parameters, the overall detection rate for aneuploidies was 73.3% (107/146), with an accuracy of informative results for aneuploidies of 93.9% (107/114). Compared to cytogenetics, the accuracy of all informative FISH results, euploid and aneuploid, was 99.8%, and the specificity was 99.9%. In those pregnancies where fetal abnormalities had been observed by ultrasound, referring physicians requested FISH plus cytogenetics at a significantly higher rate than they requested cytogenetics alone. The current prenatal FISH protocol is not designed to detect all chromosome abnormalities and should only be utilized as an adjunctive test to cytogenetics. This experience demonstrates that FISH can provide a rapid and accurate clinical method for prenatal identification of chromosome aneuploidies.     

Simultaneous visualization of rDNA clusters and the nucleolus by combining fluorescence in situ hybridization and silver staining.

We designed two procedures to visualize simultaneously clusters of ribosomal RNA genes (rDNA) and the nucleolus in plant cells. The procedures combine fluorescence in situ hybridization (FISH) to visualize the rDNA clusters and silver staining to observe the nucleolus. When FISH is followed by silver staining, many minute FISH signals are localized in the nucleolus, and several large FISH signals are seen on the nucleolar periphery. When FISH was applied to the specimens with silver nitrate staining, large FISH signals were visualized in the nucleoplasm associated with the nucleolar periphery, but no signals were seen in the nucleoli. Thus, the two combinations of FISH and silver staining provided different details regarding the arrangement of rDNA clusters in the nucleolus of plant cells.