[An improved method of genomic in situ hybridization (GISH) for distinguishing closely related genomes of tetraploid and hexaploid wheat species]

An improved modification of genomic in situ hybridization (GISH) was proposed. It allows clear and reproducible discrimination between closely related genomes of both tetraploid and hexaploid wheat species due to preannealing of labeled DNA probes and prehybridization of chromosomal samples with blocking DNA. The method was applied to analyze intergenomic translocations 6A:6B and 1A:6B identified in the IG46147 and IG116188 samples of tetraploid wheat Triticum dicoccoides by C-banding. The structure of the rearranged chromosomes was defined for two translocation variants, and the breakpoints were identified on the chromosome arms. Possible application of the developed GISH variant to study genome reorganizations during speciation of allopolyploid plants in evolution is discussed.

Phylogenetic studies of the genus Cebus (Cebidae-Primates) using chromosome painting and G-banding

BACKGROUND

Chromosomal painting, using whole chromosome probes from humans and Saguinus oedipus, was used to establish karyotypic divergence among species of the genus Cebus, including C. olivaceus, C. albifrons, C. apella robustus and C. apella paraguayanus. Cytogenetic studies suggested that the species of this genus have conservative karyotypes, with diploid numbers ranging from 2n = 52 to 2n = 54.

RESULTS

Banding studies revealed morphological divergence among some chromosomes, owing to variations in the size of heterochromatic blocks. This analysis demonstrated that Cebus species have five conserved human associations (i.e., 5/7, 2/16, 10/16, 14/15, 8/18 and 3/21) when compared with the putative ancestral Platyrrhini karyotype.

CONCLUSION

The autapomorphies 8/15/8 in C. albifrons and 12/15 in C. olivaceus explain the changes in chromosome number from 54 to 52. The association 5/16/7, which has not previously been reported in Platyrrhini, was also found in C. olivaceus. These data corroborate previous FISH results, suggesting that the genus Cebus has a very similar karyotype to the putative ancestral Platyrrhini.

Array painting reveals a high frequency of balanced translocations in breast cancer cell lines that break in cancer-relevant genes

Chromosome translocations in the common epithelial cancers are abundant, yet little is known about them. They have been thought to be almost all unbalanced and therefore dismissed as mostly mediating tumour suppressor loss. We present a comprehensive analysis by array painting of the chromosome translocations of breast cancer cell lines HCC1806, HCC1187 and ZR-75-30. In array painting, chromosomes are isolated by flow cytometry, amplified and hybridized to DNA microarrays. A total of 200 breakpoints were identified and all were mapped to 1 Mb resolution on bacterial artificial chromosome (BAC) arrays, then 40 selected breakpoints, including all balanced breakpoints, were further mapped on tiling-path BAC arrays or to around 2 kb resolution using oligonucleotide arrays. Many more of the translocations were balanced at 1 Mb resolution than expected, either reciprocal (eight in total) or balanced for at least one participating chromosome (19 paired breakpoints). Second, many of the breakpoints were at genes that are plausible targets of oncogenic translocation, including balanced breaks at CTCF, EP300/p300 and FOXP4. Two gene fusions were demonstrated, TAX1BP1-AHCY and RIF1-PKD1L1. Our results support the idea that chromosome rearrangements may play an important role in common epithelial cancers such as breast cancer.

[An analysis on chromosome X, Y and 18 in the spermatozoa of asthenospermia patients by triple-color fluorescence in situ hybridization]

OBJECTIVE

To analyze the numerical aberration of chromosome X, Y and 18 in the spermatozoa of asthenospermia patients by triple-color fluorescence in situ hybridization.

METHODS

The experiment included 10 asthenospermia patients and 5 healthy men with normal semen quality as controls. Fluorescence in situ hybridization (FISH) and probes for chromosomes including X, Y and 18 were used to determine the frequency of the aneuploid of the chromosomes in spermatozoa.

RESULTS

Of the 45,547 spermatozoa counted from the semen samples, the hybridization rate was 99.18%. The frequencies of the chromosome disomies including XX18, XY18, YY18, X1818 and Y1818 were (0.124 +/- -0.086)%, (0.360 +/- 0.380)%, (0.109 +/- 0.195)%, (0.342 +/- 0.746)% and (0.299 +/- 0.564)% in the case group and (0.014 +/- 0.019)%, (0.090 +/- 0.080)%, (0.030 +/- 0.031)%, (0.068 +/- 0.103)% and (0.075 +/- 0.083)% in the control. The sperm aneuploid rate was 9.25% in the former and 2.70% in the latter, with significant difference in between (P< 0.01).

CONCLUSION

Asthenospermia patients have a higher aneuploid rate of sperm chromosome than normal fertile men. However, larger samples are yet to be studied to obtain more scientific evidence.

Human metaphase chromosome FISH using quantum dot conjugates

Fluorescence in situ hybridization (FISH) is a powerful, molecular technique with a wide range of applications in medicine and biology. In medicine, FISH uses genomic and cDNA probes to determine the chromosomal position of genes and DNA sequences, which enables detection of ploidy levels and identification of subtle chromosomal rearrangements. Because of its exquisite sensitivity, FISH often enhances conventional cytogenetic analysis and it can provide either diagnostic or prognostic results for particular chromosomal disorders. To achieve the robust probe signals needed for routine clinical application, typical FISH probes consist of recombinant genomic DNA clones often covering multiple genes. These probes can be readily visualized on metaphase chromosomes as they span tens to hundreds of thousands of nucleotides. Visualization of shorter targets has been performed in many research laboratories, and will have significant advantages once they are available clinically. Toward that end, our goal is to make the signals from these shorter probes more intense. We are utilizing quantum dot conjugates to visualize single copy sequence DNA probes as short as 1500 nucleotides in length.

[Analysis of complex chromosomal aberrations in patients with myelodysplastic syndromes using multiplex fluorescence in situ hybridization combined with whole chromosome painting]

OBJECTIVE

To explore the value of multiplex fluorescence in situ hybridization (M-FISH) in combination with whole chromosome painting (WCP) in the detection of complex chromosomal aberrations (CCAs) in myelodysplastic syndromes (MDS).

METHODS

M-FISH was used in seven MDS patients with R-banding CCAs to refine the complex chromosomal rearrangements, and to identify cryptic translocations and characterization of marker chromosomes. Dual-color WCP procedures were further performed in 7 cases to confirm some rearrangements detected by M-FISH.

RESULTS

M-FISH confirmed all results of R-banding. The composition and origin of 6 kinds of marker chromosomes, 9 kinds of chromosomes with additional material undetermined and 5 kinds of derivative chromosomes undefined by conventional cytogenetics (CC) were defined after M-FISH analysis; four kinds of cryptic translocations overlooked by CC were found on derivative chromosomes and previously normal appearing chromosomes. In addition, M-FISH revealed some nonrandom aberrations: aberrations involving chromosome 17 and -5/5q- were the two most frequent aberrations. Some misclassified and missed chromosomal aberrations by M-FISH were corrected by WCP.

CONCLUSION

M-FISH is a powerful molecular cytogenetic tool in clarification of CCAs. Complementary WCP helps us to identify misclassified and missed chromosomal aberrations by M-FISH. CC in combination with molecular cytogenetic techniques, such as M-FISH and WCP, can unravel complex chromosomal aberrations more precisely.

Karyotype evolution in Rhinolophus bats (Rhinolophidae, Chiroptera) illuminated by cross-species chromosome painting and G-banding comparison

Rhinolophus (Rhinolophidae) is the second most speciose genus in Chiroptera and has extensively diversified diploid chromosome numbers (from 2n = 28 to 62). In spite of many attempts to explore the karyotypic evolution of this genus, most studies have been based on conventional Giemsa staining rather than G-banding. Here we have made a whole set of chromosome-specific painting probes from flow-sorted chromosomes of Aselliscus stoliczkanus (Hipposideridae). These probes have been utilized to establish the first genome-wide homology maps among six Rhinolophus species with four different diploid chromosome numbers (2n = 36, 44, 58, and 62) and three species from other families: Rousettus leschenaulti (2n = 36, Pteropodidae), Hipposideros larvatus (2n = 32, Hipposideridae), and Myotis altarium (2n = 44, Vespertilionidae) by fluorescence in situ hybridization. To facilitate integration with published maps, human paints were also hybridized to A. stoliczkanus chromosomes. Our painting results substantiate the wide occurrence of whole-chromosome arm conservation in Rhinolophus bats and suggest that Robertsonian translocations of different combinations account for their karyotype differences. Parsimony analysis using chromosomal characters has provided some new insights into the Rhinolophus ancestral karyotype and phylogenetic relationships among these Rhinolophus species so far studied. In addition to Robertsonian translocations, our results suggest that whole-arm (reciprocal) translocations involving multiple non-homologous chromosomes as well could have been involved in the karyotypic evolution within Rhinolophus, in particular those bats with low and medium diploid numbers.

Monitoring translocations by M-FISH and three-color FISH painting techniques: a study of two radiotherapy patients

PURPOSE

To compare translocation rate using either M-FISH or FISH-3 in two patients treated for head and neck cancer, with a view to retrospective dosimetry.

MATERIALS AND METHODS

Translocation analysis was performed on peripheral blood lymphocyte cultures from blood samples taken at different times during the radiotherapy (0 Gy, 12 Gy and 50 Gy) and a few months after the end of the treatment (follow-up).

RESULTS

Estimated translocation yield varied according to the FISH technique used. At 50 Gy and follow-up points, the translocation yields were higher with FISH-3 than with M-FISH. This difference can be attributed to three events. First, an increase in complex aberrations was observed for 50 Gy and follow-up points compared with 0 Gy and 12 Gy points. Second, at the end of treatment for patient A, involvement of chromosomes 2, 4, 12 in translocations was less than expected according to the Lucas formula. Third, a clone bearing a translocation involving a FISH-3 painted chromosome was detected.

CONCLUSIONS

More translocations were detected with M-FISH than with FISH-3, and so M-FISH is expected to improve the accuracy of chromosome aberration analyses in some situations.

Application of arm-specific painting probes of horse X chromosome for karyotype analysis in an infertile Hutsul mare with 64,XX/65,XX+Xp karyotype: case report

A 5-year-old infertile Hutsul mare was subjected to cytogenetic analysis. Fluorescence in situ hybridisation (FISH) using the equine Xp and Xq chromosome painting probes was carried out on chromosome preparations obtained after blood lymphocyte culture. These probes were generated by chromosome microdissection and a large number of spreads was analysed (525). The karyotype formula of the analysed mare was 64,XX/65,XX+Xp with the ratio of the two lines being 99.4 and 0.6, respectively. The goal of the study was to apply chromosome microdissection and the FISH technique for cytogenetic diagnostics.

Comparative chromosome painting map between two Ryukyu spiny rat species, Tokudaia osimensis and Tokudaia tokunoshimensis (Muridae, Rodentia)

Ryukyu spiny rats (genus Tokudaia) are indigenous species that are confined to three islands of the Nansei Shoto archipelago, Amami-Oshima, Tokunoshima and Okinawa-jima, Japan. Tokudaia tokunoshimensis from Tokunoshima Island and Tokudaia osimensis from Amami-Oshima Island are closely related taxonomically, although their karyotypes are quite different: the diploid chromosome numbers and sex chromosome constitution are 2n=45, X0/X0 for T. tokunoshimensis and 2n=25, X0/X0 for T. osimensis. We conducted comparative chromosome painting with chromosome-specific DNA probes of the laboratory mouse (Mus musculus) to molecularly examine the chromosome homology between T. tokunoshimensis and T. osimensis, and deduced a possible ancestral karyotype of Tokudaia species and the process of evolutionary chromosome rearrangements. The proposed ancestral karyotype with the diploid number of 2n=48, XX/XY was similar to the karyotype of T. tokunoshimensis, and the karyotype of T. osimensis would then have been established through at least 14 chromosomal changes, mainly centric fusion and tandem fusion, from the ancestral karyotype. The close karyological relationship between the ancestral karyotypes of Tokudaia and Apodemus also suggests that the chromosomal evolution in the Tokudaia-Apodemus lineage has been very slow and has accelerated only recently in the branch leading to T. osimensis.

Chromosome repatterning in three representative parrots (Psittaciformes) inferred from comparative chromosome painting

Parrots (order: Psittaciformes) are the most common captive birds and have attracted human fascination since ancient times because of their remarkable intelligence and ability to imitate human speech. However, their genome organization, evolution and genomic relation with other birds are poorly understood. Chromosome painting with DNA probes derived from the flow-sorted macrochromosomes (1-10) of chicken (Gallus gallus, GGA) has been used to identify and distinguish the homoeologous chromosomal segments in three species of parrots, i.e., Agapornis roseicollis (peach-faced lovebird); Nymphicus hollandicus (cockatiel) and Melopsittacus undulatus (budgerigar). The ten GGA macrochromosome paints unequivocally recognize 14 to 16 hybridizing regions delineating the conserved chromosomal segments for the respective chicken macrochromosomes in these representative parrot species. The cross-species chromosome painting results show that, unlike in many other avian karyotypes with high homology to chicken chromosomes, dramatic rearrangements of the macrochromosomes have occurred in parrot lineages. Among the larger GGA macrochromosomes (1-5), chromosomes 1 and 4 are conserved on two chromosomes in all three species. However, the hybridization pattern for GGA 4 in A. roseicollis and M. undulatus is in sharp contrast to the most common pattern known from hybridization of chicken macrochromosome 4 in other avian karyotypes. With the exception of A. roseicollis, chicken chromosomes 2, 3 and 5 hybridized either completely or partially to a single chromosome. In contrast, the smaller GGA macrochromosomes 6, 7 and 8 displayed a complex hybridization pattern: two or three of these macrochromosomes were found to be contiguously arranged on a single chromosome in all three parrot species. Overall, the study shows that translocations and fusions in conjunction with intragenomic rearrangements have played a major role in the karyotype evolution of parrots. Our inter-species chromosome painting results unequivocally illustrate the dynamic reshuffling of ancestral chromosomes among the karyotypes of Psittaciformes.

Generation of FISH probes using laser microbeam microdissection and application to clinical molecular cytogenetics

Chromosome microdissection and the reverse FISH technique is one of the most useful methods for the identification of structurally abnormal chromosomes. In particular, the laser microbeam microdissection (LMM) method allows rapid isolation of a target chromosome or a specific region of chromosomes without damage of genetic materials and contamination. Isolated chromosomes were directly amplified by the degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), and then the FISH probes labeled with spectrum green- or spectrum red-dUTP were generated by nick-translation. Whole chromosome painting (WCP) probes were successfully generated from only 5 copies of the chromosome. With this method, we produced 24 WCP probes for each human chromosome. We also tried to characterize a marker chromosome, which seemed to be originated from chromosome 11 on conventional banding technique. The marker chromosomes were isolated by the LMM method and analyzed by reverse FISH. We elucidated that the marker chromosome was originated from the short arm of chromosome 5 (5p11-->pter). A fully automated and computer-controlled LMM method is a very simple laboratory procedure, and enables rapid and precise characterization of various chromosome abnormalities.

Cross-species chromosome painting among camel, cattle, pig and human: further insights into the putative Cetartiodactyla ancestral karyotype

The great karyotypic differences between camel, cattle and pig, three important domestic animals, have been a challenge for comparative cytogenetic studies based on conventional cytogenetic approaches. To construct a genome-wide comparative chromosome map among these artiodactyls, we made a set of chromosome painting probes from the dromedary camel (Camelus dromedarius) by flow sorting and degenerate oligonucleotide primed-PCR. The painting probes were first used to characterize the karyotypes of the dromedary camel (C. dromedarius), the Bactrian camel (C. bactrianus), the guanaco (Lama guanicoe), the alpaca (L. pacos) and dromedary x guanaco hybrid karyotypes (all with 2n = 74). These FISH experiments enabled the establishment of a high-resolution GTG-banded karyotype, together with chromosome nomenclature and idiogram for C. dromedarius, and revealed that these camelid species have almost identical karyotypes, with only slight variations in the amount and distribution patterns of heterochromatin. Further cross-species chromosome painting between camel, cattle, pig and human with painting probes from the camel and human led to the establishment of genome-wide comparative maps. Between human and camel, pig and camel, and cattle and camel 47, 53 and 53 autosomal conserved segments were detected, respectively. Integrated analysis with previously published comparative maps of human/pig/cattle enabled us to propose a Cetartiodactyla ancestral karyotype and to discuss the early karyotype evolution of Cetartiodactyla. Furthermore, these maps will facilitate the positional cloning of genes by aiding the cross-species transfer of mapping information.

Fluorescence in situ hybridization using an old world monkey Y chromosome specific probe combined with immunofluorescence staining on rhesus monkey tissues

To date, there is no commercially available Y chromosome probe that can be used for fluorescence in situ hybridization (FISH) for the male rhesus monkey. We have recently generated a probe for FISH with high specificity to the short arm of the rhesus monkey Y chromosome. In this study, we further describe a method that keeps the integrity of tissue-specific antigenic structures for immunofluorescence staining subsequent to FISH on paraffin-embedded rhesus monkey tissues. We have examined this technique in combination with an epithelial cell-specific marker, cytokeratin 8/18 (CK8/18), on various tissues, including jejunum, liver, kidney, and pancreas. CK8/18 and Y chromosome signals were distinctly seen simultaneously on epithelial cells from the same tissue section from male but not female monkeys. These studies indicate that our FISH immunofluorescence technique can be reliably used to identify and phenotype male cells in paraffin-embedded rhesus monkey tissues.

COBRA: combined binary ratio labeling of nucleic-acid probes for multi-color fluorescence in situ hybridization karyotyping

Combined binary ratio labeling (COBRA) is designed to increase the multiplicity of fluorescence in situ hybridization (FISH)--i.e., the number of targets that can be distinguished simultaneously. In principle, chemical (ULS), enzymatic (nick translation or random priming) or PCR-based labeling procedures of probes can be used. The method was originally designed to label chromosome-painting probes, but has also been used for probe sets specific for subtelomeric regions. COBRA imaging requires a digital fluorescence microscope equipped for sequential excitation and recording of color images. Staining of all 24 human chromosomes is accomplished with only four fluorochromes, compared with five for methods based on combinatorial labeling. The COBRA procedure takes approximately 6 h laboratory work, 2-3 d incubation and a few hours imaging. The method is routinely applied in research (cultured cells from human or mouse origin) or to support clinical diagnosis, such as postnatal and perinatal genetic testing and in solid tumors.

Detection of equine X chromosome mosaicism in a mare using an equine X whole chromosome painting probe (WCPP)--a case report

An infertile mare with hypoplastic ovaries was subjected to cytogenetic analysis. Fluorescence in situ hybridisation (FISH) using the equine X whole chromosome painting probe (WCPP) was carried out on a chromosome preparation obtained from blood lymphocyte culture. The number of analysed spreads was high (235) and in the X chromosome aneuploidy in mosaic form was diagnosed. The karyotype formula was 63,X / 64,XX / 65,XXX. The ratio of the three lines was 15%, 82% and 3%, respectively. The application of the FISH technique with WCPP is discussed.

[The clinical application of whole chromosome painting probes in preimplantation genetic diagnosis for translocation carriers]

OBJECTIVE

To make preimplantation genetic diagnosis (PGD) for female translocation carriers by analyzing first polar bodies (1PBs) with whole chromosome painting probe (WCP).

METHODS

WCP was used in fluorescence in situ hybridization (FISH) analysis of 1PBs for four female Robertsonian carriers presented for PGD with 45 XX, der(13;14)(q10;q10) karyotype. All the patients underwent ovarian stimulation and during 6 h after oocyte retrieval 1PBs were biopsied and WCP were used in FISH. On day 3 after fertilization embryos diagnosed as normal or balanced were transferred.

RESULTS

A total of 61 oocytes were collected in 4 PGD cycles. Of the 54 matured oocytes, 50 were biopsied and 45 were fixed successfully. Results were obtained in 40 1PBs. Overall, 74.1% (40/54) oocytes were diagnosed. The fertilization rate and good embryo rate were 64.8% (35/54) and 65.7% (23/35) respectively. Two clinical pregnancies were obtained. One patient delivered a normal female baby with karyotype 46, XX in June 2006. For another patient, the fetus spontaneously aborted at 9th week of pregnancy with karyotype of 45, X confirmed by amniotic villus diagnosis.

CONCLUSION

WCP can differentiate normal, balanced and unbalanced oocytes accurately and can be used as an efficient PGD method for female carriers of translocation.

New immortalized cell lines of patients with small supernumerary marker chromosome: towards the establishment of a cell bank

Sixteen newly established cell lines with small supernumerary marker chromosomes (sSMC) derived from chromosomes 1, 2, 4, 6, 7, 8, 14, 15, 16, 18, 19, 21, and 22 are reported. Two sSMC are neocentric and derived from 15q24.1-qter and 2q35-q36, respectively. Two further cases each present with two sSMC of different chromosomal origin. sSMC were characterized by multicolor fluorescence in situ hybridization for their chromosomal origin and genetic content. Moreover, uniparental disomy of the sister chromosomes of the sSMC was excluded in all nine cases studied for that reason. The 16 cases provide information to establish a refined genotype-phenotype correlation of sSMC and are available for future studies.

Array painting using microdissected chromosomes to map chromosomal breakpoints

Molecular characterization of breakpoints of chromosomal rearrangements is a successful strategy for the identification of candidate disease genes. Mapping translocation breakpoints and rearranged chromosomal boundaries is labor intensive and/or time consuming. Here, we present a novel and rapid procedure to map such chromosomal breakpoints by hybridizing amplified microdissection derived DNA of aberrant chromosomes to arrays containing genomic clones. We illustrate the potential of the technique by molecularly delineating the breakpoints in five small supernumerary marker chromosomes (sSMC) and mapping the breakpoints of five different chromosomal translocations.

Reconstruction of the ancestral ferungulate karyotype by electronic chromosome painting (E-painting)

By comparing high-coverage and high-quality whole genome sequence assemblies it is now possible to reconstruct putative ancestral progenitor karyotypes, here called protokaryotypes. For this study we used the recently described electronic chromosome painting technique (E-painting) to reconstruct the karyotype of the 85 million-year-old (MYA) ferungulate ancestor. This model is primarily based on dog (Canis familiaris) and cattle (Bos taurus) genome data and is highly consistent with comparative gene mapping and chromosome painting data. The protokaryotype bears 23 autosomal chromosome pairs and the sex chromosomes and preserves most of the chromosomal associations described previously for the boreo-eutherian protokaryotype. The model indicates that five interchromosomal rearrangements occurred during the transition from the boreo-eutherian to the ferungulate ancestor. From there on 66 further interchromosomal rearrangements took place in the lineage leading to cattle and 61 further interchromosomal rearrangements in the lineage to dog.

Triploid origin of the gibel carp as revealed by 5S rDNA localization and chromosome painting

5S ribosomal DNA (rDNA) was isolated and sequenced from the gibel carp Carassius auratus gibelio with 162 chromosomes and crucian carp Carassius auratus with 100 chromosomes, and fluorescent probes for chromosome localization were prepared to ascertain the ploidy origin and evolutionary relationship between the two species. Using fluorescence in-situ hybridization (FISH), major 5S rDNA signals were localized to the short arms of three subtelocentric chromosomes in the gibel carp and to the short arms of two subtelocentrics in the crucian carp. In addition, some minor signals were detected on other chromosomes of both species. Simultaneously, six chromosomes were microdissected from the gibel carp metaphase spreads using glass needles, and the isolated chromosomes were amplified in vitro by degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR). Significantly, when the DOP-PCR-generated probes prepared from each single chromosome were hybridized, three same-sized chromosomes were painted in each gibel carp metaphase, whereas only two painted chromosomes were observed in each crucian carp metaphase spread. The data indicate that gibel carp is of triploid origin in comparison with diploid crucian carp.

Probing the W chromosome of the codling moth, Cydia pomonella, with sequences from microdissected sex chromatin

The W chromosome of the codling moth, Cydia pomonella, like that of most Lepidoptera species, is heterochromatic and forms a female-specific sex chromatin body in somatic cells. We collected chromatin samples by laser microdissection from euchromatin and W-chromatin bodies. DNA from the samples was amplified by degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) and used to prepare painting probes and start an analysis of the W-chromosome sequence composition. With fluorescence in situ hybridization (FISH), the euchromatin probe labelled all chromosomes, whereas the W-chromatin DNA proved to be a highly specific W-chromosome painting probe. For sequence analysis, DOP-PCR-generated DNA fragments were cloned, sequenced, and tested by Southern hybridization. We recovered single-copy and low-copy W-specific sequences, a sequence that was located only in the W and the Z chromosome, multi-copy sequences that were enriched in the W chromosome but occurred also elsewhere, and ubiquitous multi-copy sequences. Three of the multi-copy sequences were recognized as derived from hitherto unknown retrotransposons. The results show that our approach is feasible and that the W-chromosome composition of C. pomonella is not principally different from that of Bombyx mori or from that of Y chromosomes of several species with an XY sex-determining mechanism. The W chromosome has attracted repetitive sequences during evolution but also contains unique sequences.

Banding pattern of A and B chromosomes of Prochilodus lineatus (Characiformes, Prochilodontidae), with comments on B chromosomes evolution

B chromosomes in Prochilodus lineatus, a migratory neotropical fish, were analyzed in a comparative study among populations from the Dourada lagoon (State of Paraná, Brazil) and from Mogi-Guaçu river (State of São Paulo, Brazil). The data on C-banding and fluorescent in situ hybridization with a satellite DNA probe (SATH1), indicate that the small metacentric B chromosome might correspond to an isochromosome. On the other hand, both populations presented a distinct set of B chromosomes, differentiated either by their number and by the presence of variant B types in the population from Mogi-Guaçu river. The present results indicate that the B chromosomes of P. lineatus should have an ancient origin, and have undergone a differential evolutionary pathway among distinct populations.

Application of multicolor banding for identification of complex chromosome 18 rearrangements

Multicolor chromosome banding (mBAND) is a recently developed technique that allows the delineation of chromosomal regions with a resolution of a few megabase pairs. The resolution of mBAND is slightly below that of conventional chromosome banding; however, the color bands have a great value in identifying chromosomal abnormalities, particularly complex chromosome rearrangements, and intrachromosome exchanges (ie, inversions, deletions, duplications, and insertions). These abnormalities cannot be defined easily by conventional cytogenetic analysis or chromosome paint. In this report, we present the application of the mBAND analysis for identification of complex intrachromosome rearrangements of chromosome 18 in a child with dysmorphic features.

Multicolor fluorescence in situ hybridization (FISH) applied to FISH-banding

During the last decade not only multicolor fluorescence in situ hybridization (FISH) using whole chromosome paints as probes, but also numerous chromosome banding techniques based on FISH have been developed for the human and for the murine genome. This review focuses on such FISH-banding techniques, which were recently defined as 'any kind of FISH technique, which provide the possibility to characterize simultaneously several chromosomal subregions smaller than a chromosome arm. FISH-banding methods fitting that definition may have quite different characteristics, but share the ability to produce a DNA-specific chromosomal banding'. While the standard chromosome banding techniques like GTG lead to a protein-related black and white banding pattern, FISH-banding techniques are DNA-specific, more colorful and, thus, more informative. For some, even high-resolution FISH-banding techniques the development is complete and they can be used for whole genome hybridizations in one step. Other FISH-banding methods are only available for selected chromosomes and/or are still under development. FISH-banding methods have successfully been applied in research in evolution- and radiation-biology, as well as in studies on the nuclear architecture. Moreover, their suitability for diagnostic purposes has been proven in prenatal, postnatal and tumor cytogenetics, indicating that they are an important tool with the potential to partly replace the conventional banding techniques in the future.