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PubMed2026

Chromosome painting in plants: history and future perspectives.

Chromosome painting was developed in mammalian species nearly four decades ago and rapidly became a powerful tool for chromosome identification, comparative cytogenetics, and evolutionary genome analysis. Comparative chromosome painting among diverse mammals generated much of the foundational knowledge of chromosome structure, chromosomal rearrangements, and karyotype evolution before the advent of whole-genome sequencing. Although chromosome painting was first demonstrated in plants in 2001, its applications remained largely restricted to a few plant lineages until the development of oligonucleotide (oligo)-based chromosome painting in 2015. During the last decade, oligo-based chromosome painting has transformed plant cytogenetics, enabling many investigations that were previously impossible. These studies have provided new insights into meiotic chromosome pairing, crossover formation, chromosome fusion, karyotype stability, and chromosome evolution across diverse plant lineages. This review summarizes the history of technological development of chromosome painting in plants, highlights major discoveries enabled by oligo-based chromosome painting, and discusses future opportunities, particularly the integration of chromosome painting with three-dimensional chromosome and genome biology.

Chromosome Painting↗
PubMed2005

Defining the orientation of the tandem fusions that occurred during the evolution of Indian muntjac chromosomes by BAC mapping.

The Indian muntjac (Muntiacus muntjak vaginalis) has a karyotype of 2n=6 in the female and 7 in the male, the karyotypic evolution of which through extensive tandem fusions and several centric fusions has been well-documented by recent molecular cytogenetic studies. In an attempt to define the fusion orientations of conserved chromosomal segments and the molecular mechanisms underlying the tandem fusions, we have constructed a highly redundant (more than six times of whole genome coverage) bacterial artificial chromosome (BAC) library of Indian muntjac. The BAC library contains 124,800 clones with no chromosome bias and has an average insert DNA size of 120 kb. A total of 223 clones have been mapped by fluorescent in situ hybridization onto the chromosomes of both Indian muntjac and Chinese muntjac and a high-resolution comparative map has been established. Our mapping results demonstrate that all tandem fusions that occurred during the evolution of Indian muntjac karyotype from the acrocentric 2n=70 hypothetical ancestral karyotype are centromere-telomere (head-tail) fusions.

Animals↗
PubMed1988

Significance of extra 18q- chromosome in Japanese t(14;18)-positive lymphoma.

Karyotype evolution of t(14;18)-positive lymphoma was studied in 13 Japanese patients. The extra 18q- chromosome, found in six of ten patients with complex karyotypes, was the most common change subsequent to a t(14;18)(q32;q21) chromosome translocation. The additional change was interpreted as being a duplication of an 18q- derived from a t(14;18). The six patients had transformed histology of follicular small cleaved cell lymphoma or diffuse large cell lymphoma, and five of them had extranodal expansion associated with a poor prognosis. These findings indicate that the extra 18q-, together with other chromosome abnormalities, is closely associated with the advanced grade disease of t(14;18)-positive lymphoma, and the extra chromosome is evolutionally comparable with the second Philadelphia (Ph1) chromosome often found in the blastic phase of chronic myelocytic leukemia carrying a t(9;22)(q34;q11). In addition, since the extra 18q- is rarely found in American patients with t(14;18)-positive lymphoma, there appears to be a difference in the karyotype evolution between Japanese and American patients.

Chromosome Aberrations↗
PubMed1997

Mapping the distribution of the telomeric sequence (T2AG3)n in rock-wallabies, Petrogale (Marsupialia: Macropodidae), by fluorescence in situ hybridization. I. The penicillata complex.

The eight Petrogale (rock-wallaby) species of the penicillata complex have a variable rate of karyotypic evolution, with species differing from the ancestral karyotype by two to six rearrangements. The distribution of the predominant vertebrate telomeric sequence (T2AG3)n was examined by fluorescence in situ hybridization (FISH) to determine if this sequence is retained during centric fusion events or is involved in other rearrangements. In all submetacentric chromosomes derived by centric fusions, the telomeric sequence was identified at or near the centromere, indicating that the (T2AG3)n sequence is consistently retained. In two acrocentric chromosomes, derived by centromeric transpositions from submetacentric fusion chromosomes, an interstitial signal was observed at the presumed site of the fusion. This represents the identification of a novel mechanism by which the (T2AG3)n sequence may become interstitial. Other interstitial telomeric signals were identified just below the centromere of chromosome 1 and interstitially on chromosome 4 in all eight species of the penicillata complex. These may be related to, respectively, the formation of euchromatic short arms on chromosome 1 and a more ancient rearrangement of chromosome 4 within marsupials.

Animals↗
PubMed2002

[Comparative chromosome painting].

The review of the data on comparative chromosomal painting in mammals is presented. The development of new molecular-cytogenetic methods has resulted in the accumulation of the detailed information on homology of chromosomal segments of more than 50 species from 11 orders. In this review, modern methods of obtaining painting probes are considered in detail, and the basic tendencies of karyotype evolution in different taxa are discussed. Putative karyotypes of the ancestors of primates, carnivores, and placental mammals are considered.

Animals↗
PubMed1993

Clinical and cytogenetic significance of myelodysplastic syndromes with disease evolution.

We performed a retrospective study of 83 patients with myelodysplastic syndrome (MDS) to clarify the clinical and cytogenetic implications of disease evolution. Twenty-three patients showed disease progression; six of the 11 patients whose disease evolved within 100 days showed complex cytogenetic aberrations and most of them died within 300 days. Of the patients who survived more than 300 days, those with high bone marrow (BM) blast percentages experienced significant disease progression, but we noted no cytogenetic indicators for disease evolution at the later phase. Sixty percent of patients showing karyotypic evolution without disease evolution had deletion-type chromosome changes. The most frequent anomaly in patients with disease evolution who survived more than 300 days was an additional numerical change, whereas patients with disease evolution who survived less than 300 days showed karyotypic instability. It was difficult to predict disease progression for patients whose disease evolved more than 300 days after diagnosis, but in some patients the presence of additional numerical changes was related to disease progression. The cutoff level of early disease evolution was 100 days after diagnosis, and most patients with complex abnormalities survived less than 300 days with or without disease evolution.

Adult↗
PubMed2026

Highly Contiguous Is Not Chromosomally Accurate: Integrated Cytogenetic and Genomic Mapping in Two Turtle Genome.

High-quality genome assemblies are essential for robust research across biological and medical fields. Assembly errors can have far-reaching consequences for downstream analyses, including gene annotation and the inference of synteny. In contrast to the rapid growth of genomic data volume, there is a notable lag in the integration of chromosome-level assemblies with cytogenetic data. We conducted the first direct genome-to-genome comparison, integrating comparative chromosome painting, the alignment of chromosome-specific probes to available genome assemblies, and synteny-based comparison of independent chromosome-level assemblies of the loggerhead sea turtle (Caretta caretta, 2n = 56) and the red-eared slider (Trachemys scripta elegans, 2n = 50). Using two independent sets of flow-sorted chromosome-specific probes in cross-species hybridizations, together with the sequencing and mapping of chromosome-derived DNA libraries, we assigned assembled scaffolds to all physical chromosomes of both species. In C. caretta, chromosomal assignments and genome-wide synteny were fully consistent with the published assembly, except for the reduced sizes of two microchromosome scaffolds, which we attribute to under-representation of repetitive DNA. In contrast, in T. s. elegans, cytogenetic validation of the assemblies revealed a false rearrangement compared to a missed one. Our results show that even highly contiguous vertebrate genome assemblies can misrepresent chromosome structure. When cytogenetic analyses reveal such inaccuracies, updated reference genomes should be generated for widely studied species to enable accurate inference of karyotype evolution and downstream comparative genomic analyses.

FISH↗
PubMed1988

The chromosome complement of Sorex granarius--the ancestral karyotype of the common shrew (Sorex araneus)?

We present the G-band karyotype of Sorex granarius (Miller, 1910). With minor exceptions, each of the acrocentric autosomes in this karyotype is completely homologous to one of the chromosome arms in the karyotype of the common shrew (Sorex araneus L., 1758). If, as is the simplest interpretation, the karyotypic evolution in S. araneus is by repeated Robertsonian fusion, the karyotype in S. granarius represents the ancestral condition. We urge breeding studies to establish whether the designation of S. granarius as a full species is justified.

Animals↗
PubMed2004

Karyotype analysis and achiasmatic meiosis in pseudoscorpions of the family Chthoniidae (Arachnida: Pseudoscorpiones).

Karyotypes of pseudoscorpions (Arachnida, Pseudoscorpiones) are largely unknown. Here we describe for the first time karyotypes of the suborder Epiocheirata, represented by 9 European species of two genera of Chthoniidae, Chthonius and Mundochthonius. Diploid chromosome numbers of males range from 21 to 37. Karyotypes of both genera differ substantially. Acrocentric chromosomes predominate in karyotypes of the genus Chthonius, whereas M. styriacus exhibits a predominance of metacentric chromosomes. These differences suggest that the two genera belong probably to distant branches of the family Chthoniidae. It is proposed that karyotype evolution of the genus Chthonius was characterised by a reduction of chromosome numbers by tandem and centric fusions as well as gradual conversion of acrocentric chromosomes to biarmed ones, mostly by pericentric inversions. A tendency towards reduced chromosome numbers is evident in the subgenus Ephippiochthonius. All species display X0 sex chromosome system that is probably ancestral in pseudoscorpions. The X chromosome exhibits conservative morphology. It is metacentric in all species examined, and in the majority of them, a subterminal secondary constriction was found at one of its arms. In contrast to chthoniids, secondary constriction was not reported on sex chromosomes of other pseudoscorpions. Analysis of prophase I chromosomes in males revealed an achiasmatic mode of meiosis. Findings of the achiasmatic meiosis in both genera, Chthonius and Mundochthonius, indicate that this mode of meiosis might be characteristic of the family Chthoniidae. Amongst arachnids, achiasmatic meiosis has only been described in some scorpions, acariform mites, and spiders.

Animals↗
PubMed1991

[Heterogeneity of the Canidae Bsp-repeats family: discovery of the EcoRI subfamily].

A 1600 bp EcoRI fragment was cloned from genome of raccoon dog. The structure obtained is homologous to the Canidae Bsp-repeats family. Comparative blot hybridization of the EcoRI fragment and BamHI repeat from fox genome with restricted hydrolysates of the total of raccoon dog and fox DNAs revealed differences both in structure and genomic organization between these two Bsp-repeats versions. Evidently, the EcoRI fragment contains a sequence lacking from the BamHI fragment of the fox Bsp-repeats. Quantitative differences in contents of two Bsp versions in various canid genomes were revealed as well. The EcoRI version is most abundant in raccoon dog genome, while the BamHI fox version is most representative in polar fox genome. With other species studied, quantitative differences in version contents are not so dramatic, and the EcoRI fragment is always present in lower copy numbers. The discovery of the EcoRI subfamily of the Bsp-repeats is in accordance with the "library hypothesis" advanced by Salser in 1976. Connection of the Bsp-repeats' evolution with centric fusions and breaks characteristic of karyotype evolution of canids is being discussed. Comparative study of cloned EcoRI and BamHI fragments of Bsp-repeats in cytogenetical and molecular aspects may be useful, when investigating the role of tandem repeats in large chromosome rearrangements.

Animals↗
PubMed1977

Chromosomal repatterning in Acrididae.

Studies on the chromosomes of the acridid grasshoppers Acrida turrita, Poekilocerus pictus and Chrotogonus oxypterus have led the authors to surmise that structural re-arrangements must have played a major role in chromosomal repatterning and karyotypic evolution. Moreover, the telocentricity noticed in the Cryptosacci was evident in the Chasmosacci without the presence of the metacentric chromosomes to account for the reduction in the chromosome number. Possible trends in the evolution are discussed.

Animals↗
PubMed1991

Structure, mitotic and meiotic behaviour, and stability of centromere-like elements devoid of chromosome arms in the fly Megaselia scalaris (Phoridae).

Minute elements detected in Megaselia scalaris (Phoridae, Diptera) lack chromosome arms but carry centromeres and possess kinetochore microtubules in mitosis as well as in meiosis. These centromere-like elements (CLEs) were present in two geographically independent strains of the fly. This indicates that their origin is not a recent event in the karyotype evolution of M. scalaris and that they are rather stable constituents of the karyotype. Most often, two CLEs were found in gonial and somatic mitosis. Spermatocytes contained one CLE. Two individuals examined deviated from this rule in that a metaphase spermatogonium showed three and an anaphase spermatogonium eight CLEs. These animals are believed to have been aneuploid relative to the CLEs. An analysis of spermatogonial division revealed that the CLEs behave like the centromeres of the regular chromosomes but seem to separate precociously, since they were closer to the spindle poles in late anaphase cells. Whereas the size of the CLEs was not significantly different between mitotic cells and secondary spermatocytes, the CLEs in primary spermatocytes were larger in volume by a factor of about 4.5 than those in mitosis and meiosis II. The additional material is interpreted as a glue that holds two CLEs together. This, in turn, is a prerequisite for orderly segregation. The function of the CLEs is not known. They are considered as B chromosomes reduced to the minimum required for segregation, the centromere.

Animals↗
PubMed1985

Chromosomes and causation of human cancer and leukemia. LIV. Near-tetraploidy in acute leukemia.

Near-tetraploid cell populations were observed in a case of T-cell acute lymphoblastic leukemia (T-ALL) and in one of acute myeloblastic leukemia (AML). In the ALL case, hyperdiploid chromosomal changes, characterized by an isochromosome 17q [i(17q)], as well as other changes, were seen at the onset of the disease. At the first relapse, hypertetraploid cells appeared in about 10% of the mitoses in the bone marrow (BM), and by the second and third relapses, the hypertetraploidy was present in more than 90% of the mitoses in the BM. Even though karyotypic instability was evident, all abnormal karyotypes contained one or two i(17q) at every sampling. In spite of karyotypic instability at each relapse, karyotypic evolution was observed whenever relapse occurred. A normal female karyotype was confirmed in the BM of each period. Immunologic examinations performed at each sampling revealed no recognizable changes before and after the appearance of tetraploidy. In the AML case, which was classified as FAB M2, cytogenetic examination was performed at diagnosis and relapse. In both, hypotetraploid cells were observed in over 60% of the BM cells; the modal chromosome number was 90. Banding analysis was successful at relapse, and a pseudodiploid clone characterized by t(8;21) and a hypotetraploid clone with two t(8;21) and a loss of two Y chromosomes were observed in the same BM sample. A normal male karyotype was also observed in BM cells. In both cases, giant and bizarre blasts were seen in the BM. A close correlation between near-tetraploid mitoses and giant and bizarre blast cells in BM smears of the same samples was observed. Previously published tetraploid acute leukemia cases analyzed with banding methods were accumulated and compared with our two cases.

Adolescent↗
PubMedDate not supplied

Genomic rearrangements in trypanosomatids: an alternative to the "one gene" evolutionary hypotheses?

Most molecular trees of trypanosomatids are based on point mutations within DNA sequences. In contrast, there are very few evolutionary studies considering DNA (re) arrangement as genetic characters. Waiting for the completion of the various parasite genome projects, first information may already be obtained from chromosome size-polymorphism, using the appropriate algorithms for data processing. Three illustrative models are presented here. First, the case of Leishmania (Viannia) braziliensis/L. (V.) peruviana is described. Thanks to a fast evolution rate (due essentially to amplification/deletion of tandemly repeated genes), molecular karyotyping seems particularly appropriate for studying recent evolutionary divergence, including eco-geographical diversification. Secondly, karyotype evolution is considered at the level of whole genus Leishmania. Despite the fast chromosome evolution rate, there is qualitative congruence with MLEE- and RAPD-based evolutionary hypotheses. Significant differences may be observed between major lineages, likely corresponding to major and less frequent rearrangements (fusion/fission, translocation). Thirdly, comparison is made with Trypanosoma cruzi. Again congruence is observed with other hypotheses and major lineages are delineated by significant chromosome rearrangements. The level of karyotype polymorphism within that "species" is similar to the one observed in "genus" Leishmania. The relativity of the species concept among these two groups of parasites is discussed.

Animals↗
PubMed2004

Segmental duplication associated with the human-specific inversion of chromosome 18: a further example of the impact of segmental duplications on karyotype and genome evolution in primates.

The human-specific pericentric inversion of chromosome 18 was analysed using breakpoint-spanning BACs from the chimpanzee and human genome. Sequence and FISH analyses disclosed that the breakpoints map to an inverted segmental duplication of 19-kb, which most likely mediated the inversion by intrachromosomal homologous recombination. The 19-kb duplication encompasses the 3' end of the ROCK1 gene and occurred in the human lineage. Only one copy of this segment is found in the chimpanzee. Due to the inversion, the genomic context of the ROCK1 and USP14 genes is altered. ROCK1 flanks USP14 in the long arm of the chimpanzee chromosome 17, which is homologous to human chromosome 18. This order is interrupted by the inversion in humans. ROCK1 is localized close to the pericentromeric region in 18q11 and USP14 is inverted to distal 18p11.3 in direct neighbourhood to LSAU-satellites, beta-satellites and telomere-associated repeats. Our findings essentially confirm the analysis of Dennehey et al. (2004). Intriguingly, USP14 is differentially expressed in human and chimpanzee cortex as well as fibroblast cell lines determined previously by the analysis of oligonucleotide arrays. Either position effects mediated by the proximity to the telomeric region or nucleotide divergence in regulatory regions might account for the differential expression of USP14. The assignment of the breakpoint region to a segmental duplication underlines the significance of the genomic architecture in the context of genome and karyotype evolution in hominoids.

Animals↗
PubMed2006

Reconstruction of a 450-My-old ancestral vertebrate protokaryotype.

From recent work the putative eutherian karyotype from 100 Mya has been derived. Here, we have applied a new in silico technique, electronic chromosome painting (E-painting), on a large data set of genes whose positions are known in human, chicken, zebrafish and pufferfish. E-painting identifies conserved syntenies in the data set, and it enables a stepwise reconstruction of the ancestral vertebrate protokaryotype comprising 11 protochromosomes. During karyotype evolution in land vertebrates interchromosomal rearrangements by translocation are relatively frequent, whereas the karyotypes of birds and fish are much more conserved. Although the human karyotype is one of the most conserved in eutherians, it can no longer be considered highly conserved from a vertebrate-wide perspective.

Animals↗
PubMed1994

Extended cytogenetic follow-up and clinical progress in patients with myelodysplastic syndromes (MDS).

198 patients with MDS were followed cytogenetically for up to 90 months. There were significant differences in survival between patients with a normal karyotype, single abnormalities (p < 0.05) and multiple abnormalities (p < 0.0001). Survival differences were also seen in each of the FAB sub-types but were only significant in RAEB/RAEB-t and CMML (p = 0.001) where a normal karyotype was associated with prolonged survival. Single and multiple abnormalities of chromosomes 7 and 8 but only multiple abnormalities of chromosome 5 were also associated with reduced survival. 126 patients were successfully investigated on more than one occasion. Karyotype evolution occurred in 15 and was associated with reduced overall survival in those patients who had previously been karyotypically normal (p < 0.05). Median survival following evolution was only 10 months. 29 patients developed leukaemia. The incidence of transformation was significantly higher in patients with multiple abnormalities than in those with a normal karyotype (p < 0.05) or single abnormalities (p < 0.05).

Adult↗
PubMed1994

Rapidly evolving repetitive DNAs in a conservative genome: a test of factors that affect chromosomal evolution.

The hypothesis that tandemly repeated DNA sequences may facilitate chromosomal rearrangements was tested by comparing a conservatively evolving karyotype of a bat species (Macrotus waterhousii) with data published for a rapidly evolving karyotype of an equid species (Equus zebra). Empirical data generated from the phylogenetic screening of rapidly evolving repetitive DNAs from approximately 0.1% of the M. waterhousii genome showed only one sequence that was repetitive in M. waterhousii but low in copy number or absent from the outgroup Artibeus jamaicensis. This compares to 34 such clones containing sequences which were repetitive in E. zebra but were low in copy number or absent from the outgroup Ceratotherium simum. The bat sequence represents a single family of repeated sequences, whereas six families of sequences were identified in E. zebra. Southern blot analysis suggested that the sequence from M. waterhousii is interspersed rather than tandemly repeated, as are the sequences in E. zebra. These data support the above hypothesis and suggest that species with conservatively evolving karyotypes have fewer numbers and families of rapidly evolving DNA sequences than do species such as the equids that possess a karyotype that is considered to have undergone rapid karyotypic evolution.

Animals↗