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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↗
PubMed2004

A centromere-specific retroviral element associated with breaks of synteny in macropodine marsupials.

Studies of chromosome evolution have focused heavily on the evolution of conserved syntenic, gene-rich domains. It is obvious, however, that the centromere plays an equally important role in chromosome evolution, through its involvement in fissions, centric fusions, translocations, inversions and centric shifts. It is unclear how the centromere, either as a functioning unit of the chromosome or as a DNA sequence motif, has been involved in these processes. Marsupials of the family Macropodidae (kangaroos, wallabies, rat kangaroos and potoroos) offer unique insights into current theories expositing centromere emergence during karyotypic diversification and speciation. Tracing the genomic distribution of centromeric sequences in a model macropodine (subfamily Macropodinae: kangaroos and wallabies) species, Macropus eugenii (tammar wallaby), indicates these sequences have played an important role in chromosome evolution through possible segmental duplications associated with phylogenetically conserved breaks of synteny, pericentromeric and subtelomeric regions. Hybrids between different kangaroo species provide evidence that the centromere is unstable within this group of mammals and is involved in a large number of chromosome aberrations. A better understanding of the genetic and epigenetic factors that define centromeres and how centromeres may mediate changes in chromosome architecture are critical not only to our understanding of basic cellular functioning but also to our understanding of the process of speciation.

Animals↗
PubMed2006

Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigs.

BACKGROUND: Evolutionary centromere repositioning and human analphoid neocentromeres occurring in clinical cases are, very likely, two stages of the same phenomenon whose properties still remain substantially obscure. Chromosome 13 is the chromosome with the highest number of neocentromeres. We reconstructed the mammalian evolutionary history of this chromosome and characterized two human neocentromeres at 13q21, in search of information that could improve our understanding of the relationship between evolutionarily new centromeres, inactivated centromeres, and clinical neocentromeres. RESULTS: Chromosome 13 evolution was studied, using FISH experiments, across several diverse superordinal phylogenetic clades spanning >100 million years of evolution. The analysis revealed exceptional conservation among primates (hominoids, Old World monkeys, and New World monkeys), Carnivora (cat), Perissodactyla (horse), and Cetartiodactyla (pig). In contrast, the centromeres in both Old World monkeys and pig have apparently repositioned independently to a central location (13q21). We compared these results to the positions of two human 13q21 neocentromeres using chromatin immunoprecipitation and genomic microarrays. CONCLUSION: We show that a gene-desert region at 13q21 of approximately 3.9 Mb in size possesses an inherent potential to form evolutionarily new centromeres over, at least, approximately 95 million years of mammalian evolution. The striking absence of genes may represent an important property, making the region tolerant to the extensive pericentromeric reshuffling during subsequent evolution. Comparison of the pericentromeric organization of chromosome 13 in four Old World monkey species revealed many differences in sequence organization. The region contains clusters of duplicons showing peculiar features.

Animals↗
PubMed1992

Chromosomal rearrangements in rock wallabies, Petrogale (Marsupialia: Macropodidae). VII. G-banding analysis of Petrogale brachyotis and P. concinna: species with dramatically altered karyotypes.

G-banded metaphase preparations of cultured fibroblasts were used to construct the karyotypes of Petrogale brachyotis (2n = 18) and P. concinna (2n = 16). The two karyotypes differ significantly from the plesiomorphic karyotype of the genus and from those of all other Petrogale species examined. Petrogale brachyotis and P. concinna are characterised by three synapomorphies: a 1-10 centric fusion, a 3a-6 centric fusion, and a submetacentric chromosome 2 (2s). Both species also possess autapomorphies. Petrogale brachyotis is characterised by submetacentric chromosomes 5 (5s) and 4 (4sm), whereas P. concinna is characterised by a 5-9 centric fusion and a submetacentric chromosome 8 (8m). The 2s, 5s, 4sm, and 8m chromosomes all appear to be derived from their plesiomorphic homologs by centromeric transpositions. Although the rate of chromosome evolution varies considerably in Petrogale, the genus clearly exhibits karyotypic orthoselection, with all the autosomal rearrangements identified being either centric fusions or centromeric transpositions. This study also illustrates the potential for convergent evolution in chromosomally diverse groups and demonstrates the importance of G-banding studies for accurate identification of chromosome rearrangements.

Animals↗
PubMed2004

B chromosomes and Robertsonian fusions of Dichroplus pratensis (Acrididae): intraspecific support for the centromeric drive theory.

We tested the centromeric drive theory of karyotypic evolution in the grasshopper Dichroplus pratensis, which is simultaneously polymorphic for eight Robertsonian fusions and two classes of B chromosomes. A logistic regression analysis performed on 53 natural populations from Argentina revealed that B chromosomes are more probably found in populations with a higher proportion of acrocentric chromosomes, as the theory predicts. Furthermore, frequencies of B-carrying individuals are significantly negatively correlated with the mean frequency of different Robertsonian fusions per individual. No significant correlations between presence/absence or frequency of Bs, and latitude or altitude of the sampled populations, were found. We thus provide the first intraspecific evidence supporting the centromeric drive theory in relation to the establishment of B chromosomes in natural populations.

Animals↗
PubMed1999

Structural bistability of repetitive DNA elements featuring CA/TG dinucleotide steps and mode of evolution of satellite DNA.

Satellite DNA sequences are known to be important components required for the construction of centromeres and are common to all higher eukaryotes. Nevertheless, their nucleotide sequences vary significantly, even in evolutionarily related species. In order to elucidate how the nucleotide sequences define the conformational character of centromeric satellite DNA, an evolutionary path toward repetitive units has been hypothesized. In that context, the DNA conformation of fish satellite DNA was evaluated in two ways: the organization of subrepeats and sequence characteristics were compared, and the differences in stacking energies between A-helix and B-helix and the sequence-dependent bendability of the helices were evaluated. Our findings suggest that the monomeric units making up currently observed repetitive sequences have evolved through stepwise amplification of shorter, ancestral sequences by increasing the length of the units. In addition, we suggest that potentially key sequences required for DNA amplification comprise highly flexible structures. Thus flexibility of the DNA structure may be a primary prerequisite for DNA amplification.

Animals↗
PubMed1996

A stable marker chromosome with a cryptic centromere: evidence for centromeric sequences associated with an inverted duplication.

Centromere activation, an important mechanism in karyotype evolution, is occasionally observed in some human chromosome rearrangements. We report a possible occurrence of centromere activation in a marker chromosome containing an atypical centromere associated with an inverted duplication of the region 14q32 --> qter. The marker chromosome's reduced centromere lacks both the alpha and beta satellite sequences usually found at normal centromeres. In an attempt to identify the centromeric sequences, the marker chromosome was flow-sorted and amplified by a degenerate oligonucleotide primer polymerase chain reaction. Reverse chromosome painting experiments showed that the marker chromosome contains sequences that are unique to the distal region of chromosome 14, as well as a low copy number of (centromeric) sequences that are also highly represented in the centromeres of chromosomes 18 and 19. These data suggest the activation of a novel centromere in the 14q32 --> qter region, very likely consequent to the duplication of the region itself.

Adult↗
PubMed2006

Evolutionary movement of centromeres in horse, donkey, and zebra.

Centromere repositioning (CR) is a recently discovered biological phenomenon consisting of the emergence of a new centromere along a chromosome and the inactivation of the old one. After a CR, the primary constriction and the centromeric function are localized in a new position while the order of physical markers on the chromosome remains unchanged. These events profoundly affect chromosomal architecture. Since horses, asses, and zebras, whose evolutionary divergence is relatively recent, show remarkable morphological similarity and capacity to interbreed despite their chromosomes differing considerably, we investigated the role of CR in the karyotype evolution of the genus Equus. Using appropriate panels of BAC clones in FISH experiments, we compared the centromere position and marker order arrangement among orthologous chromosomes of Burchelli's zebra (Equus burchelli), donkey (Equus asinus), and horse (Equus caballus). Surprisingly, at least eight CRs took place during the evolution of this genus. Even more surprisingly, five cases of CR have occurred in the donkey after its divergence from zebra, that is, in a very short evolutionary time (approximately 1 million years). These findings suggest that in some species the CR phenomenon could have played an important role in karyotype shaping, with potential consequences on population dynamics and speciation.

Animals↗
PubMed1995

Comparative mapping of human alphoid sequences in great apes using fluorescence in situ hybridization.

Twenty-seven human alphoid DNA probes have been hybridized in situ to metaphase spreads of the common chimpanzee (PTR), the pigmy chimpanzee (PPA), and the gorilla (GGO) to investigate the evolutionary relationship between the centromeric regions of the great ape chromosomes. The surprising results showed that the vast majority of the probes did not recognize their corresponding homologous chromosomes. Alphoid sequences belonging to the suprachromosomal family 1 (chromosomes 1, 3, 5, 6, 7, 10, 12, 16, and 19) yielded very heterogeneous results: some probes gave intense signals, but always on nonhomologous chromosomes; others did not produce any hybridization signal. Almost all probes belonging to the suprachromosomal family 2 (chromosomes 2, 4, 8, 9, 13, 14, 15, 18, 20, 21, and 22) recognized a single chromosome: chromosome 11 (phylogenetic IX) in PTR and PPA and chromosome 19 (phylogenetic V) in GGO. Localization of probes of suprachromosomal family 3 (chromosomes 1, 11, 17, and X) was found to be substantially conserved in PTR and PPA, but not in GGO. Probe pDMX1, specific for the human X chromosome, was the only sequence detecting its corresponding chromosome in all three species. PPA chromosomes I, IIp, IIq, IV, V, VI, and XVIII were never labeled, even under low-stringency hybridization conditions, by the 27 alphoid probes used in this study. These results, with particular reference to differences found in the two related species PTR and PPA, suggest that alphoid centromeric sequences underwent a very rapid evolution.

Animals↗
PubMed1993

Nonrandom localization of recombination events in human alpha satellite repeat unit variants: implications for higher-order structural characteristics within centromeric heterochromatin.

Tandemly repeated DNA families appear to undergo concerted evolution, such that repeat units within a species have a higher degree of sequence similarity than repeat units from even closely related species. While intraspecies homogenization of repeat units can be explained satisfactorily by repeated rounds of genetic exchange processes such as unequal crossing over and/or gene conversion, the parameters controlling these processes remain largely unknown. Alpha satellite DNA is a noncoding tandemly repeated DNA family found at the centromeres of all human and primate chromosomes. We have used sequence analysis to investigate the molecular basis of 13 variant alpha satellite repeat units, allowing comparison of multiple independent recombination events in closely related DNA sequences. The distribution of these events within the 171-bp monomer is nonrandom and clusters in a distinct 20- to 25-bp region, suggesting possible effects of primary sequence and/or chromatin structure. The position of these recombination events may be associated with the location within the higher-order repeat unit of the binding site for the centromere-specific protein CENP-B. These studies have implications for the molecular nature of genetic recombination, mechanisms of concerted evolution, and higher-order structure of centromeric heterochromatin.

Base Sequence↗
PubMed2005

Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the Aegilops-Triticum alliance.

The origin of tetraploid wheat and the divergence of diploid ancestors of wheat A and D genomes were estimated to have occurred 0.36 and 2.7 million years ago, respectively. These estimates and the evolutionary history of 3159 gene loci were used to estimate the rates with which gene loci have been deleted and duplicated during the evolution of wheat diploid ancestors and during the evolution of polyploid wheat. During diploid evolution, the deletion rate was 2.1 x 10(-3) locus(-1) MY(-1) for single-copy loci and 1.0 x 10(-2) locus(-1) MY(-1) for loci in paralogous sets. Loci were duplicated with a rate of 2.9 x 10(-3) locus(-1) MY(-1) during diploid evolution. During polyploid evolution, locus deletion and locus duplication rates were 1.8 x 10(-2) and 1.8 x 10(-3) locus(-1) MY(-1), respectively. Locus deletion and duplication rates correlated positively with the distance of the locus from the centromere and the recombination rate during diploid evolution. The functions of deleted and duplicated loci were inferred to gain insight into the surprisingly high rate of deletions of loci present apparently only once in a genome. The significance of these findings for genome evolution at the diploid and polyploid level is discussed.

Centromere↗
PubMed1998

To pair or not to pair: chromosome pairing and evolution.

Chromosome pairing in wild-type wheat closely resembles the process in both yeast and Drosophila. The recent characterisation of a mutant Ph1 wheat and the observation that chromosome pairing in the absence of Ph1 more closely resembles that of mammals and maize has shed light on the evolution of chromosome pairing in the cereals.

Centromere↗
PubMed2006

High-density comparative BAC mapping in the black muntjac (Muntiacus crinifrons): molecular cytogenetic dissection of the origin of MCR 1p+4 in the X1X2Y1Y2Y3 sex chromosome system.

The black muntjac (Muntiacus crinifrons, 2n = 8[female symbol]/9[male symbol]) is a critically endangered mammalian species that is confined to a narrow region of southeastern China. Male black muntjacs have an astonishing X1X2Y1Y2Y3 sex chromosome system, unparalleled in eutherian mammals, involving approximately half of the entire genome. A high-resolution comparative map between the black muntjac (M. crinifrons) and the Chinese muntjac (M. reevesi, 2n = 46) has been constructed based on the chromosomal localization of 304 clones from a genomic BAC (bacterial artificial chromosome) library of the Indian muntjac (M. muntjak vaginalis, 2n = 6[female symbol]/7[male symbol]). In addition to validating the chromosomal homologies between M. reevesi and M. crinifrons defined previously by chromosome painting, the comparative BAC map demonstrates that all tandem fusions that have occurred in the karyotypic evolution of M. crinifrons are centromere-telomere fusions. The map also allows for a more detailed reconstruction of the chromosomal rearrangements leading to this unique and complex sex chromosome system. Furthermore, we have identified 46 BAC clones that could be used to study the molecular evolution of the unique sex chromosomes of the male black muntjacs.

Animals↗
PubMed2004

Recurrent sites for new centromere seeding.

Using comparative FISH and genomics, we have studied and compared the evolution of chromosome 3 in primates and two human neocentromere cases on the long arm of this chromosome. Our results show that one of the human neocentromere cases maps to the same 3q26 chromosomal region where a new centromere emerged in a common ancestor of the Old World monkeys approximately 25-40 million years ago. Similarly, the locus in which a new centromere was seeded in the great apes' ancestor was orthologous to the site in which a new centromere emerged in the New World monkeys' ancestor. These data suggest the recurrent use of longstanding latent centromeres and that there is an inherent potential of these regions to form centromeres. The second human neocentromere case (3q24) revealed unprecedented features. The neocentromere emergence was not accompanied by any chromosomal rearrangement that usually triggers these events. Instead, it involved the functional inactivation of the normal centromere, and was present in an otherwise phenotypically normal individual who transmitted this unusual chromosome to the next generation. We propose that the formation of neocentromeres in humans and the emergence of new centromeres during the course of evolution share a common mechanism.

Animals↗
PubMed2002

Chromosome banding in Amphibia. XXV. Karyotype evolution and heterochromatin characterization in Australian Mixophyes (Anura, Myobatrachidae).

The mitotic chromosomes of the Australian ground frogs Mixophyes fasciolatus and M. schevilli were analyzed by means of banding techniques and restriction endonuclease digestions. Chromosomal differentiation in these two species occurred exclusively by considerable changes in the amount of telomeric and centromeric heterochromatin, whereas the sizes and locations of interstitial heterochromatic regions, the sizes of all euchromatic segments as well as the positions of centromeres remained nearly identical during karyotype evolution. The major heterochromatic regions in the karyotypes of M. fasciolatus and M. schevilli amount to 30.2% and 20.7%, respectively. They consist of AT base pair-rich repetitive DNA sequences that are brightly labeled by AT-specific fluorochromes and display quenched fluorescence after staining with GC-specific fluorochromes. The heterochromatic regions can be differentiated by treatment of metaphase chromosomes and interphase cell nuclei with various restriction enzymes which either disclose the complete set of C-band patterns in the karyotypes of both species, or else reveal several subsets of these C-bands.

Animals↗
PubMed2004

Evolutionary dynamics of transposable elements at the centromere.

Transposable elements are the single most abundant class of genetic material in higher eukaryotes. These elements show a genome-wide distribution but are found in disproportionate abundance at the centromeric and/or pericentric regions in a wide range of phylogenetic species. We propose at least three possible ways in which these elements could have directly contributed to the evolution of the architecture and function of the centromere in various organisms. An "extradition" mechanism also appears to have evolved, which enables the developing or established centromere to deal with the potentially disruptive effects of any subsequently arising transposable elements.

Centromere↗
PubMed1982

Cloning and analysis of ribosomal DNA of Chironomus thummi piger and Chironomus thummi thummi. The nontranscribed spacer of Ch. th. thummi contains a highly repetitive DNA sequence.

The ribosomal DNAs from Ch. thummi piger and Ch. th. thummi were cloned and analysed by a variety of restriction endonucleases. Comparison of rDNA clones from the two subspecies revealed a considerable length difference: the length of the analysed rDNA cistrons is approximately 9.0 kb for Ch. th. piger and approximately 14.5 kb for Ch. th. thummi. The nearly 5 kb additional DNA in Ch. th. thummi is clearly located within the non-transcribed spacer region, and consists of AT-rich, repetitive DNA elements. These elements with a basic repeat length of approximately 120 bp, are arranged tandemly in stretches of up to about 50 identical copies, which are characterized by a cleavage site for ClaI restriction endonuclease. They are found only in the Ch. th. thummi rDNA clones and not in the Ch. th. piger clones. Southern hybridizations between cloned ribosomal DNA and "centromeric" highly repetitive DNA have shown that the ribosomal repetitive Cla-elements are closely related to a highly repetitive DNA sequence family, which is present in various chromosomal sites particularly the centromeres. Sequence analysis has revealed more than 90% homology between the ribosomal Cla-elements and the "centromeric" Cla-elements.--Since it is clear from cytological investigations that Ch. th. piger with the small rDNA repeating unit is the phylogenetically older subspecies, we postulate a transposition of Cla-elements into the nucleolar DNA during the evolution of Ch. th. thummi.

Animals↗