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PubMed1989

Cloning and characterization of a tandemly repeated DNA sequence in the crane family (Gruidae).

A tandemly repeated DNA sequence possessing a unique PstI site has been characterized in several species of the crane family. The "Pst family" comprises at least 8800 monomer units 187 base pairs (bp) in length and constitutes 0.14% of the genome of the sarus crane (Grus antigone). The array is located in the centromeric heterochromatin of chromosome 2 in the two species where in situ hybridizations of a cloned monomer to metaphase chromosome spreads were carried out. DNA sequence comparisons between five monomer units from G. antigone revealed a high degree of homology between four of the individual repeats, while the fifth was somewhat divergent. The G + C content deduced from the DNA sequence makes it likely that the Pst family constitutes part of a density satellite seen in profiles of crane DNA centrifuged to equilibrium in CsCl. The common occurrence of tandem arrays such as the Pst family, with repeat lengths close to 200 bp, leads us to an hypothesis implicating nucleosomes in the evolution of such families.

Animals↗
PubMed2003

Chromosomal studies on sphaerodactyl lizards of genera Gonatodes and Coleodactylus (Squamata, Gekkonidae) using differential staining and fragile sites analyses.

The karyotypes of three species of sphaerodactyl gekkonid lizards are described after conventional and differential staining. Karyotypes of Gonatodeshumeralis and G. hasemani are formed by a gradual series of 32 acrocentric chromosomes, similar to those already published for other species of the genus. G. humeralis shows multiple Ag-NORs with intra-individual variability, and positive C-bands located at centromeric and telomeric regions of several chromosome pairs. Coleodactylus amazonicus, the first non-Gonatodes sphaerodactyl studied so far karyologically, exhibits 36 acrocentric/subtelocentric chromosomes and a single pair of Ag- NORs. Fragile sites were detected on two medium-sized chromosome pairs in the karyotype of G. humeralis, most of them obtained in BrdU-treated culture preparations. These sites may represent a putative fission/fusion spot involved in the differentiation of G. humeralis-like 2n = 32 and C. amazonicus-like 2n = 36 karyotypes. Our results, especially on the location of Ag-NORs and the description of fragile sites, are relevant in improving our knowledge about the events of chromosome evolution in this extremely variable and poorly known group of lizards.

Animals↗
PubMed1998

Microdissected bovine X chromosome segment delineates homoeologous chromosomal regions in sheep, goat and buffalo.

The terminal part of the long arm of the bovine X chromosome (bands Xq41-q43) was microdissected. The DNA thus obtained was PCR amplified, labelled and used as painting probe on cattle, sheep, goat and buffalo chromosomes. In cattle, as expected, distinct hybridization signals were observed on bands Xq41-q43. In sheep and goat, the painting signals were observed on the proximal part of the long arm of the X chromosome, adjacent to the centromere (Xp12-q12). In buffalo, however, the terminal part of the X chromosome involving bands q44-q47 was painted. The findings contribute towards developing a better understanding of the comparative organization of the X chromosome in the four bovidae species. Proposed models of evolutionary rearrangements within the X chromosome of the four species are examined in light of the results obtained.

Animals↗
PubMed1989

Chromosome maps of man and mouse. IV.

Current knowledge of man-mouse genetic homology is presented in the form of chromosomal displays, tables and a grid, which show locations of the 322 loci now assigned to chromosomes in both species, as well as 12 DNA segments not yet associated with gene loci. At least 50 conserved autosomal segments with two or more loci have been identified, twelve of which are over 20 cM long in the mouse, as well as five conserved segments on the X chromosome. All human and mouse chromosomes now have conserved regions; human 17 still shows the least evidence of rearrangement, with a single long conserved segment which apparently spans the centromere. The loci include 102 which are known to be associated with human hereditary disease; these are listed separately. Human parental effects which may well be the result of genomic imprinting are reviewed and the location of the factors concerned displayed in relation to mouse chromosomal regions which have been implicated in imprinting phenomena.

Animals↗
PubMed1996

Chromosomal relationships and phylogenetic and clustering analyses on genes Callithrix group argentata (Callitrichidae, Primates).

The karyotypes of three species of marmosets of the Callithrix argentata group (C. argentata, C. humeralifera and C. chrysoleuca) were studied. Comparisons were made among species and with the previously described karyotypes of C. emiliae, C. mauesi (argentata group) and C. jacchus (jacchus group). Two chromosomes rearrangements differentiate the argentata (2n=44) and jacchus (2n=46) groups: fusion or fission and a paracentric invasion. The argentata group is also characterized by the addition of large amounts of distal constitutive heterochromatin (CH) in some chromosomes, while the jacchus group shows mainly centromeric heterochromatin. The five species of the argentata group differ in the amount or location of the distal CH. Interspecific differences were converted to a Basic Data Matrix (BDM), that was submitted to phenetic and cladistic analyses. For cladistic analyses C. jacchus was the outgroup. The results agree with morphological and geographical data.

Animals↗
PubMed1996

Cytogenetic and molecular analysis of the satellite DNA of the genus Ctenomys (Rodentia Octodontidae) from Uruguay.

The genus of subterranean rodents Ctenomys presents the widest range of variability in diploid number among mammals (from 2n = 10 to 2n = 70). In Uruguay, this variability is observed in karyotypes with 2n = 44, 50 or 58 and two geographically isolated populations with 70 chromosomes but different karyotypic structure. The last three populations were analyzed in the present study. They present a satellite DNA, which was isolated from genomic DNA after AluI digestion. In situ hybridization showed that this satellite DNA is located in the centromeric region of a few chromosomes, coincident with Hoechst 33258 staining and C-banding patterns. A similar satellite DNA was detected in Argentinian species of this genus. We established that, in spite of differences in number of positive heterochromatic blocks per karyotype, the C value is the same in the three populations studied. The nature and possible evolutionary path of this repeated DNA is discussed.

Animals↗
PubMed2001

Chromosomal rearrangements and oncogene amplification precede aneuploidization in the genetic evolution of breast cancer.

Breast carcinoma is thought to arise because of multiple successive changes in the genome of the normal epithelial cells. However, little is known of the order of appearance of different types of genetic aberrations We studied the ERBB2 (Her-2/neu) and CCND1 (cyclin D1) oncogene amplification in flow cytometrically sorted diploid and nondiploid tumor cell populations by fluorescence in situ hybridization (FISH). The purity of the cell sorting was confirmed by static DNA image cytometry. Spectral karyotyping was used to define differences in a genome-wide manner between two distinctly different aneuploid cell clones found in each of two breast cancer cell lines. FISH indicated the presence of gene amplification both in diploid and nondiploid cell clones in 17 of the 21 amplification-containing tumors analyzed. The oncogene copy numbers remained unchanged throughout aneuploidization in 11 of 17 tumors. The remaining six tumors showed an increase in oncogene copy number as well as the number of chromosome 11 or 17 centromeres (the original location of CCNDI and ERBB2, respectively). Breast carcinoma cell lines MDA-157 and MDA-436 showed a significant number of chromosomal rearrangements in the near-diploid clones, which were present in duplicate in the corresponding aneuploid (polyploid) clones. These results indicate that ploidy shift, ie., aneuploidization, in breast cancer is a late genetic event which is preceded by both oncogene amplifications as well as many chromosomal rearrangements.

Aneuploidy↗
PubMed2000

A comparative study of chromosome morphology among the nine annual species of Cicer L.

Thirty-six accessions, representing the full complement of all the nine annual Cicer L. species, viz C. arietinum, C. reticulatum, C. echinospermum, C. pinnatifidum, C. judaicum, C. bijugum, C. chorassanicum, C. yamashitae and C. cuneatum, were subjected to karyotype analysis for the first time in a single comprehensive study. The detailed karyotype of C. chorassanicum was also investigated for the first time. A 12 h cold water pretreatment and 13 min 60 degrees C 1 N HCl hydrolysis confirmed a somatic chromosome number of 2n = 16 in all the species. Within species interchromosomal size variation was observed to be quite large in C. arietinum, C. reticulatum and C. echinospermum, but not in the remaining six species. Individual chromosome size ranged from 3.77 microns in C. echinospermum to 1.32 microns in C. arietinum while the haploid genome length ranged from 20.65 microns in C. echinospermum to 14.92 microns in C. cuneatum. Ample rearrangement of chromatin among chromosomes within a species was implied to have played a role in Cicer genome evolution. The nine species were classified in two groups based on karyotypic similarity, with the first group comprising the inter-crossable species C. arietinum, C. reticulatum and C. echinospermum, while the remaining species forming the second group. The first group species are also genetically close to each other as deduced by other morphological, biochemical and DNA based studies. Circumstantial evidence has lead to the speculation that perhaps karyotypic similarity and interspecific crossability are positively related to each other.

Centromere↗
PubMed2002

Genomic organization and chromosome localization of the murine and human allantoicase gene.

Allantoicase is one of the enzymes involved in uricolysis. The enzymes of this catabolic pathway (i.e. allantoinase, allantoicase, ureidoglycolate lyase and urease) were lost during vertebrate evolution and the causes for this loss are still unclear. In mammals, as well as in birds and reptiles, the activity of allantoicase is absent; notwithstanding, we recently cloned human and mouse cDNA sequences with high similarity with previously characterized allantoicases. In the present paper, we report the genomic organization of the allantoicase gene in mouse and in man. Both genes are constituted by 11 exons that appear to be very conserved; introns are more variable in length while maintain the same phase but for intron 4. We have also detected a second transcript of the human allantoicase gene in which exon 1 is absent. Moreover, the mouse gene maps in chromosome 12 at 13.0 cM from the centromere.

Animals↗
PubMed1997

Nucleotide sequence analysis of the HLA class I region spanning the 237-kb segment around the HLA-B and -C genes.

To elucidate the detailed gene organization of the human leukocyte antigen (HLA) class I region on chromosome 6, seven contiguous cosmid genomic clones covering the 237-kb segment around the HLA-B and -C loci were subjected to DNA sequencing by the shotgun strategy to give a single contig of 236,822 bp from the MICA gene (58.2 kb centromeric of HLA-B) to 90.8 kb telomeric of HLA-C. This region was confirmed to contain four known genes, MICA, HLA-17, HLA-B, and HLA-C, from centromere to telomere. Further, a new member of the P5 multicopy genes was found to be about 1.3 kb upstream of the HLA-17 gene and designated P5.8. Five novel genes designated NOB1-5 were identified by RT-PCR and Northern blot hybridization. In addition, two pseudogenes, dihydrofolate reductase pseudogene (DHFRP) and ribosomal protein L3 homologous gene (RPL3-Hom), were also found in the vicinity of the HLA-B and -C genes, respectively. The two segments (about 40 kb) downstream of the HLA-B and HLA-C genes showed high sequence homology to each other, suggesting that segmental genome duplication including the major histocompatibility complex (MHC) class I gene must have occurred during the evolution of the MHC.

Blotting, Northern↗
PubMed2006

A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms.

BACKGROUND: The development of large genomic resources has become a prerequisite to elucidate the wide-scale evolution of genomes and the molecular basis of complex traits. Linkage maps represent a first level of integration and utilization of such resources and the primary framework for molecular analyses of quantitative traits. Previously published linkage maps have already outlined the main peculiarities of the rainbow trout meiosis and a correspondance between linkage groups and chromosome arms has been recently established using fluorescent in situ hybridization. The number of chromosome arms which were covered by these maps remained unknown. RESULTS: We report an updated linkage map based on segregation analysis of more than nine hundred microsatellite markers in two doubled haploid gynogenetic lines. These markers segregated into 31 linkage groups spanning an approximate total map length of 2750 cM. Centromeres were mapped for all the linkage groups using meiogenetic lines. For each of the 31 linkage groups, the meta or acrocentric structure infered from centromere mapping was identical with those recently found with fluorescent in situ hybridization results. The present map is therefore assumed to cover the 52 chromosome arms which constitute the rainbow trout karyotype. Our data confirm the occurrence of a high interference level in this species. Homeologous regions were identified in eleven linkage groups, reflecting the tetraploid nature of the salmonid genome. The data supported the assumption that gene orders are conserved between duplicated groups and that each group is located on a single chromosome arm. Overall, a high congruence with already published rainbow trout linkage maps was found for both gene syntenies and orders. CONCLUSION: This new map is likely to cover the whole set of chromosome arms and should provide a useful framework to integrate existing or forthcoming rainbow trout linkage maps and other genomic resources. Since very large numbers of EST containing microsatellite sequences are available in databases, it becomes feasible to construct high-density linkage maps localizing known genes. This will facilitate comparative mapping and, eventually, identification of candidate genes in QTL studies.

Animals↗
PubMed1996

The chromosome complement of Acomys spp. (Rodentia, Muridae) from Oursi, Burkina Faso--the ancestral karyotype of the cahirinus-dimidiatus group?

We present here data on chromosome banding analysis (R- and C-bands) of Acomys sp. (Rodentia, Muridae) from Oursi, Burkina Faso, characterized by 2n = FN = 68 and comparison of its banding patterns with those of Acomys dimidiatus from Saudi Arabia (2n = 38, FN = 70), studied previously. The study revealed complete homology between acrocentric chromosomes of Acomys sp. and chromosome arms of 16 pairs of metacentric and two pairs of acrocentric chromosomes of A. dimidiatus. In addition to monobrachial homology, one tandem translocation accompanied by a centromeric shift was identified in the karyotype of the latter species. The data obtained show that karyotypes of all the species of the Acomys cahirinus-dimidiatus group studied previously may be derived from that of Acomys sp. from Oursl by means of numerous non-homologous Rb translocations and 1-2 tandem transiocations, and thus its karyotype may be considered as ancestral for the cahirinus-dimidiatus group.

Animals↗
PubMed2002

Micronuclei, nucleoplasmic bridges and nuclear buds induced in folic acid deficient human lymphocytes-evidence for breakage-fusion-bridge cycles in the cytokinesis-block micronucleus assay.

We have validated the analysis of nucleoplasmic bridges (NPBs) and nuclear buds as biomarkers of genomic instability within the cytokinesis-block micronucleus assay in long-term lymphocyte cultures. Lymphocytes from 20 subjects were cultured in medium containing 12-120 nM folic acid for 9 days. Binucleate cells were scored for micronuclei (MN), NPBs and nuclear budding on day nine after 24h incubation in the presence of the cytokinesis inhibitor cytochalasin-B. Folic acid concentration was correlated significantly (P<0.0001) and negatively (r=-0.63 to -0.74) with all these markers of chromosome damage. Chromosome damage was minimised at 60-120 nM folic acid, which is greater than the concentration of folate normally observed in plasma (<30 nM). Current evidence suggests that (a) NPBs originate from dicentric chromosomes in which the centromeres have been pulled to the opposite poles of the cell at anaphase and are therefore, indicative of chromosome rearrangement and (b) that the nuclear budding process is the mechanism by which cells remove amplified DNA and is therefore a marker of gene amplification. The strong correlation between micronucleus formation, nuclear budding and NPBs (r=0.75-0.77, P<0.001) is supportive of the hypothesis that folic acid deficiency causes genomic instability and gene amplification by the initiation of breakage-fusion-bridge (BFB) cycles. These results also suggest that the CBMN assay may be a useful model for the study of the BFB cycle which may be one of the key mechanisms for the hypermutability phenotype required for the rapid evolution of cancer cells.

Cell Division↗
PubMed2005

Why do human diversity levels vary at a megabase scale?

Levels of diversity vary across the human genome. This variation is caused by two forces: differences in mutation rates and the differential impact of natural selection. Pertinent to the question of the relative importance of these two forces is the observation that both diversity within species and interspecies divergence increase with recombination rates. This suggests that mutation and recombination are either directly coupled or linked through some third factor. Here, we test these possibilities using the recently generated sequence of the chimpanzee genome and new estimates of human diversity. We find that measures of GC and CpG content, simple-repeat structures, as well as the distance from the centromeres and the telomeres predict diversity as well as divergence. After controlling for these factors, large-scale recombination rates measured from pedigrees are still significant predictors of human diversity and human-chimpanzee divergence. Furthermore, the correlation between human diversity and recombination remains significant even after controlling for human-chimpanzee divergence. Two plausible and non-mutually exclusive explanations are, first, that natural selection has shaped the patterns of diversity seen in humans and, second, that recombination rates across the genome have changed since humans and chimpanzees shared a common ancestor, so that current recombination rates are a better predictor of diversity than of divergence. Because there are indications that recombination rates may have changed rapidly during human evolution, we favor the latter explanation.

Animals↗
PubMed2001

Trigenomic origin of the hexaploid Psammopyrum athericum (Triticeae: Poaceae) revealed by in-situ hybridization.

The genomic constitution of the hexaploid Psammopyrum athericum was studied with in-situ DNA hybridization using both genomic DNA and isolated cloned sequences as probes. A genomic probe from Thinopyrum bessarabicum (E genome) hybridized successfully to 14 chromosomes of Ps. athericum and a probe from Festucopsis serpentinii (L genome) hybridized to another 14 chromosomes. The remaining chromosomes did not hybridize, apart from in the centromeric region, to any of the genomic probes used. It is thus proposed that Ps. athericum contains the genomes E, L and X where X stands for a so-far unknown genome. Psammopyrum athericum has three pairs of pTa71 sites and approximately 30 pSc119:2 sites. The origin of the third genome will be a matter for further research using genomic and genome-specific probes.

Biological Evolution↗
PubMed2000

The chromosomes of Rhynchosciara baschanti (Diptera: Sciaridae): molecular cytogenetic comparisons with taxa in the americana-like group.

Polytene chromosome analysis is presented for Rhynchosciara baschanti, a species belonging to the americana-like group of Rhynchosciara. R. baschanti chromosomes show morphological differences in centromeric and telomeric regions compared to two other members within the group, R. americana and R. hollaenderi. In addition, fixed band and autosomal inversion differences were noted. Physical mapping data showed synteny among the taxa under study for DNA puffs and single-copy or histone gene probes, whereas rDNA and poly-(r)A probes showed different diagnostic patterns. The activity of developmentally active genes and the pattern of thymidine incorporation into DNA puff sites of R. baschanti are consistent with those found in the two previously studied species, except for lower levels of expression at some of these sites. These results suggest that differential duplication of specific DNA sequences, in particular repetitive and homopolymeric DNA, has played a role in the chromosomal evolution of these Rhynchosciara species. Inversions and band dimorphisms have also occurred, but the processes leading to their maintenance and fixation appear to have been slow, since these three species are in general chromosomally monomorphic.

Animals↗
PubMed2005

Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana.

Over 1000 genetically linked RFLP loci in Brassica napus were mapped to homologous positions in the Arabidopsis genome on the basis of sequence similarity. Blocks of genetically linked loci in B. napus frequently corresponded to physically linked markers in Arabidopsis. This comparative analysis allowed the identification of a minimum of 21 conserved genomic units within the Arabidopsis genome, which can be duplicated and rearranged to generate the present-day B. napus genome. The conserved regions extended over lengths as great as 50 cM in the B. napus genetic map, equivalent to approximately 9 Mb of contiguous sequence in the Arabidopsis genome. There was also evidence for conservation of chromosome landmarks, particularly centromeric regions, between the two species. The observed segmental structure of the Brassica genome strongly suggests that the extant Brassica diploid species evolved from a hexaploid ancestor. The comparative map assists in exploiting the Arabidopsis genomic sequence for marker and candidate gene identification within the larger, intractable genomes of the Brassica polyploids.

Arabidopsis↗
PubMed1989

[Organization of Bsp-repeats in the fox genome].

Bsp repeats comprise approximately 1% of silver for total DNA and are preferentially localized in centromeric regions. Two of Bsp fragments cloned earlier, such as non-homologous rsV1 and rsV3, make up together a Bsp unit (680 bp) and possess a set of sites known to have regulatory functions in eucaryotic genomes. In this work, tandem organization of Bsp repeats is demonstrated. A stretched Bsp sequence (approximately 1460 bp, dimeric form) flanked by BamHI sites was cloned and its restriction map was plotted. With use of rsV1 and rsV3 probes the new sequence exhibited linked structure: rsV1-rsV3-rsV1-rsV3-rsV1. Blot-hybridization with the restriction fragments of fox total DNA suggested hierarchical order of Bsp clustes in the genome. It is supposed that the processes of selective amplification of individual fragments had been of real importance during evolution of Bsp repeats.

Animals↗