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PubMed2001

The molecular phylogeny of the Sparidae (Pisces, Perciformes) based on two satellite DNA families.

In this study, the phylogenetic relationships and which the taxonomic status of the species belonging to the Sparidae family (Pisces: Perciformes) are analysed and revised. This study includes species of this family that are distributed by the North-eastern Atlantic and Mediterranean coasts, is based on the analysis of two satellite DNA families. While one satellite DNA, the centromeric EcoRI family, extends to all the species analysed, the other, the subtelomeric DraI family, is restricted to only six of the 16 species studied. Based on phylogenetic use of these two markers, we conclude that the Sparidae family is composed by two major lineages: one comprising the species of the genera Sparus, Diplodus, Lithognathus, Boops, Sarpa and Spondyliosoma, and one species of Pagellus (P. bogaraveo); and the other lineage is comprised of the species of Pagrus and Dentex, and one species of Pagellus (P. erythrinus). This classification is consistent across the two markers used and clearly contradicts previous morphological phylogenies based mainly on dentition. In addition, the current status and the phylogenetic position of some of the species analysed (i.e. species of Pagrus, Dentex and Pagellus) are not supported by our analyses. Finally, we discuss the value of the morphological characters used until now for the classification of this group of fish.

Animals↗
PubMed2003

Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII.

Chromosome segregation at mitosis depends critically on the accurate assembly of kinetochores and their stable attachment to microtubules. Analysis of Saccharomyces cerevisiae kinetochores has shown that they are complex structures containing >/=50 protein components. Many of these yeast proteins have orthologs in animal cells, suggesting that key aspects of kinetochore structure have been conserved through evolution, despite the remarkable differences between the 125-base pair centromeres of budding yeast and the Mb centromeres of animal cells. We describe here an analysis of S. cerevisiae Ndc10p, one of the four protein components of the CBF3 complex. CBF3 binds to the CDEIII element of centromeric DNA and initiates kinetochore assembly. Whereas CDEIII binding by Ndc10p requires the other components of CBF3, Ndc10p can bind on its own to CDEII, a region of centromeric DNA with no known binding partners. Ndc10p-CDEII binding involves a dispersed set of sequence-selective and -nonselective contacts over approximately 80 base pairs of DNA, suggesting formation of a multimeric structure. CDEII-like sites, active in Ndc10p binding, are also present along chromosome arms. We propose that a polymeric Ndc10p complex formed on CDEII and CDEIII DNA is the foundation for recruiting microtubule attachment proteins to kinetochores. A similar type of polymeric structure on chromosome arms may mediate other chromosome-spindle interactions.

Base Sequence↗
PubMed2025

Genetic Differentiation is Constrained to Chromosomal Inversions and Putative Centromeres in Locally Adapted Populations With Higher Gene Flow.

The impact of genome structure on adaptation is a growing focus in evolutionary biology, revealing an important role for structural variation and recombination landscapes in shaping genetic diversity across genomes and among populations. This is particularly relevant when local adaptation occurs despite gene flow, where clustering of differentiated loci can maintain locally adapted variants by reducing recombination between them. However, the limited genomic resources for nonmodel species, including reference genomes and recombination maps, have constrained our understanding of these patterns. In this study, we leverage the Atlantic silverside-a nonmodel fish with extensive local adaptation across a steep latitudinal gradient-as an ideal system to explore how genome structure influences adaptation under varying levels of gene flow, using a newly available reference genome and multiple recombination maps. Analyzing 168 genomes from four populations, we found a continuum of genome-wide differentiation increasing from south to north, reflecting higher connectivity among southern populations and reduced gene flow at northern latitudes. With increasing gene flow, the number and clustering of FST outlier loci also increased, with differentiated loci found exclusively within large haploblocks harboring inversions and smaller peaks overlapping putative centromeric regions. Notably, sequence divergence was only evident in inversions, supporting their role in adaptive divergence with gene flow, whereas centromeric regions appeared differentiated because of low recombination and diversity, with no indication of elevated divergence. Our results support the hypothesis that clustered genomic architectures evolve with high gene flow and enhance our understanding of how inversions and centromeres are linked to different evolutionary processes.

Gene Flow↗
PubMed1980

Novel classes of mouse repeated DNAs.

Mouse DNA cleaved with Eco R11 (bst NI) displays two prominent restriction bands of 1.5 and 1.7 kb in agarose gels stained with ethidium bromide. These constitute novel subsets of repeated DNA in the mouse. Sequential Hoechst 33258-CsCl gradient fractionation of mouse DNA, yielding more GC rich main band DNA, and AT rich satellite DNA, revealed that both these fragments copurified with GC rich main band DNA. They were not detected in purified satellite preparations. Together these restriction bands constituted larger than or equal to 0.2% of main band DNAs. Hybridization of 32p labelled satellite DNA to blots of Eco R11 restricted mouse DNA showed positive hybridization only to smaller satellite restriction fragments, indicating satellite DNA had little or no homology with either the 1.5 or 1.7 kb fragments. The 1.5 and 1.7 kb fragments were isolated from gels and labelled with 32p by nick translation. Using a series of restriction endonucleases each of these two fragments showed different cleavage patterns. Filter hybridization confirmed that these two fragments were distinct subsets as they did not cross hybridize with each other. They also did not hybridize to other more minor repeated non-satellite DNA bands noted in ethidium bromide stained gels. Neither of them could be assigned to ribosomal genes as they did not hybridize to 32p kinase labelled 18S and 28S RNA. Isolation of DNA from male and female mice showed comparable amounts of both the 1.5 and 1.7 kb fragments. Thus neither was Y chromosome specific. From restriction patterns, and preliminary chromosome hybridization studies, these fragments are thought to represent "interspersed" repeated sequences rather than very long tandem (satellite like) centromeric arrays. The relationship between these repeated sequence subsets, their evolution and detailed organization, and their representation in different mouse species, remain to be determined.

Animals↗
PubMed1991

Characterisation of a tandem repetitive sequence cloned from the deer Capreolus capreolus and its chromosomal localisation in two muntjac species.

The isolation and characterisation of a highly repetitive DNA sequence from the genome of the Roe deer Capreolus capreolus is reported. This sequence is characterised by tandem repetition and located within centric heterochromatin as demonstrated by non isotopic in situ hybridisation to the karyotypes of the Indian and Chinese muntjacs. Amplification and/or clustering of these sequences during the drastic karyotype evolution of the genus Muntiacus was noted in the large centromere of the X chromosome of the Indian muntjac. Partial sequence analysis revealed a 62% sequence homology with the sat 1A sequences of Muntiacus muntjak vaginalis.

Animals↗
PubMed1985

Human U1 small nuclear RNA genes: extensive conservation of flanking sequences suggests cycles of gene amplification and transposition.

The DNA immediately flanking the 164-base-pair U1 RNA coding region is highly conserved among the approximately 30 human U1 genes. The U1 multigene family also contains many U1 pseudogenes (designated class I) with striking although imperfect flanking homology to the true U1 genes. Using cosmid vectors, we now have cloned, characterized, and partially sequenced three 35-kilobase (kb) regions of the human genome spanning U1 homologies. Two clones contain one true U1 gene each, and the third bears two class I pseudogenes 9 kb apart in the opposite orientation. We show by genomic blotting and by direct DNA sequence determination that the conserved sequences surrounding U1 genes are much more extensive than previously estimated: nearly perfect sequence homology between many true U1 genes extends for at least 24 kb upstream and at least 20 kb downstream from the U1 coding region. In addition, the sequences of the two new pseudogenes provide evidence that class I U1 pseudogenes are more closely related to each other than to true genes. Finally, it is demonstrated elsewhere (Lindgren et al., Mol. Cell. Biol. 5:2190-2196, 1985) that both true U1 genes and class I U1 pseudogenes map to chromosome 1, but in separate clusters located far apart on opposite sides of the centromere. Taken together, these results suggest a model for the evolution of the U1 multigene family. We speculate that the contemporary family of true U1 genes was derived from a more ancient family of U1 genes (now class I U1 pseudogenes) by gene amplification and transposition. Gene amplification provides the simplest explanation for the clustering of both U1 genes and class I pseudogenes and for the conservation of at least 44 kb of DNA flanking the U1 coding region in a large fraction of the 30 true U1 genes.

Base Sequence↗
PubMed2006

Duplication of centromeric histone H3 (HTR12) gene in Arabidopsis halleri and A. lyrata, plant species with multiple centromeric satellite sequences.

Arabidopsis halleri and lyrata have three different major centromeric satellite sequences, a unique finding for a diploid Arabidopsis species. Since centromeric histones coevolve with centromeric satellites, these proteins would be predicted to show signs of selection when new centromere satellites have recently arisen. We isolated centromeric protein genes from A. halleri and lyrata and found that one of them, HTR12 (CENP-A), is duplicated, while CENP-C is not. Phylogenetic analysis indicates that the HTR12 duplication occurred after these species diverged from A. thaliana. Genetic mapping shows that HTR12 copy B has the same genomic location as the A. thaliana gene; the other copy (A, at the other end of the same chromosome) is probably the new copy. To test for selection since the duplication, we surveyed diversity at both HTR12 loci within A. lyrata. Overall, there is no strong evidence for an "evolutionary arms race" causing multiple replacement substitutions. The A. lyrata HTR12B sequences fall into three classes of haplotypes, apparently maintained for a long time, but they all encode the same amino acid sequence. In contrast, HTR12A has low diversity, but many variants are amino acid replacements, possibly due to independent selective sweeps within populations of the species.

Arabidopsis↗
PubMed2000

Artificial chromosomes: a blueprint for the future?

Recent developments in molecular genetics have led to the synthesis of an artificial human chromosome. Because the chromosome replicates and divides normally in human cells, this has exciting possibilities in terms of mankind's ability to influence evolutionary processes and to modify the human genome.

Centromere↗
PubMed1995

Characterization and chromosomal location of two repeated DNAs in three Gerbillus species.

Two tandemly repeated DNA sequences of Gerbillus nigeriae (Rodentia) (GN1 and GN2) were isolated and characterized. Both share a 36bp repeated unit, which includes a 20bp motif also found in primate alphoid and other repeated DNAs. The localization of GN1 and GN2 sequences on metaphase chromosomes of three Gerbillus species, G. nigeriae, G. aureus and G. nanus, was studied by fluorescence in situ hybridization (FISH). In the G. nigeriae and G. aureus karyotypes, which were shown to possess large amounts of heterochromatin and to have undergone multiple rearrangements during evolution, both GN1 and GN2 sequences were observed at various chromosomal sites: centromeric, telomeric and intercalary. In contrast, the karyotypically stable G. nanus, which does not possess large amounts of heterochromatin and seems to be a more ancestral species, possesses only GN1 sequences, localized in the juxtacentromeric regions.

Animals↗
PubMed2003

Chromosome homology between chicken (Gallus gallus domesticus) and the red-legged partridge (Alectoris rufa); evidence of the occurrence of a neocentromere during evolution.

Chromosome-specific paints from macrochromosomes 1-9 and Z of the chicken were hybridised to metaphases of the red-legged partridge and revealed no inter-chromosomal rearrangements. The results from chromosome painting are similar to previous studies on the Japanese quail but different from findings in guinea fowl and several species of pheasant. The difference in centromere position in chicken and partridge chromosome 4, previously assumed to be the result of an inversion, was confirmed. However, FISH mapping of BAC clones from chicken chromosome 4 revealed that the order of loci was the same in both species, indicating the occurrence of a neocentromere during divergence.

Animals↗
PubMed2005

ERVK9, transposons and the evolution of MHC class I duplicons within the alpha-block of the human and chimpanzee.

The genomic sequences within the alpha-block (approximately 288-310 kb) of the human and chimpanzee MHC class I region contains ten MHC class I genes and three MIC gene fragments grouped together within alternating duplicated genomic segments or duplicons. In this study, the chimpanzee and human genomic sequences were analyzed in order to determine whether the remnants of the ERVK9 and other retrotransposon sequences are useful genomic markers for reconstructing the evolutionary history of the duplicated MHC gene families within the alpha-block. A variety of genes, pseudogenes, autologous DNA transposons and retrotransposons such as Alu and ERVK9 were used to categorize the ten duplicons into four distinct structural groups. The phylogenetic relationship of the ten duplicons was examined by using the neighbour joining method to analyze transposon sequence topologies of selected Alu members, LTR16B and Charlie9. On the basis of these structural groups and the phylogeny of the duplicated transposon sequences, a duplication model was reconstructed involving four multipartite tandem duplication steps to explain the organization and evolution of the ten duplicons within the alpha-block of the chimpanzee and human. The phylogenetic analysis and inferred duplication history suggests that the Patr/HLA-F was the first MHC class I gene to have been fixed and not required as a precursor for further duplication within the alpha-block of the ancestral species.

Animals↗
PubMed2005

Functional mapping of a trypanosome centromere by chromosome fragmentation identifies a 16-kb GC-rich transcriptional "strand-switch" domain as a major feature.

Trypanosomatids are an ancient family that diverged from the main eukaryotic lineage early in evolution, which display several unique features of gene organization and expression. Although genome sequencing is now complete, the nature of centromeres in these and other parasitic protozoa has not been resolved. Here, we report the functional mapping of a centromere in the American trypanosome, Trypanosoma cruzi, a parasite with an unusual mechanism of genetic exchange that involves the generation of aneuploidy by nuclear hybridization. Using a telomere-associated chromosome fragmentation approach, we show that the region required for the mitotic stability of chromosome 3 encompasses a transcriptional "strand-switch" domain constituted by a 16-kb GC-rich island. The domain contains several degenerate retrotransposon-like insertions, but atypically, lacks the arrays of satellite repeats normally associated with centromeric regions. This unusual type of organization may represent a paradigm for centromeres in T. cruzi and other primitive eukaryotes.

Animals↗
PubMed2006

A Survey of the Brassica rapa genome by BAC-end sequence analysis and comparison with Arabidopsis thaliana.

Brassica rapa ssp. pekinensis (Chinese cabbage) is an economically important crop and a model plant for studies on polyploidization and phenotypic evolution. To gain an insight into the structure of the B. rapa genome we analyzed 12,017 BAC-end sequences for the presence of transposable elements (TEs), SSRs, centromeric satellite repeats and genes, and similarity to the closely related genome of Arabidopsis thaliana. TEs were estimated to occupy 14% of the genome, with 12.3% of the genome represented by retrotransposons. It was estimated that the B. rapa genome contains 43,000 genes, 1.6 times greater than the genome of A. thaliana. A number of centromeric satellite sequences, representing variations of a 176-bp consensus sequence, were identified. This sequence has undergone rapid evolution within the B. rapa genome and has diverged among the related species of Brassicaceae. A study of SSRs demonstrated a non-random distribution with a greater abundance within predicted intergenic regions. Our results provide an initial characterization of the genome of B. rapa and provide the basis for detailed analysis through whole-genome sequencing.

Arabidopsis↗
PubMed1996

The physical and genomic organization of microsatellites in sugar beet.

Microsatellites, tandem arrays of short (2-5 bp) nucleotide motifs, are present in high numbers in most eukaryotic genomes. We have characterized the physical distribution of microsatellites on chromosomes of sugar beet (Beta vulgaris L.). Each microsatellite sequence shows a characteristic genomic distribution and motif-dependent dispersion, with site-specific amplification on one to seven pairs of centromeres or intercalary chromosomal regions and weaker, dispersed hybridization along chromosomes. Exclusion of some microsatellites from 18S-5.8S-25S rRNA gene sites, centromeres, and intercalary sites was observed. In-gel and in situ hybridization patterns are correlated, with highly repeated restriction fragments indicating major centromeric sites of microsatellite arrays. The results have implications for genome evolution and the suitability of particular microsatellite markers for genetic mapping and genome analysis.

Base Sequence↗
PubMed1988

Reproducible compartmentalization of individual chromosome domains in human CNS cells revealed by in situ hybridization and three-dimensional reconstruction.

Specific chromosome domains in interphase nuclei of neurons and glia were studied by three-dimensional (3-D) reconstruction of serial optical sections from in situ hybridized human CNS tissue. Overall patterns of centromere organization, delineated with alphoid repeats, were comparable to those seen in mouse, and are clearly conserved in mammalian evolution. Cloned probes from other individual chromosome domains were used to define interphase organization more precisely. Homologous chromosomes were spatially separated in nuclei. In large neurons, probes specific for 9q12, or 1q12 showed that at least one homolog was always compartmentalized together with centromeres on the nucleolus, while the second signal either abutted the nucleolus or was on the nuclear membrane. A telomeric Yq12 sequence also localized together with perinucleolar centromeres in a completely non-Rabl orientation. In astrocytes, these three chromosome regions were on the membrane and not necessarily associated with nucleoli. Therefore there are different patterns of interphase chromosome organization in functionally distinct cell types. In contrast to the above domains, a 1p36.3 telomeric sequence embedded in a large Alu-rich and early replicating chromosome region, was always found in an interior euchromatic nuclear compartment in both neurons and glial cells. In double hybridizations with 1q12 and 1p36.3 probes, 1p arms were clearly separated in all cells, and arms projected radially into the interior nucleoplasm with non-Rabl orientations. There was no absolute or rigid position for each 1p arm with respect to each other or to the major dendrite, indicating that individual chromosome arms may be dynamically positioned even in highly differentiated cell types. We suggest that centromeric and other highly repeated non-transcribed sequence domains may act as general organizing centers for cell type specific interphase patterns that are conserved in mammalian evolution. Such centers would allow selected groups of chromosome arms to extend into (and contract from) an interior, presumably transcriptionally active, nuclear compartment.

Astrocytes↗