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PubMed2025

Cytotype classification and genetic diversity of Platostoma palustre revealed by rDNA localization and chloroplast genome.

BACKGROUND: Platostoma palustre A. J. Paton is an edible medicinal plant that plays a significant role in traditional food production and medicinal applications. However, the genetic basis of P. palustre remains unclear, thereby hampering research on its genome and polyploid evolution. RESULTS: To characterize the karyotype and ploidy of P. palustre, we performed fluorescence in situ hybridization (FISH) by using 35 S and 5 S rDNA probes in P. palustre. FISH results indicated that 35 S rDNA mapped to the end of the chromosome (chromosome satellite, heterochromatic region) and that 5 S rDNA was located close to the centromere of the chromosomes. Based on the rDNA sites, we identified three distinct cytotypes of P. palustre: diploid (2n = 2x = 30, x = 15), triploid (2n = 3x = 45, x = 15), and tetraploid (2n = 4x = 60, x = 15). To further explore the genetic evolutionary relationship among these P. palustre cytotypes, we conducted Illumina sequencing and assembled the chloroplast (CP) genome. The CP genomes of P. palustre accessions maintained a conserved single circular molecule with a length of 152,534 - 152,788 bp, comprising a large single-copy region (LSC) and small single-copy region (SSC) separated by two inverted repeat regions (IRs). Phylogenetic trees were also created based on CP and nuclear molecular markers, showing that most P. palustre accessions clustered together corresponding to their collection regions. Of these, GDZC2 (2n = 2x = 30) clustered with several triploid accessions, suggesting that it may share a common ancestor with these triploid accessions. CONCLUSIONS: This is the first study to characterize the karyotype, identify three cytotypes of P. palustre using FISH, and provide molecular evidence for an evolutionary relationship among different P. palustre accessions. These findings will be useful for further genomic studies and polyploid evolution of P. palustre.

Genome, Chloroplast↗
PubMed2026

Evolution of maize recombination landscape during domestication.

Despite the plethora of knowledge about the benefits of meiotic recombination and numerous theoretical studies examining how recombination rates evolve, there is a general lack of empirical support and consensus across species. To fill this knowledge gap, we characterized the evolution of recombination landscape in maize during its domestication from teosinte and related the observed changes to established theoretical frameworks. Through examining recombination in experimental populations of maize and teosinte and the population genomics approach of identifying historical recombination events using ancestral recombination graph inference to generate saturated maize and teosinte recombination maps, we found that during domestication, maize experienced a 12% increase in its genome-wide recombination rate. Furthermore, maize evolved higher recombination rates on the long arms of chromosomes in regions closer to centromeres, where recombination is generally very low. The repatterning of crossover events came from changes in global crossover positioning rather than alterations in cis-acting chromatin factors. Consequently, we found evidence of selection acting on trans-acting recombination modifiers affecting crossover interference and controlling the interference-dependent class I crossover pathway. We show that CO repatterning was likely beneficial for maize fitness, as significant recombination rate increases were predominantly in gene-rich regions, which harbor domestication-related variation. This work suggests genomic and mechanistic processes leading to the evolution of meiotic recombination landscape in response to directional selection pressure and provides evidence for the evolutionary advantage of recombination.

Zea mays↗
PubMed1991

Tg (9 HSA-MYC), a homozygous lethal insertion in the mouse.

Transgenic mice generated with different DNA sequences were surveyed for possible homozygous mutant phenotypes. We found an embryonic lethal mutation in the transgenic mouse strain (MT-MYC12.4) containing the human c-myc gene. Embryos homozygous for the transgene die shortly after implantation. The strain MT-MYC12.4 carries approximately 50 tandem copies of the recombinant plasmid sequence. The 3' flanking sequence has been cloned and analyzed. It contains a unique sequence that has been conserved during evolution and maps to Chromosome (Chr) 9. This mutant has been designated Tg 9 (HSA-MYC).

Animals↗
PubMed2000

Evolutionary conservation of kinetochore protein sequences in plants.

The evolutionary conservation of structural/functional kinetochore proteins has been studied on isolated nuclei and pro-/metaphase chromosomes of mono- and dicot plants. The cross-reactivities of antibodies against human CENPC, CENPE and CENPF, and against maize CENPCa with the centromeric regions of mitotic chromosomes of Vicia faba and/or Hordeum vulgare are shown. Putative homologs of the kinetochore protein SKP1 (suppressor of kinetochore protein 1p of yeast) were found in both species and of CBF5p (centromere binding factor 5 of yeast) in barley. Antibodies against synthetic peptides derived from partial sequences encoding these proteins were produced and recognized the centromeric regions on mitotic chromosomes as detected by indirect immunofluorescence.

Amino Acid Sequence↗
PubMed2000

Apparently unrelated clones shown by spectral karyotyping to represent clonal evolution of cryptic t(10;11)(p13;q23) in a patient with acute monoblastic leukemia.

The accurate genetic classification of acute leukemia is of the utmost clinical importance for treatment stratification. In the present study, we report on a young girl with aggressive acute monoblastic leukemia (AML) (M5b) with skin, lymph node, and bone marrow involvement, in whom cytogenetic analysis revealed three clones with different secondary chromosomal changes. Two clones had the secondary +8 and del(9q) aberrations, with the der(11)t(1;11) in the second one; the third clone was apparently unrelated to the others, and had add(7)(p?21),-13,+22. Using the spectral karyotyping (SKY) technique, we found that all three clones originated from a common clone that harbored the hidden primary t(10;11)(p13;q23) or its derivatives, suggesting clonal evolution. The first clone had the balanced t(10;11), the second had its derivative, der(10)t(10;11), and the third had the other derivative, der(11)t(10;11). On fluorescence in situ hybridization (FISH), MLL gene splitting, with translocation of its centromeric portion to 10p, and deletion of its telomeric portion, was demonstrated. In conclusion, the detection of the very poor prognostic t(10;11) aberration in AML, was possible by complementing the traditional cytogenetic analysis with SKY and FISH.

Bone Marrow Cells↗
PubMed1980

Chromosomal interrelationship of hamster species of the genus Mesocricetus.

The similarity of chromosomes and the mode by which differences occurred in the chromosomes of the species comprising the genus Mesocricetus, M. auratus (2n = 44), two "cryptic" species of M. brandti (2n = 44 and 2n = 42) and M. newtoni (2n = 38) were determined. Most of the autosomes and the sex chromosomes have either complete or partial G-band correspondence and thus provide definitive evidence for the taxonomic relationship of these species. The karyotypic differences occurred primarily as a result of deletion of sex chromosome heterochromatin and of autosomal translocations that frequently involved chromosomes with heterochromatic short arms or chromosomes bearing NOR's. Only one Robertsonian centric fusion occurred. Despite the conservatism of arrangement of the genetic material, the chromosomal distribution of heterochromatin diverged during the evolution of these species. M. brandti and newtoni each have a metacentric chromosome with a common long arm matching a submetacentric M. auratus autosome, but a short arm corresponding to two different M. auratus chromosomes. These translocations are crucial for explaining the direction of chromosomal evolution of these species and indicate that M. auratus was the commmon ancestral species and that M. brandti and newtoni subsequently evolved independently.

Animals↗
PubMed1996

Chromosomal localization of the major and 5S rRNA genes in the European eel (Anguilla anguilla).

The major (18S, 5.8S, and 28S) and 5S rRNA genes have been mapped by double fluorescent in situ hybridization to European eel metaphase chromosomes. The major rRNA genes were localized to a submetacentric pair of chromosomes that showed a consistent size polymorphism among the individuals studied. The 5S rRNA genes were clustered in a single locus that mapped to the centromeric region of an acrocentric pair. In contrast to the major rRNA genes, no detectable polymorphism, in either size or intensity of the fluorescent signal, was observed. The chromosomal organization of both families of rRNA genes are discussed in terms of genomic organization and chromosomal evolution.

Anguilla↗
PubMed1989

Evolution of mouse chromosome 17 and the origin of inversions associated with t haplotypes.

Mouse t haplotypes are variant forms of chromosome 17 that exist at high frequencies in worldwide populations of several species of house mouse. They are known to differ from wild-type chromosomes with respect to two relative inversions referred to as proximal and distal. An untested assumption has been that these two inversions originated in the chromosomal lineage leading to present-day t haplotypes. To investigate the evolutionary origins of these inversions and the possibility of additional inversions, interspecific crosses were performed between Mus spretus or Mus abbotti and laboratory strains of Mus domesticus that carried wild-type and t haplotypes forms of chromosome 17. The results provide evidence for the existence of two additional nonoverlapping inversions--one between the proximal and distal inversions and one between the centromere and the proximal inversion. These four inversions span nearly the entire region of t haplotype recombination suppression. Considering the distribution of these inversions among the species studied as well as the organization of the D17Leh66 family of DNA elements, we infer that the proximal inversion occurred on the lineage leading to the common ancestor of M. domesticus and M. abbotti, and that the other three inversions occurred on the separate lineage leading to present-day t haplotypes. Alternative models for the evolution of t haplotypes are discussed in light of these findings.

Animals↗
PubMed1993

Pathological and biological relevance of cytophotometric DNA content to breast carcinoma genetic progression.

Correlating cytophotometrically detectable genetic alterations to events of known biological and pathological significance in breast carcinoma has been challenging, in large part owing to the difficulty in isolating and analyzing premalignant (i.e., hyperplastic) or preinvasive (i.e., in situ carcinoma) lesions. This problem may be addressed by using histologically directed evaluation of intact, paraffin-embedded tissue sections. Using image cytophotometry in preserved sections, we have identified clonal DNA content abnormalities (i.e., aneuploidy) in up to three-fourths of preinvasive breast carcinomas. Moreover, comparison of ploidy determinations between residual in situ and corresponding invading neoplastic populations suggests that host invasion is accompanied by measurable DNA content shifts in many cases. Image cytophotometric DNA content abnormalities are also detectable in florid/atypical proliferative lesions, albeit less frequently (-25% of cases) and to a lesser extent (i.e., near-diploid) than in situ carcinomas. Taken together, these findings imply an association between clonal DNA content aberrations and histologic disease progression. Although the sensitivity of cytophotometric ploidy assessments in tissue sections is limited by nuclear sectioning artifact and overlap, the presence of genomic instability in precursor lesions is supported by evidence of individual chromosome aneuploidy, which can be demonstrated in tissue sections by interphase cytogenetics with fluorescent, centromere-specific probes. Further, presence of intra-tumoral clonal DNA content heterogeneity is confirmed by cytogenetic studies showing co-existing near-diploid chromosome number modes in many tumors with hyperdiploid stemlines. Karyotypic stemline analyses imply polyploidization events are an important mechanism of clonal evolution leading to genetic heterogeneity.(ABSTRACT TRUNCATED AT 250 WORDS)

Breast Neoplasms↗
PubMed1986

[Various characteristics of gene localization in eukaryotic chromosomes. Formulation of a problem and analysis of non-random localization of mating type loci in fungi].

We have denoted two possible models of gene order evolution as the "card" and "chess" models. The first suggests random shuffling of genes during evolution, the second--non-random gene transposition, gene order being checked by natural selection. We discuss here localization of the mating type locus in fungal genomes. In 8 of 10 genetically well studied species of ascomycetous fungi, the mating type locus is linked to a centromere; in one species, it segregates regularly during the second meiotic division, and only one species does not show any regularity in the mating type locus segregation. Centromeric linkage of the mating type locus maintains heterozygosity of all centromeric genome regions during intratetrad fertilization observed in some fungi. Non-random localization of mating type locus can be considered as the means for conservation of heterozygosity.

Chromosome Mapping↗
PubMed2003

Cytogenetic characterization of tumors of the vulva and vagina.

Neoplasms of the vulva and vagina account for less than 5% of all female genital tract cancers. Squamous cell carcinoma (SCC) represents more than 70% of the cases in both locales, followed by melanoma, basal cell carcinoma, Paget's disease, and other carcinoma subtypes. Until recently, only few cases had been analyzed by chromosome banding techniques and karyotyped, and also the number subjected to molecular cytogenetic analysis remains low. To understand better the genetic changes harbored by the neoplastic cells in cancer of the vulva and vagina, we analyzed cytogenetically 51 such tumors, finding karyotypic abnormalities in 37. All tumors were analyzed by G-banding, sometimes supplemented by multicolor fluorescence in situ hybridization, and a subset of tumors was also analyzed by comparative genomic hybridization. The two cytogenetically abnormal cases of Paget's disease both had two clones, one with gain of chromosome 7 as the sole change, the other with loss of the X chromosome among, in one case, other aberrations. The four cytogenetically abnormal malignant melanomas (three of the vulva, one of the vagina) presented complex karyotypes with aberrations involving different chromosomes but most often chromosome 1, specifically 1p12-q41. In the 31 cytogenetically abnormal SCCs, different clonal karyotypic abnormalities were seen. Intratumor heterogeneity with multiple clones was observed in 11 cases. The clones were cytogenetically unrelated in eight tumors but related in three, indicating that in the latter clonal evolution had taken place from a single malignantly transformed cell. The main chromosomal imbalances were gains of, or from, chromosome arms 3q, 5p, 8q, 9q, and 19q, and loss from 11q. Breakpoint clusters were seen in 11q13-23, 2q22-35, and 19q13, as well as in the centromeres and pericentromeric bands of chromosomes 3, 8, 9, 13, 14, and 22.

Carcinoma in Situ↗
PubMed2001

Isolation of SDS-stable complexes of the intermediate filament protein vimentin with repetitive, mobile, nuclear matrix attachment region, and mitochondrial DNA sequence elements from cultured mouse and human fibroblasts.

Crosslinkage of vimentin to DNA in mouse L929 cells by formaldehyde and isolation of SDS-stable DNA-vimentin complexes from normal L929 cells and mouse and human embryo fibroblasts indicated close spatial relations between these components in the intact cell. The adducts, obtained by immunoprecipitation with anti-vimentin antibody, contained substantial quantities, not only of repetitive and mobile sequence elements such as centromeric satellite DNA, telomere DNA, microsatellites and minisatellites, long and short interspersed nucleotide elements, and retroposons, but also of mitochondrial (mt) DNA. Because the SDS-stable complexes could be isolated with distinctly higher yields from oxidatively stressed, senescent fibroblasts and were dissociated by boiling, they possibly arose from accidental condensation reactions mediated by unsaturated and dialdehydes, products of free radical-induced lipid peroxidation. They can therefore be considered vestiges of a general interaction of vimentin with cellular DNA. The sequence patterns of their DNA fragments were similar to those of extrachromosomal circular and linear DNA, including retroviral elements, markers and enhancers of genomic instability that also occur in the cytoplasm and are able to transport vimentin into the nucleus. Many of the fragments were also remarkably similar to AT-rich nuclear matrix attachment regions (MARs) in that they contained, in addition to various mobile elements, a palette of typical MAR motifs. With its tendency to multimerize and to interact with single-stranded and supercoiled DNA, vimentin thus behaves like a nuclear matrix protein and may as such participate in a variety of nuclear matrix-associated processes such as replication, recombination, repair, and transcription of DNA. These activities seem to be extendible to the mitochondrial compartment, as vimentin was also crosslinked to mtDNA, preferentially to its D-loop and hypervariable main control region. These sites are prone to point and deletion mutations and, like nuclear MARs, are associated with the cyto-karyomatrix. Moreover, as a developmentally regulated and tissue-specific cyto-karyomatrix protein, vimentin may contribute to the organization of chromatin, including centromeric and telomeric heterochromatin at the nuclear periphery, with all its consequences for genomic activities during embryogenesis and in adulthood of vertebrates. However, because of its high affinity for hypervariable, recombinogenic DNA sequences, vimentin is proposed to play a major role in both the preservation and the evolution of the nuclear and mitochondrial genome.

Animals↗
PubMed1998

The structure and evolution of angiosperm nuclear genomes.

Despite several decades of investigation, the organization of angiosperm genomes remained largely unknown until very recently. Data describing the sequence composition of large segments of genomes, covering hundreds of kilobases of contiguous sequence, have only become available in the past two years. Recent results indicate commonalities in the characteristics of many plant genomes, including in the structure of chromosomal components like telomeres and centromeres, and in the order and content of genes. Major differences between angiosperms have been associated mainly with repetitive DNAs, both gene families and mobile elements. Intriguing new studies have begun to characterize the dynamic three-dimensional structures of chromosomes and chromatin, and the relationship between genome structure and co-ordinated gene function.

Chromosomes↗
PubMed2004

The mouse secreted gel-forming mucin gene cluster.

Using genomic cosmid and BAC clones and genome shotgun supercontigs available in GenBank, we determined the complete gene structure of the four mouse secreted gel-forming mucin genes Muc2, Muc5ac, Muc5b and Muc6 and the organization of the genomic locus harboring these genes. The mouse secreted gel-forming mucin gene is 215 kb on distal chromosome 7 to 69.0 cM from the centromere and organized as: Muc6-Muc2-Muc5ac-Muc5b with Muc2, Muc5ac and Muc5b arranged in the same orientation and Muc6 in opposite. Mouse mucin genes have highly similar genomic organization to each other and to their respective human homologues indicating that they have been well conserved through evolution. Deduced peptides showed striking sequence similarities in their N- and C-terminal regions whereas the threonine/serine/proline-rich central region is specific for each other and for species. Expression studies also showed that they have expression patterns similar to human mucin genes with Muc2 expressed in small and large intestines, Muc5ac and Muc6 in stomach, and Muc5b in laryngo-tracheal tract. These data constitute an important initial step for investigation of mucin gene regulation and mucin function through the use of animal models.

Amino Acid Sequence↗
PubMed2001

Telomere dysfunction triggers extensive DNA fragmentation and evolution of complex chromosome abnormalities in human malignant tumors.

Although mechanisms for chromosomal instability in tumors have been described in animal and in vitro models, little is known about these processes in man. To explore cytogenetic evolution in human tumors, chromosomal breakpoint profiles were constructed for 102 pancreatic carcinomas and 140 osteosarcomas, two tumor types characterized by extensive genomic instability. Cases with few chromosomal alterations showed a preferential clustering of breakpoints to the terminal bands, whereas tumors with many changes showed primarily interstitial and centromeric breakpoints. The terminal breakpoint frequency was negatively correlated to telomeric TTAGGG repeat length, and fluorescence in situ hybridization with telomeric TTAGGG probes consistently indicated shortened telomeres and >10% of chromosome ends lacking telomeric signals. Because telomeric dysfunction may lead to formation of unstable ring and dicentric chromosomes, mitotic figures were also evaluated. Anaphase bridges were found in all cases, and fluorescence in situ hybridization demonstrated extensive structural rearrangements of chromosomes, with terminal transferase detection showing fragmented DNA in 5-20% of interphase cells. Less than 2% of cells showed evidence of necrosis or apoptosis, and telomerase was expressed in the majority of cases. Telomeric dysfunction may thus trigger chromosomal fragmentation through persistent bridge-breakage events in pancreatic carcinomas and osteosarcomas, leading to a continuous reorganization of the tumor genome. Telomerase expression is not sufficient for completely stabilizing the chromosome complement but may be crucial for preventing complete genomic deterioration and maintaining cellular survival.

Adolescent↗
PubMed2004

Evolutionary history of chromosome 20.

The evolutionary history of human chromosome 20 in primates was investigated using a panel of human BAC/PAC probes spaced along the chromosome. Oligonucleotide primers derived from the sequence of each human clone were used to screen horse, cat, pig, and black lemur BAC libraries to assemble, for each species, a panel of probes mapping to chromosomal loci orthologous to the loci encompassed by the human BACs. This approach facilitated marker-order comparison aimed at defining marker arrangement in primate ancestor. To this goal, we also took advantage of the mouse and rat draft sequences. The almost perfect colinearity of chromosome 20 sequence in humans and mouse could be interpreted as evidence that their form was ancestral to primates. Contrary to this view, we found that horse, macaque, and two New World monkeys share the same marker-order arrangement from which the human and mouse forms can be derived, assuming similar but distinct inversions that fully account for the small difference in marker arrangement between humans and mouse. The evolutionary history of this chromosome unveiled also two centromere repositioning events in New World monkey species.

Animals↗
PubMed2006

Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes.

Most genes are conserved in mammals, but certain gene families have acquired large numbers of lineage-specific loci through repeated rounds of gene duplication, divergence, and loss that have continued in each mammalian group. One such family encodes KRAB-zinc finger (KRAB-ZNF) proteins, which function as transcriptional repressors. One particular subfamily of KRAB-ZNF genes, including ZNF91, has expanded specifically in primates to comprise more than 110 loci in the human genome. Genes of the ZNF91 subfamily reside in large gene clusters near centromeric regions of human chromosomes 19 and 7 with smaller clusters or isolated copies in other locations. Phylogenetic analysis indicates that many of these genes arose before the split between the New and Old World monkeys, but the ZNF91 subfamily has continued to expand and diversify throughout the evolution of apes and humans. Paralogous loci are distinguished by divergence within their zinc finger arrays, indicating selection for proteins with different regulatory targets. In addition, many loci produce multiple alternatively spliced transcripts encoding proteins that may serve separate and perhaps even opposing regulatory roles because of the modular motif structure of KRAB-ZNF genes. The tissue-specific expression patterns and rapid structural divergence of ZNF91 subfamily genes suggest a role in determining gene expression differences between species and the evolution of novel primate traits.

Animals↗
PubMed2026

Divergent trajectories of genome architecture and chromosome evolution in ferns and angiosperms.

Ferns and angiosperms represent the two largest vascular plant lineages but exhibit striking genomic and ecological contrasts. We investigated whether differences in genome size, chromosome architecture, GC content, and stomatal traits reveal divergent evolutionary trajectories between these lineages. We assembled the most comprehensive dataset to date, integrating genome size, chromosome number and size, GC content, and stomatal traits for over 1100 fern species and compared it with an extensive angiosperm dataset. Ferns exhibited markedly lower variability and c. 16-fold slower rates of chromosome size evolution than angiosperms. A persistent positive relationship between genome size and chromosome number in ferns suggests limited cytological post-polyploid diploidization. While ferns generally possess larger stomata, this difference disappears after accounting for genome size, indicating that nucleotypic constraints, rather than lineage-specific physiology, dictate stomatal dimensions. Both groups share a unimodal GC-genome size relationship peaking at c. 14 Gbp. Larger fern chromosomes imply lower genome-wide recombination rates, potentially limiting genetic reshuffling and adaptive potential. Our results highlight fundamentally divergent evolutionary trajectories, likely shaped by meiotic symmetry in ferns and meiotic asymmetry, possibly centromere drive, and post-polyploid diploidization in angiosperms, defining the functional and genomic landscapes of these lineages across deep evolutionary timescales.

Genome, Plant↗