Showing papers on "Karyotype published in 2013"

Validation of targeted sequencing of single-nucleotide polymorphisms for non-invasive prenatal detection of aneuploidy of chromosomes 13, 18, 21, X, and Y

Abstract: Objective To assess the performance of cell-free DNA (cfDNA) testing in maternal blood for detection of fetal aneuploidy of chromosomes 13, 18, 21, X, and Y using targeted sequencing of single-nucleotide polymorphisms. Methods Prospective study in 242 singleton pregnancies undergoing chorionic villus sampling at 11 to 13weeks. Maternal blood was collected before chorionic villus sampling and sent to Natera (San Carlos, CA, USA). cfDNA was isolated from maternal plasma, and targeted multiplex PCR amplification followed by sequencing of 19488 polymorphic loci covering chromosomes 13, 18, 21, X, and Y was performed. Sequencing data were analyzed using the NATUS algorithm that determines the copy number and calculates a sample-specific accuracy for each of the five chromosomes tested. Laboratory personnel were blinded to fetal karyotype. Results Results were provided for 229 (94.6%) of the 242 cases. Thirty-two cases were correctly identified as aneuploid, including trisomy 21 [n=25; sensitivity=100% (CI: 86.3–100%), specificity=100% (CI: 98.2–100%)], trisomy 18 (n=3), trisomy 13 (n=1), Turner syndrome (n=2), and triploidy (n=1), with no false positive or false negative results. Median accuracy was 99.9% (range: 96.0–100%). Conclusions cfDNA testing in maternal blood using targeted sequencing of polymorphic loci at chromosomes 13, 18, 21, X, and Y holds promise for accurate detection of fetal autosomal trisomies, sex chromosome aneuploidies, and triploidy. © 2013 John Wiley & Sons, Ltd.

ISCN 2013 : an international system for human cytogenetic nomenclature (2013) : recommendations of the International Standing Committee on Human Cytogenetic Nomenclature

Abstract: Historical Introduction Normal Chromosomes Symbols and Abbreviated Terms Karyotype Designation Uncertainty in Chromosome or Band Designation Order of Chromosome Abnormalities in the Karyotype Normal Variable Chromosome Features Numerical Chromosome Abnormalities Structural Chromosome Rearrangements Chromosome Breakage Neoplasia Meiotic Chromosomes In situ Hybridization Microarrays Region-Specific Assays.

Reversal of an ancient sex chromosome to an autosome in Drosophila

Abstract: Although transitions of sex-determination mechanisms are frequent in species with homomorphic sex chromosomes, heteromorphic sex chromosomes are thought to represent a terminal evolutionary stage owing to chromosome-specific adaptations such as dosage compensation or an accumulation of sex-specific mutations. Here we show that an autosome of Drosophila, the dot chromosome, was ancestrally a differentiated X chromosome. We analyse the whole genome of true fruitflies (Tephritidae), flesh flies (Sarcophagidae) and soldier flies (Stratiomyidae) to show that genes located on the dot chromosome of Drosophila are X-linked in outgroup species, whereas Drosophila X-linked genes are autosomal. We date this chromosomal transition to early drosophilid evolution by sequencing the genome of other Drosophilidae. Our results reveal several puzzling aspects of Drosophila dot chromosome biology to be possible remnants of its former life as a sex chromosome, such as its minor feminizing role in sex determination or its targeting by a chromosome-specific regulatory mechanism. We also show that patterns of biased gene expression of the dot chromosome during early embryogenesis, oogenesis and spermatogenesis resemble that of the current X chromosome. Thus, although sex chromosomes are not necessarily evolutionary end points and can revert back to an autosomal inheritance, the highly specialized genome architecture of this former X chromosome suggests that severe fitness costs must be overcome for such a turnover to occur.

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

Abstract: We report intron chromosomal expression FISH (iceFISH), a multiplex imaging method for measuring gene expression and chromosome structure simultaneously on single chromosomes. We find substantial differences in transcriptional frequency between genes on a translocated chromosome and the same genes in their normal chromosomal context in the same cell. Correlations between genes on a single chromosome pointed toward a cis chromosome-level transcriptional interaction spanning 14.3 megabases.

Non-invasive prenatal testing of fetal whole chromosome aneuploidy by massively parallel sequencing.

Abstract: Objective To determine whether non-invasive prenatal testing by maternal plasma DNA sequencing can uncover all fetal chromosome aneuploidies in one simple sequencing event. Methods Plasma samples from 435 pregnant women at high risk for Down syndrome were collected prior to amniocentesis in three hospitals in China between March 2009 and June 2011. We sequenced the plasma DNA extracted from these samples at low coverage. We discovered that the genome representation of each of the 24 chromosomes obeyed a linear relationship to its GC content. Applying this relationship, we analysed the copy number of each of the 24 chromosomes. Full fetal karyotyping was compared with maternal plasma DNA sequencing results. Results Among the 435 samples, 412 samples (94.7%) have full karyotyping and sequencing results. Sixty-seven samples containing a fetal chromosome aneuploidy, including trisomy 21, trisomy 18, trisomy 13, trisomy 9, monosomy X or others, can be accurately identified with a detection sensitivity of 100% and a detection specificity of 99.71%. Normalization of the chromosome representation values against chromosomal guanine/cytosine base content is the key issue to ensure the accuracy. Conclusions Our results indicate that non-invasive detection of fetal chromosome aneuploidies for all 24 chromosomes in one single sequencing event is feasible. © 2013 John Wiley & Sons, Ltd.

Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat.

Abstract: Allopolyploidization has been a driving force in plant evolution. Formation of common wheat (Triticum aestivum L.) represents a classic example of successful speciation via allopolyploidy. Nevertheless, the immediate chromosomal consequences of allopolyploidization in wheat remain largely unexplored. We report here an in-depth investigation on transgenerational chromosomal variation in resynthesized allohexaploid wheats that are identical in genome constitution to common wheat. We deployed sequential FISH, genomic in situ hybridization (GISH), and homeolog-specific pyrosequencing, which enabled unequivocal identification of each of the 21 homologous chromosome pairs in each of >1,000 individual plants from 16 independent lines. We report that whole-chromosome aneuploidy occurred ubiquitously in early generations (from selfed generation S1 to >S20) of wheat allohexaploidy although at highly variable frequencies (20–100%). In contrast, other types of gross structural variations were scant. Aneuploidy included an unexpected hidden type, which had a euploid chromosome number of 2n = 42 but with simultaneous loss and gain of nonhomeologous chromosomes. Of the three constituent subgenomes, B showed the most lability for aneuploidy, followed by A, but the recently added D subgenome was largely stable in most of the studied lines. Chromosome loss and gain were also unequal across the 21 homologous chromosome pairs. Pedigree analysis showed no evidence for progressive karyotype stabilization even with multigenerational selection for euploidy. Profiling of two traits directly related to reproductive fitness showed that although pollen viability was generally reduced by aneuploidy, the adverse effect of aneuploidy on seed-set is dependent on both aneuploidy type and synthetic line.

Cancer cells preferentially lose small chromosomes.

Abstract: Genetic and genomic aberrations are the primary cause of cancer. Chromosome missegregation leads to aneuploidy and provides cancer cells with a mechanism to lose tumor suppressor loci and gain extra copies of oncogenes. Using cytogenetic and array-based comparative genomic hybridization data, we analyzed numerical chromosome aneuploidy in 43,205 human tumors and found that 68% of solid tumors are aneuploid. In solid tumors, almost all chromosomes are more frequently lost than gained with chromosomes 7, 12 and 20 being the only exceptions with more frequent gains. Strikingly, small chromosomes are lost more readily than large ones, but no such inverse size correlation is observed with chromosome gains. Because of increasing levels of proteotoxic stress, chromosome gains have been shown to slow cell proliferation in a manner proportional to the number of extra gene copies gained. However, we find that the extra chromosome in trisomic tumors does not preferentially have a low gene copy number, suggesting that a proteotoxicity-mediated proliferation barrier is not sustained during tumor progression. Paradoxically, despite a bias toward chromosome loss, gains of chromosomes are a poor prognostic marker in ovarian adenocarcinomas. In addition, we find that solid and non-solid cancers have markedly distinct whole-chromosome aneuploidy signatures, which may underlie their fundamentally different etiologies. Finally, preferential chromosome loss is observed in both early and late stages of astrocytoma. Our results open up new avenues of enquiry into the role and nature of whole-chromosome aneuploidy in human tumors and will redirect modeling and genetic targeting efforts in patients.

Aneuploidy and chromosomal instability: a vicious cycle driving cellular evolution and cancer genome chaos

Abstract: Aneuploidy and chromosomal instability frequently co-exist, and aneuploidy is recognized as a direct outcome of chromosomal instability. However, chromosomal instability is widely viewed as a consequence of mutations in genes involved in DNA replication, chromosome segregation, and cell cycle checkpoints. Telomere attrition and presence of extra centrosomes have also been recognized as causative for errors in genomic transmission. Here, we examine recent studies suggesting that aneuploidy itself can be responsible for the procreation of chromosomal instability. Evidence from both yeast and mammalian experimental models suggests that changes in chromosome copy number can cause changes in dosage of the products of many genes located on aneuploid chromosomes. These effects on gene expression can alter the balanced stoichiometry of various protein complexes, causing perturbations of their functions. Therefore, phenotypic consequences of aneuploidy will include chromosomal instability if the balanced stoichiometry of protein machineries responsible for accurate chromosome segregation is affected enough to perturb the function. The degree of chromosomal instability will depend on specific karyotypic changes, which may be due to dosage imbalances of specific genes or lack of scaling between chromosome segregation load and the capacity of the mitotic system. We propose that the relationship between aneuploidy and chromosomal instability can be envisioned as a “vicious cycle,” where aneuploidy potentiates chromosomal instability leading to further karyotype diversity in the affected population.

Chromosomal Mapping of Repetitive DNAs in the Grasshopper Abracris flavolineata Reveal Possible Ancestry of the B Chromosome and H3 Histone Spreading

Abstract: Supernumerary chromosomes (B chromosomes) occur in approximately 15% of eukaryote species. Although these chromosomes have been extensively studied, knowledge concerning their specific molecular composition is lacking in most cases. The accumulation of repetitive DNAs is one remarkable characteristic of B chromosomes, and the occurrence of distinct types of multigene families, satellite DNAs and some transposable elements have been reported. Here, we describe the organization of repetitive DNAs in the A complement and B chromosome system in the grasshopper species Abracris flavolineata using classical cytogenetic techniques and FISH analysis using probes for five multigene families, telomeric repeats and repetitive C0t-1 DNA fractions. The 18S rRNA and H3 histone multigene families are highly variable and well distributed in A. flavolineata chromosomes, which contrasts with the conservation of U snRNA genes and less variable distribution of 5S rDNA sequences. The H3 histone gene was an extensively distributed with clusters occurring in all chromosomes. Repetitive DNAs were concentrated in C-positive regions, including the pericentromeric region and small chromosomal arms, with some occurrence in C-negative regions, but abundance was low in the B chromosome. Finally, the first demonstration of the U2 snRNA gene in B chromosomes in A. flavolineata may shed light on its possible origin. These results provide new information regarding chromosomal variability for repetitive DNAs in grasshoppers and the specific molecular composition of B chromosomes.

Fertilization and Uniparental Chromosome Elimination during Crosses with Maize Haploid Inducers

Abstract: Producing maternal haploids via a male inducer can greatly accelerate maize (Zea mays) breeding process. However, the mechanism underlying haploid formation remains unclear. In this study, we constructed two inducer lines containing cytogenetic marker B chromosome or alien centromeric histone H3 variant-yellow fluorescent protein vector to investigate the mechanism. The two inducer lines as the pollinators were crossed with a hybrid ZhengDan958. B chromosomes were detected in F1 haploids at a low frequency, which was direct evidence to support the occurrence of selective chromosome elimination during haploid formation. We found that most of the inducer chromosomes were eliminated in haploid embryonic cells during the first week after pollination. The gradual elimination of chromosomes was also detected in the endosperm of defective kernels, although it occurred only in some endosperm cells as late as 15 d after pollination. We also performed a genome-wide identification of single nucleotide polymorphism markers in the inducers, noninducer inbred lines, and 42 derived haploids using a 50K single nucleotide polymorphism array. We found that an approximately 44-Mb heterozygous fragment from the male parent was detected in a single haploid, which further supported the occurrence of paternal introgression. Our results suggest that selective elimination of uniparental chromosomes leads to the formation of haploid and possible defective kernels in maize as well, which is accompanied with unusual paternal introgression in haploid cells.

Karyotype Diversity and Evolutionary Trends in Angiosperms

Abstract: Karyotypic change constitutes an important evolutionary mechanism contributing to in angiosperm diversification and speciation. Comparative analyses of the karyotype usually include numerical features (chromosome number) and their changes (dysploidy, aneuploidy, polyploidy), as well as morphological features (chromosome size, karyotype length and genome size, centromere position and karyotype symmetry, secondary constrictions, supernumerary chromosomal material). More detailed characterization of angiosperm karyotypes involves also analyses of the abundance, distribution, and organization of specific molecular landmarks of different types (heterochromatin, ribosomal DNA, telomeric sequences, transposable elements, tandemly repeated DNA) and sizes (ranging from small genomic blocks to entire chromosome sets). This chapter describes the above mentioned karyotypic features and discusses their variation and evolutionary trends within angiosperms with respect to, for instance, their phylogenetic distribution and significance, directionality of chromosome number changes, or the nature and function of genetic elements involved in genome diploidization.

Karyotype heterogeneity and unclassified chromosomal abnormalities.

Abstract: In a departure from traditional gene-centric thinking with regard to cytogenetics and cytogenomics, the recently introduced genome theory calls upon a re-focusing of our attention on karyotype analyses of disease conditions. Karyotype heterogeneity has been demonstrated to be directly involved in the somatic cell evolution process which is the basis of many common and complex diseases such as cancer. To correctly use karyotype heterogeneity and apply it to monitor system instability, we need to include many seemingly unimportant non-specific chromosomal aberrations into our analysis. Traditionally, cytogenetic analysis has been focused on identifying recurrent types of abnormalities, particularly those that have been linked to specific diseases. In this perspective, drawing on the new framework of 4D-genomics, we will briefly review the importance of studying karyotype heterogeneity. We have also listed a number of overlooked chromosomal aberrations including defective mitotic figures, chromosome fragmentation as well as genome chaos. Finally, we call for the systematic discovery/characterization and classification of karyotype abnormalities in human diseases, as karyotype heterogeneity is the common factor that is essential for somatic cell evolution.

Intrinsic karyotype stability and gene copy number variations may have laid the foundation for tetraploid wheat formation

Abstract: Polyploidy or whole-genome duplication is recurrent in plant evolution, yet only a small fraction of whole-genome duplications has led to successful speciation. A major challenge in the establishment of nascent polyploids is sustained karyotype instability, which compromises fitness. The three putative diploid progenitors of bread wheat, with AA, SS (S ∼ B), and DD genomes occurred sympatrically, and their cross-fertilization in different combinations may have resulted in fertile allotetraploids with various genomic constitutions. However, only SSAA or closely related genome combinations have led to the speciation of tetraploid wheats like Triticum turgidum and Triticum timopheevii. We analyzed early generations of four newly synthesized allotetraploid wheats with genome compositions SshSshAmAm, SlSlAA, SbSbDD, and AADD by combined fluorescence and genomic in situ hybridization-based karyotyping. Results of karyotype analyses showed that although SshSshAmAm and SlSlAA are characterized by immediate and persistent karyotype stability, massive aneuploidy and extensive chromosome restructuring are associated with SbSbDD and AADD in which parental subgenomes showed markedly different propensities for chromosome gain/loss and rearrangements. Although compensating aneuploidy and reciprocal translocation between homeologs prevailed, reproductive fitness was substantially compromised due to chromosome instability. Strikingly, localized genomic changes in repetitive DNA and copy-number variations in gene homologs occurred in both chromosome stable lines, SshSshAmAm and SlSlAA. Our data demonstrated that immediate and persistent karyotype stability is intrinsic to newly formed allotetraploid wheat with genome combinations analogous to natural tetraploid wheats. This property, coupled with rapid gene copy-number variations, may have laid the foundation of tetraploid wheat establishment.

A ZZ/ZW microchromosome system in the spiny softshell turtle, Apalone spinifera, reveals an intriguing sex chromosome conservation in Trionychidae

Abstract: Reptiles display a wide diversity of sex-determining mechanisms ranging from temperature-dependent sex determination (TSD) to genotypic sex determination (GSD) with either male (XY) or female (ZW) heterogamety. Despite this astounding variability, the origin, structure, and evolution of sex chromosomes remain poorly understood. In turtles, TSD is purportedly ancestral while GSD arose multiple times independently. Here we test whether independent (XY or ZW) or morphologically divergent heterogametic sex chromosome systems evolved in tryonichids (Cryptodira) using the GSD spiny softshell turtle, Apalone spinifera, a species with previously unidentified sex chromosomes. A female-specific signal from comparative genomic hybridization (CGH) was detected in a Giemsa/4′,6-diamidino-2-phenylindole faint portion of a microchromosome, indicating the presence of a ZZ/ZW system in A. spinifera. In situ hybridization of a fluorescently labeled 18S rRNA probe identified a large nucleolar organizer region block in the female-specific region of the W (co-localizing with the female-specific CGH signal) and a smaller block on the Z. The heteromorphic ZZ/ZW micro-sex chromosome system detected here is identical to that found in another tryonichid, the Chinese softshell turtle Pelodiscus sinensis, from which A. spinifera diverged ∼95 million years ago. These results reveal a striking sex chromosome conservation in tryonichids, compared to the divergent sex chromosome morphology observed among younger XX/XY systems in pleurodiran turtles. Our findings highlight the need to understand the drivers behind sex chromosome lability and conservation in different lineages and contribute to our knowledge of sex chromosome evolution in reptiles and vertebrates.

Homoeologous chromosomes of Xenopus laevis are highly conserved after whole-genome duplication.

Abstract: It has been suggested that whole-genome duplication (WGD) occurred twice during the evolutionary process of vertebrates around 450 and 500 million years ago, which contributed to an increase in the genomic and phenotypic complexities of vertebrates. However, little is still known about the evolutionary process of homoeologous chromosomes after WGD because many duplicate genes have been lost. Therefore, Xenopus laevis (2n=36) and Xenopus (Silurana) tropicalis (2n=20) are good animal models for studying the process of genomic and chromosomal reorganization after WGD because X. laevis is an allotetraploid species that resulted from WGD after the interspecific hybridization of diploid species closely related to X. tropicalis. We constructed a comparative cytogenetic map of X. laevis using 60 complimentary DNA clones that covered the entire chromosomal regions of 10 pairs of X. tropicalis chromosomes. We consequently identified all nine homoeologous chromosome groups of X. laevis. Hybridization signals on two pairs of X. laevis homoeologous chromosomes were detected for 50 of 60 (83%) genes, and the genetic linkage is highly conserved between X. tropicalis and X. laevis chromosomes except for one fusion and one inversion and also between X. laevis homoeologous chromosomes except for two inversions. These results indicate that the loss of duplicated genes and inter- and/or intrachromosomal rearrangements occurred much less frequently in this lineage, suggesting that these events were not essential for diploidization of the allotetraploid genome in X. laevis after WGD.

New insights on the origin and relevance of aneuploidy in human spermatozoa

Abstract: In humans, the most common chromosomal abnormality is aneuploidy. Because the majority of aneuploid conceptuses die during the early stages of embryonic development, an accurate estimate of the frequency of aneuploidy at conception can only be assessed by directly studying the gametes. The vast majority of aneuploidies arise de novo as a result of sporadic chromosome missegregation in paternal or maternal meiosis. In this review, we present the basic current knowledge about the incidence of aneuploidy in human spermatozoa in the general population and in patient populations where elevated levels of sperm aneuploidy are observed. These include infertile patients, patients with abnormal somatic karyotypes, and individuals exposed to certain environmental/lifestyle hazards. The clinical impact of increased levels of aneuploidy is discussed. We then focus on the non-disjunction mechanisms that cause aneuploidy during spermatogenesis and the factors that predispose to non-disjunction in male germ cells followed by an analysis of the sex differences in the incidence of gamete aneuploidy. Recent meiotic studies using multiplex-FISH on three fertile men have revealed that the frequency of conservative aneuploidy of metaphase II spermatocytes is similar to that observed in non-inseminated oocytes of young women. These findings suggest that the differences in the incidence of aneuploidy between spermatozoa and oocytes are not due to differences in chromosome segregation errors but rather to more effective checkpoint mechanisms in spermatogenesis than in oogenesis.

Linkage map of the peppered moth, Biston betularia (Lepidoptera, Geometridae): a model of industrial melanism.

Abstract: We have constructed a linkage map for the peppered moth (Biston betularia), the classical ecological genetics model of industrial melanism, aimed both at localizing the network of loci controlling melanism and making inferences about chromosome dynamics. The linkage map, which is based primarily on amplified fragment length polymorphisms (AFLPs) and genes, consists of 31 linkage groups (LGs; consistent with the karyotype). Comparison with the evolutionarily distant Bombyx mori suggests that the gene content of chromosomes is highly conserved. Gene order is conserved on the autosomes, but noticeably less so on the Z chromosome, as confirmed by physical mapping using bacterial artificial chromosome fluorescence in situ hybridization (BAC-FISH). Synteny mapping identified three pairs of B. betularia LGs (11/29, 23/30 and 24/31) as being orthologous to three B. mori chromosomes (11, 23 and 24, respectively). A similar finding in an outgroup moth (Plutella xylostella) indicates that the B. mori karyotype (n=28) is a phylogenetically derived state resulting from three chromosome fusions. As with other Lepidoptera, the B. betularia W chromosome consists largely of repetitive sequence, but exceptionally we found a W homolog of a Z-linked gene (laminin A), possibly resulting from ectopic recombination between the sex chromosomes. The B. betularia linkage map, featuring the network of known melanization genes, serves as a resource for melanism research in Lepidoptera. Moreover, its close resemblance to the ancestral lepidopteran karyotype (n=31) makes it a useful reference point for reconstructing chromosome dynamic events and ancestral genome architectures. Our study highlights the unusual evolutionary stability of lepidopteran autosomes; in contrast, higher rates of intrachromosomal rearrangements support a special role of the Z chromosome in adaptive evolution and speciation.

Molecular Cytogenetics (FISH, GISH) of Coccinia grandis: A ca. 3 myr-Old Species of Cucurbitaceae with the Largest Y/Autosome Divergence in Flowering Plants

Abstract: The independent evolution of heteromorphic sex chromosomes in 19 species from 4 families of flowering plants permits studying X/Y divergence after the initial recombination suppression. Here, we document autosome/Y divergence in the tropical Cucurbitaceae Coccinia grandis, which is ca. 3 myr old. Karyotyping and C-value measurements show that the C. grandis Y chromosome has twice the size of any of the other chromosomes, with a male/female C-value difference of 0.094 pg or 10% of the total genome. FISH staining revealed 5S and 45S rDNA sites on autosomes but not on the Y chromosome, making it unlikely that rDNA contributed to the elongation of the Y chromosome; recent end-to-end fusion also seems unlikely given the lack of interstitial telomeric signals. GISH with different concentrations of female blocking DNA detected a possible pseudo-autosomal region on the Y chromosome, and C-banding suggests that the entire Y chromosome in C. grandis is heterochromatic. During meiosis, there is an end-to-end connection between the X and the Y chromosome, but the X does not otherwise differ from the remaining chromosomes. These findings and a review of plants with heteromorphic sex chromosomes reveal no relationship between species age and degree of sex chromosome dimorphism. Its relatively small genome size (0.943 pg/2C in males), large Y chromosome, and phylogenetic proximity to the fully sequenced Cucumis sativus make C. grandis a promising model to study sex chromosome evolution.

Transcription of a protein-coding gene on B chromosomes of the Siberian roe deer (Capreolus pygargus)

Abstract: Background: Most eukaryotic species represent stable karyotypes with a particular diploid number. B chromosomes are additional to standard karyotypes and may vary in size, number and morphology even between cells of the same individual. For many years it was generally believed that B chromosomes found in some plant, animal and fungi species lacked active genes. Recently, molecular cytogenetic studies showed the presence of additional copies of protein-coding genes on B chromosomes. However, the transcriptional activity of these genes remained elusive. We studied karyotypes of the Siberian roe deer (Capreolus pygargus) that possess up to 14 B chromosomes to investigate the presence and expression of genes on supernumerary chromosomes. Results: Here, we describe a 2 Mbp region homologous to cattle chromosome 3 and containing TNNI3K (partial), FPGT, LRRIQ3 and a large gene-sparse segment on B chromosomes of the Siberian roe deer. The presence of the copy of the autosomal region was demonstrated by B-specific cDNA analysis, PCR assisted mapping, cattle bacterial artificial chromosome (BAC) clone localization and quantitative polymerase chain reaction (qPCR). By comparative analysis of B-specific and non-B chromosomal sequences we discovered some B chromosome-specific mutations in protein-coding genes, which further enabled the detection of a FPGT-TNNI3K transcript expressed from duplicated genes located on B chromosomes in roe deer fibroblasts. Conclusions: Discovery of a large autosomal segment in all B chromosomes of the Siberian roe deer further corroborates the view of an autosomal origin for these elements. Detection of a B-derived transcript in fibroblasts implies that the protein coding sequences located on Bs are not fully inactivated. The origin, evolution and effect on host of B chromosomal genes seem to be similar to autosomal segmental duplications, which reinforces the view that supernumerary chromosomal elements might play an important role in genome evolution.

Chromosomal evolution in tortricid moths: conserved karyotypes with diverged features.

Abstract: Moths of the family Tortricidae constitute one of the major microlepidopteran groups in terms of species richness and economic importance. Yet, despite their overall significance, our knowledge of their genome organization is very limited. In order to understand karyotype evolution in the family Tortricidae, we performed detailed cytogenetic analysis of Grapholita molesta, G. funebrana, Lobesia botrana, and Eupoecilia ambiguella, representatives of two main tortricid subfamilies, Olethreutinae and Tortricinae. Besides standard cytogenetic methods, we used fluorescence in situ hybridization for mapping of major rRNA and histone gene clusters and comparative genomic hybridization to determine the level of molecular differentiation of the W and Z sex chromosomes. Our results in combination with available data in the codling moth, Cydia pomonella, and other tortricids allow us a comprehensive reconstruction of chromosomal evolution across the family Tortricidae. The emerging picture is that the karyotype of a common ancestor of Tortricinae and Olethreutinae differentiated from the ancestral lepidopteran chromosome print of n = 31 by a sex chromosome-autosome fusion. This rearrangement resulted in a large neo-sex chromosome pair and a karyotype with n = 30 conserved in most Tortricinae species, which was further reduced to n = 28 observed in Olethreutinae. Comparison of the tortricid neo-W chromosomes showed differences in their structure and composition presumably reflecting stochasticity of molecular degeneration of the autosomal part of the neo-W chromosome. Our analysis also revealed conservative pattern of the histone distribution, which is in contrast with high rDNA mobility. Despite the dynamic evolution of rDNA, we can infer a single NOR-chromosome pair as an ancestral state not only in tortricids but probably in all Lepidoptera. The results greatly expand our knowledge of the genome architecture in tortricids, but also contribute to the understanding of chromosomal evolution in Lepidoptera in general.

Karyotype evolution in monitor lizards: cross-species chromosome mapping of cDNA reveals highly conserved synteny and gene order in the Toxicofera clade

Abstract: The water monitor lizard (Varanus salvator macromaculatus (VSA), Platynota) has a chromosome number of 2n = 40: its karyotype consists of 16 macrochromosomes and 24 microchromosomes To delineate the process of karyotype evolution in V salvator macromaculatus, we constructed a cytogenetic map with 86 functional genes and compared it with those of the butterfly lizard (Leiolepis reevesii rubritaeniata (LRE); 2n = 36) and Japanese four-striped rat snake (Elaphe quadrivirgata (EQU); 2n = 36), members of the Toxicofera clade The syntenies and gene orders of macrochromosomes were highly conserved between these species except for several chromosomal rearrangements: eight pairs of VSA macrochromosomes and/or chromosome arms exhibited homology with six pairs of LRE macrochromosomes and eight pairs of EQU macrochromosomes Furthermore, the genes mapped to microchromosomes of three species were all located on chicken microchromosomes or chromosome 4p No reciprocal translocations were found in the species, and their karyotypic differences were caused by: low frequencies of interchromosomal rearrangements, such as tandem fusions, or centric fissions/fusions between macrochromosomes and between macro- and microchromosomes; and intrachromosomal rearrangements, such as paracentric inversions or centromere repositioning The chromosomal rearrangements that occurred in macrochromosomes of the Varanus lineage were also identified through comparative cytogenetic mapping of V salvator macromaculatus and V exanthematicus Morphologic differences in chromosomes 6–8 between the two species could have resulted from pericentric inversion or centromere repositioning

Mapping five repetitive DNA classes in sympatric species of Hypostomus (Teleostei: Siluriformes: Loricariidae): analysis of chromosomal variability

Abstract: Fish belonging to the genus Hypostomus are known for exhibiting a striking diversity in its karyotype structure, however the knowledge concerning the distribution patterns of heterochromatin and location of repetitive DNA sequences in the karyotypes is still limited. Aiming a better understanding of the chromosomal organization in this group, we analyzed three sympatric species of Hypostomus collected in the Hortela stream, a component of the Paranapanema River basin, Botucatu/SP/Brazil. The analyses involved the cytogenetic characterization and chromosomal mapping of repetitive sequences and intra/interspecific comparisons using sequences of the cytochrome C oxidase subunit I. The results revealed that H. ancistroides presents a karyotype with 2n = 68 chromosomes, H. strigaticeps 2n = 72 chromosomes, and H. nigromaculatus 2n = 76 chromosomes. In addition to differences found in the diploid number, it was also observed variations in karyotypic formulae, amount of constitutive heterochromatin, and location of nucleolus organizer regions. The cytogenetic mapping of 5S and 18S rDNA, as well as of the H3 histone gene, disclosed a differential dispersion process among the three species. In some cases the Rex1 transposable element showed to be co-located with 5S rDNA sites. The molecular analyses support the cytogenetic data and represent an additional tool for the characterization of the analyzed species. The results evidenced that chromosomal variations are not restricted to differences in diploid number or karyotypic macrostructure in the genus Hypostomus, indicating that events such as transposition of heterochromatin and rDNA segments may participate in the differentiation process occurred in these species.

Activation of autophagy in cells with abnormal karyotype

Abstract: The presence of even one extra chromosome severely impairs cellular growth. This effect of aneuploidy (a term describing chromosome numbers deviating from multiples of haploid chromosome content) has been observed in many different organisms, from yeast to humans. Accordingly, abnormal karyotypes are detected in nearly 30% of spontaneously aborted embryos. The rarely surviving infants, such as with trisomy of chromosome 21, are severely handicapped. The causes remain enigmatic, although recent studies exploiting yeast and mouse models provided first glimpses of the imbalanced inner life of aneuploid cells. Using comparative genomics, transcriptomics and proteomics we have analyzed the fate of the transcripts and proteins coded on the extra chromosomes as well as the general response to aneuploidy in human cells.

Mechanisms of Chromosome Rearrangements

Abstract: The striking diversity of land plants is associated with immense genetic variation manifested also by a wide range of genome sizes and chromosome numbers. Nuclear genome size across land plants varies more than 2,300-fold from ~64 Mb (Genlisea aurea; Greilhuber et al. 2006) to ~150,000 Mb (Paris japonica; Pellicer et al. 2010). Accordingly, chromosome numbers can vary from n = 2 in six angiosperm species (Vanzela et al. 1996; Cremonini 2,005) to n > 320 in the angiosperm Sedum suaveolens (Uhl 1978) and n = c. 720 in the fern Ophioglossum reticulatum (Khandelwal 1990). This extensive variation of chromosome numbers among land plants is driven by two main trends in opposite directions: chromosome numbers increase through polyploidy (whole-genome duplications, WGD) and decrease through structural chromosome rearrangements (descending dysploidy). Genomic and cytogenetic analyses indicate that probably all land plants have experienced at least one WGD event (Jaillon et al. 2009; Soltis et al. 2009; Van de Peer et al. 2009; see also Fawcett et al. 2012, this volume) followed by more or less extensive karyotype reshuffling towards diploid-like genomes (e.g. Wolfe 2001; Thomas et al. 2006; Cenci et al. 2010; Mandakova et al. 2010a). Karyotypic changes at a given ploidy level are mediated by chromosome rearrangements such as insertions, duplications, deletions, inversions and translocations altering the size and morphology of chromosomes. Centric fissions and different types of reciprocal translocations combined with meiotic (mis)segregation may lead to a reduction or increase of chromosome number (descending/ascending dysploidy).

Evolution of karyotype, sex chromosomes, and meiosis in mygalomorph spiders (Araneae: Mygalomorphae)

Abstract: Spider diversity is partitioned into three primary clades, namely Mesothelae, Mygalomorphae, and Araneomorphae. Mygalomorph cytogenetics is largely unknown. Our study revealed a remarkable karyotype diversity of mygalomorphs. Unlike araneomorphs, they show no general trend towards a decrease of 2n, as the chromosome number was reduced in some lineages and increased in others. A biarmed karyotype is a symplesiomorphy of mygalomorphs and araneomorphs. Male meiosis of some mygalomorphs is achiasmatic, or includes the diffuse stage. The sex chromosome system X1X20, which is supposedly ancestral in spiders, is uncommon in mygalomorphs. Many mygalomorphs exhibit more than two (and up to 13) X chromosomes in males. The evolution of X chromosomes proceeded via the duplication of chromosomes, fissions, X–X, and X-autosome fusions. Spiders also exhibit a homomorphic sex chromosome pair. In the germline of mygalomorph males these chromosomes are often deactivated; their deactivation and pairing is initiated already at spermatogonia. Remarkably, pairing of sex chromosomes in mygalomorph females is also initiated at gonial cells. Some mygalomorphs have two sex chromosome pairs. The second pair presumably arose in early-diverging mygalomorphs, probably via genome duplication. The unique behaviour of spider sex chromosomes in the germline may promote meiotic pairing of homologous sex chromosomes and structural differentiation of their duplicates, as well as the establishment of polyploid genomes. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 377–408.

Alterations and Abnormal Mitosis of Wheat Chromosomes Induced by Wheat-Rye Monosomic Addition Lines

Abstract: Background Wheat-rye addition lines are an old topic However, the alterations and abnormal mitotic behaviours of wheat chromosomes caused by wheat-rye monosomic addition lines are seldom reported Methodology/Principal Findings Octoploid triticale was derived from common wheat T aestivum L ‘Mianyang11’×rye S cereale L ‘Kustro’ and some progeny were obtained by the controlled backcrossing of triticale with ‘Mianyang11’ followed by self-fertilization Genomic in situ hybridization (GISH) using rye genomic DNA and fluorescence in situ hybridization (FISH) using repetitive sequences pAs1 and pSc1192 as probes were used to analyze the mitotic chromosomes of these progeny Strong pSc1192 FISH signals could be observed at the telomeric regions of 3DS arms in ‘Mianyang11’ However, the pSc1192 FISH signals were disappeared from the selfed progeny of 4R monosomic addition line and the changed 3D chromosomes could be transmitted to next generation stably In one of the selfed progeny of 7R monosomic addition line, one 2D chromosome was broken and three 4A chromosomes were observed In the selfed progeny of 6R monosomic addition line, structural variation and abnormal mitotic behaviour of 3D chromosome were detected Additionally, 1A and 4B chromosomes were eliminated from some of the progeny of 6R monosomic addition line Conclusions/Significance These results indicated that single rye chromosome added to wheat might cause alterations and abnormal mitotic behaviours of wheat chromosomes and it is possible that the stress caused by single alien chromosome might be one of the factors that induced karyotype alteration of wheat

Biology and Evolution of B Chromosomes

Abstract: B chromosomes are dispensable and often selfish elements of the genome which follow their own evolutionary pathway. B chromosomes are a major source of intraspecific variation in nuclear DNA amounts in numerous species and the distribution of Bs among different groups of angiosperms is not random. B chromosome inheritance is irregular and non-Mendelian, and therefore polymorphisms exist with respect to the number of Bs within populations or even within different cell lines of an individual carrying Bs. Drive mechanisms play a major role in the equilibrium of B frequency in populations. The most widely accepted view is that Bs are derived from the A chromosome complement. Some evidence also suggests that Bs can be spontaneously generated in response to the new genomic conditions after interspecific hybridization. The molecular processes that gave rise to Bs during evolution remain unclear. Here, we survey current knowledge on the DNA/chromatin composition, origin, and mitotic and meiotic drive mechanisms of B chromosomes and discuss effects and transcripts associated with Bs.

Chromosome Studies of European Cyprinid Fishes: Cross-Species Painting Reveals Natural Allotetraploid Origin of a Carassius Female with 206 Chromosomes

Abstract: A single female with 206 chromosomes and another 26 females with 156 chromosomes identified as Prussian carp, Carassius gibelio, and 5 individuals with 100 chromosomes identified as crucian carp, C. carassius, were sampled during field survey in one locality in the upper Elbe River. To identify the origin of females with high chromosome numbers, comparative karyotype analysis, GISH, with whole C. carassius DNA as probe and phylogenetic positions of sampled individuals revealed by cytochrome b mitochondrial marker were performed. GISH showed consistently bright labeling of 50 chromosomal elements out of 206, corresponding to the haploid chromosome number of C. carassius. The position of these females with high chromosome numbers in a reconstructed phylogenetic tree was within the clade of C. gibelio, documenting its affiliation to C. gibelio mitochondrial, i.e. maternal lineage. Our findings indicated that the mother of the female with high chromosome numbers was a gynogenetically reproducing 156-chromosome C. gibelio female and the father a bisexually reproducing C. carassius male. We, therefore, hypothesized that the C. gibelio × C. carassius allopolyploid female with 206 chromosomes arose by a mechanism of sperm genome addition to an unreduced egg of the mother.