scholarly journals Further observations on the activity of Y chromosome heterochromatin in Rumex thyrsiflorus

2015 ◽  
Vol 40 (3) ◽  
pp. 513-518
Author(s):  
J. Żuk ◽  
Z. Bolkhovskikh
Keyword(s):  
Life Cycle ◽  
Y Chromosome ◽  
Rna Synthesis ◽  
High Rate ◽  
Uridine Incorporation ◽  
Y Chromosomes ◽  
Genetic Activity ◽  
Tapetal Cells ◽  
Fuzzy State

Observation of premeiotic nuclei of plants containing different numbers (from one to five) of Y chromosomes reveal that is such plants prior to meiosis all Y chromosomes are in fuzzy state, while in nuclei of tapetal cells or nuclei from anther stalk the number of big chromocentres is directly correlated with the number of Y chromosomes in given plants. This finding provides a further indication of genetic activity of Y chromosomes in this particular stage of the life cycle (premeiosis). Another indication of genetical activity of Y chromosomes was obtained from analysis of the rate of RNA synthesis in premeiosis. It was found that PMC's in the last premeioitc interphase exhibit a high rate of 3H-uridine incorporation. Thus in PMC's the fuzzy appearance of Y chromosomes coincides with intensive RNA synthesis.

scholarly journals Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lingzhan Xue ◽  
Yu Gao ◽  
Meiying Wu ◽  
Tian Tian ◽  
Haiping Fan ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Chromosome Pair ◽  
Sex Chromosome ◽  
Structural Variations ◽  
Recombination Suppression ◽  
Chromosome Differentiation ◽  
Y Chromosomes ◽  
Recent Origin ◽  
Mastacembelus Armatus

Abstract Background The origin of sex chromosomes requires the establishment of recombination suppression between the proto-sex chromosomes. In many fish species, the sex chromosome pair is homomorphic with a recent origin, providing species for studying how and why recombination suppression evolved in the initial stages of sex chromosome differentiation, but this requires accurate sequence assembly of the X and Y (or Z and W) chromosomes, which may be difficult if they are recently diverged. Results Here we produce a haplotype-resolved genome assembly of zig-zag eel (Mastacembelus armatus), an aquaculture fish, at the chromosomal scale. The diploid assembly is nearly gap-free, and in most chromosomes, we resolve the centromeric and subtelomeric heterochromatic sequences. In particular, the Y chromosome, including its highly repetitive short arm, has zero gaps. Using resequencing data, we identify a ~7 Mb fully sex-linked region (SLR), spanning the sex chromosome centromere and almost entirely embedded in the pericentromeric heterochromatin. The SLRs on the X and Y chromosomes are almost identical in sequence and gene content, but both are repetitive and heterochromatic, consistent with zero or low recombination. We further identify an HMG-domain containing gene HMGN6 in the SLR as a candidate sex-determining gene that is expressed at the onset of testis development. Conclusions Our study supports the idea that preexisting regions of low recombination, such as pericentromeric regions, can give rise to SLR in the absence of structural variations between the proto-sex chromosomes.

Muller’s ratchet of the Y chromosome with gene conversion

Genetics ◽  
2021 ◽  
Author(s):  
Takahiro Sakamoto ◽  
Hideki Innan
Keyword(s):  
Gene Duplication ◽  
Gene Conversion ◽  
Y Chromosome ◽  
Conversion Rate ◽  
Single Copy ◽  
Duplicated Genes ◽  
Fitness Effect ◽  
Muller's Ratchet ◽  
Y Chromosomes ◽  
Muller’S Ratchet

Abstract Muller’s ratchet is a process in which deleterious mutations are fixed irreversibly in the absence of recombination. The degeneration of the Y chromosome, and the gradual loss of its genes, can be explained by Muller’s ratchet. However, most theories consider single-copy genes, and may not be applicable to Y chromosomes, which have a number of duplicated genes in many species, which are probably undergoing concerted evolution by gene conversion. We developed a model of Muller’s ratchet to explore the evolution of the Y chromosome. The model assumes a non-recombining chromosome with both single-copy and duplicated genes. We used analytical and simulation approaches to obtain the rate of gene loss in this model, with special attention to the role of gene conversion. Homogenization by gene conversion makes both duplicated copies either mutated or intact. The former promotes the ratchet, and the latter retards, and we ask which of these counteracting forces dominates under which conditions. We found that the effect of gene conversion is complex, and depends upon the fitness effect of gene duplication. When duplication has no effect on fitness, gene conversion accelerates the ratchet of both single-copy and duplicated genes. If duplication has an additive fitness effect, the ratchet of single-copy genes is accelerated by gene duplication, regardless of the gene conversion rate, whereas gene conversion slows the degeneration of duplicated genes. Our results suggest that the evolution of the Y chromosome involves several parameters, including the fitness effect of gene duplication by increasing dosage and gene conversion rate.

scholarly journals The life cycle of Drosophila orphan genes

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Nicola Palmieri ◽  
Carolin Kosiol ◽  
Christian Schlötterer
Keyword(s):  
Life Cycle ◽  
Time Scales ◽  
High Rate ◽  
Sequence Evolution ◽  
Functional Requirements ◽  
Evolutionary Time ◽  
Orphan Genes ◽  
Functional Conservation ◽  
Close Relatives ◽  
Obscura Group

Orphans are genes restricted to a single phylogenetic lineage and emerge at high rates. While this predicts an accumulation of genes, the gene number has remained remarkably constant through evolution. This paradox has not yet been resolved. Because orphan genes have been mainly analyzed over long evolutionary time scales, orphan loss has remained unexplored. Here we study the patterns of orphan turnover among close relatives in the Drosophila obscura group. We show that orphans are not only emerging at a high rate, but that they are also rapidly lost. Interestingly, recently emerged orphans are more likely to be lost than older ones. Furthermore, highly expressed orphans with a strong male-bias are more likely to be retained. Since both lost and retained orphans show similar evolutionary signatures of functional conservation, we propose that orphan loss is not driven by high rates of sequence evolution, but reflects lineage-specific functional requirements.

scholarly journals Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

2021 ◽  
Author(s):  
Ching-Ho Chang ◽  
Lauren E. Gregory ◽  
Kathleen E. Gordon ◽  
Colin D. Meiklejohn ◽  
Amanda M. Larracuente
Keyword(s):  
Positive Selection ◽  
Y Chromosome ◽  
Related Species ◽  
De Novo ◽  
Gene Families ◽  
Chromosome Organization ◽  
End Joining ◽  
Sexual Antagonism ◽  
Closely Related Species ◽  
Y Chromosomes

AbstractY chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposable elements, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism generally contributes to the convergent evolution of Y chromosome organization.

scholarly journals The Large Delta Antigen of Hepatitis Delta Virus Potently Inhibits Genomic but Not Antigenomic RNA Synthesis: a Mechanism Enabling Initiation of Viral Replication

2000 ◽  
Vol 74 (16) ◽  
pp. 7375-7380 ◽  
Author(s):  
Lucy E. Modahl ◽  
Michael M. C. Lai
Keyword(s):  
Life Cycle ◽  
Hepatitis Delta Virus ◽  
Rna Synthesis ◽  
Rna Replication ◽  
Dominant Negative ◽  
Genomic Rna ◽  
Inhibitory Effects ◽  
Hepatitis Delta ◽  
Artificial Dna ◽  
Delta Virus

ABSTRACT Hepatitis delta virus (HDV) contains two types of hepatitis delta antigens (HDAg) in the virion. The small form (S-HDAg) is required for HDV RNA replication, whereas the large form (L-HDAg) potently inhibits it by a dominant-negative inhibitory mechanism. The sequential appearance of these two forms in the infected cells regulates HDV RNA synthesis during the viral life cycle. However, the presence of almost equal amounts of S-HDAg and L-HDAg in the virion raised a puzzling question concerning how HDV can escape the inhibitory effects of L-HDAg and initiate RNA replication after infection. In this study, we examined the inhibitory effects of L-HDAg on the synthesis of various HDV RNA species. Using an HDV RNA-based transfection approach devoid of any artificial DNA intermediates, we showed that a small amount of L-HDAg is sufficient to inhibit HDV genomic RNA synthesis from the antigenomic RNA template. However, the synthesis of antigenomic RNA, including both the 1.7-kb HDV RNA and the 0.8-kb HDAg mRNA, from the genomic-sense RNA was surprisingly resistant to inhibition by L-HDAg. The synthesis of these RNAs was inhibited only when L-HDAg was in vast excess over S-HDAg. These results explain why HDV genomic RNA can initiate replication after infection even though the incoming viral genome is complexed with equal amounts of L-HDAg and S-HDAg. These results also suggest that the mechanisms of synthesis of genomic versus antigenomic RNA are different. This study thus resolves a puzzling question about the early events of the HDV life cycle.

scholarly journals Chromosome Y Isodicentrics in two Cases with Ambiguous genitalia and Features of Turner Syndrome

2008 ◽  
Vol 11 (2) ◽  
pp. 51-58
Author(s):  
A Lungeanu ◽  
A Arghir ◽  
S Arps ◽  
G Cardos ◽  
N Dumitriu ◽  
...  
Keyword(s):  
Turner Syndrome ◽  
Y Chromosome ◽  
Ambiguous Genitalia ◽  
Peripheral Blood Lymphocytes ◽  
Chromosome Y ◽  
Y Chromosomes ◽  
New Information ◽  
Pathway Perturbation

Chromosome Y Isodicentrics in two Cases with Ambiguous genitalia and Features of Turner SyndromeKaryotype investigations using classical cytogenetics, fluorescencein situhybridization (FISH) and polymerase chain reaction (PCR) techniques were used for the characterization of Y chromosome structural anomalies found in two patients with ambiguous genitalia and features of Turner syndrome. Both exhibited mosaic karyotypes of peripheral blood lymphocytes. The karyotype was 45, X[90]/ 46, X, idic(Y)(p11.3).ish idic(Y) (wcpY+, DXYS130++,SRY++,DYZ3++,DYZ1++, DYS224++)[10] in one case, and the karyotype was 45, X[65]/46, X, idic(Y) (q11).ish idic(Y)(SRY++, RP11-140H23-)[35] in the other case. Derivative Y chromosomes were different in shape and size and positive for the SRY gene, a common underlying element of ambiguous genitalia phenotypes. These results add new information concerning the role of Y chromosome structural abnormalities in sex determination pathway perturbation which are poorly understood, and highlight the importance of the sex chromosomes integrity for a normal sex phenotype development.

An unusual Y chromosome of Drosophila simulans carrying amplified rDNA spacer without rRNA genes.

Genetics ◽  
1990 ◽  
Vol 125 (2) ◽  
pp. 399-406
Author(s):  
A R Lohe ◽  
P A Roberts
Keyword(s):  
Y Chromosome ◽  
Initiation Site ◽  
Drosophila Simulans ◽  
Rrna Genes ◽  
Rdna Transcription ◽  
Nontranscribed Spacer ◽  
Protein Factor ◽  
Y Chromosomes ◽  
Full Complement ◽  
Polymerase I

Abstract The X and Y chromosomes of Drosophila melanogaster each contain a cluster of several hundred ribosomal RNA genes (rDNA). A nontranscribed spacer region separates adjacent rRNA genes and contains tandem copies of 240 bp repeats that include the initiation site for RNA polymerase I transcription. We show here that Drosophila simulans, a sibling species of D. melanogaster, contains few, if any, rRNA genes on its Y chromosome but carries instead a large block (3,000 kb or 12,500 copies) of 240 bp nontranscribed spacer repeats. The repeats are located at the tip of the long arm of the simulans Y chromosome, in contrast to their location among rRNA genes on the short arm of the Y chromosome of D. melanogaster. The bobbed mutation in homozygous females of D. melanogaster shortens and thins the bristles, owing to a partial deletion of rRNA genes on the X chromosome. The bristles of bobbed/Y males are normal owing to the presence of a full complement of rRNA genes on the Y chromosome. Peculiarly, in bobbed/Y males of D. simulans the short bristle phenotype does not return to normal but is enhanced by the presence of the Y chromosome. We propose that the 12,500 nontranscribed spacer repeats on the Y chromosome are responsible for this biological effect by competition for a protein factor(s) essential for normal levels of rDNA transcription at the X-linked locus.

scholarly journals Locating the Sex Determining Region of Linkage Group 12 of Guppy (Poecilia reticulata)

2020 ◽  
Vol 10 (10) ◽  
pp. 3639-3649
Author(s):  
Deborah Charlesworth ◽  
Roberta Bergero ◽  
Chay Graham ◽  
Jim Gardner ◽  
Lengxob Yong
Keyword(s):  
Poecilia Reticulata ◽  
Population Genomics ◽  
False Positive Rate ◽  
Natural Populations ◽  
Proximal Region ◽  
High Rate ◽  
Chromosome 12 ◽  
Small Samples ◽  
Autosomal Region ◽  
Y Chromosomes

Despite over 100 years of study, the location of the fully sex-linked region of the guppy (Poecilia reticulata) carrying the male-determining locus, and the regions where the XY pair recombine, remain unclear. Previous population genomics studies to determine these regions used small samples from recently bottlenecked captive populations, which increase the false positive rate of associations between individuals’ sexes and SNPs. Using new data from multiple natural populations, we show that a recently proposed candidate for this species’ male-determining gene is probably not completely sex-linked, leaving the maleness factor still unidentified. Variants in the chromosome 12 region carrying the candidate gene sometimes show linkage disequilibrium with the sex-determining factor, but no consistently male-specific variant has yet been found. Our genetic mapping with molecular markers spread across chromosome 12 confirms that this is the guppy XY pair. We describe two families with recombinants between the X and Y chromosomes, which confirm that the male-determining locus is in the region identified by all previous studies, near the terminal pseudo-autosomal region (PAR), which crosses over at a very high rate in males. We correct the PAR marker order, and assign two unplaced scaffolds to the PAR. We also detect a duplication, with one copy in the male-determining region, explaining signals of sex linkage in a more proximal region.

scholarly journals Differences in Viral RNA Synthesis but Not Budding or Entry Contribute to the In Vitro Attenuation of Reston Virus Compared to Ebola Virus

2020 ◽  
Vol 8 (8) ◽  
pp. 1215
Author(s):  
Bianca S. Bodmer ◽  
Josephin Greßler ◽  
Marie L. Schmidt ◽  
Julia Holzerland ◽  
Janine Brandt ◽  
...  
Keyword(s):  
Life Cycle ◽  
Rna Synthesis ◽  
Ebola Virus ◽  
Severe Disease ◽  
Case Fatality ◽  
Viral Rna ◽  
Pathogenic Potential ◽  
Rnp Complex ◽  
Reston Virus

Most filoviruses cause severe disease in humans. For example, Ebola virus (EBOV) is responsible for the two most extensive outbreaks of filovirus disease to date, with case fatality rates of 66% and 40%, respectively. In contrast, Reston virus (RESTV) is apparently apathogenic in humans, and while transmission of RESTV from domestic pigs to people results in seroconversion, no signs of disease have been reported in such cases. The determinants leading to these differences in pathogenicity are not well understood, but such information is needed in order to better evaluate the risks posed by the repeated spillover of RESTV into the human population and to perform risk assessments for newly emerging filoviruses with unknown pathogenic potential. Interestingly, RESTV and EBOV already show marked differences in their growth in vitro, with RESTV growing slower and reaching lower end titers. In order to understand the basis for this in vitro attenuation of RESTV, we used various life cycle modeling systems mimicking different aspects of the virus life cycle. Our results showed that viral RNA synthesis was markedly slower when using the ribonucleoprotein (RNP) components from RESTV, rather than those for EBOV. In contrast, the kinetics of budding and entry were indistinguishable between these two viruses. These data contribute to our understanding of the molecular basis for filovirus pathogenicity by showing that it is primarily differences in the robustness of RNA synthesis by the viral RNP complex that are responsible for the impaired growth of RESTV in tissue culture.

Polymorphism and differentiation of rainbow trout Y chromosomes

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1105-1113 ◽  
Author(s):  
Alicia Felip ◽  
Atushi Fujiwara ◽  
William P Young ◽  
Paul A Wheeler ◽  
Marc Noakes ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Y Chromosome ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Morphological Differentiation ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Y Chromosomes ◽  
Cytogenetic Analyses ◽  
Clonal Lines ◽  
Sex Locus

Most fish species show little morphological differentiation in the sex chromosomes. We have coupled molecular and cytogenetic analyses to characterize the male-determining region of the rainbow trout (Oncorhynchus mykiss) Y chromosome. Four genetically diverse male clonal lines of this species were used for genetic and physical mapping of regions in the vicinity of the sex locus. Five markers were genetically mapped to the Y chromosome in these male lines, indicating that the sex locus was located on the same linkage group in each of the lines. We also confirmed the presence of a Y chromosome morphological polymorphism among these lines, with the Y chromosomes from two of the lines having the more common heteromorphic Y chromosome and two of the lines having Y chromosomes morphologically similar to the X chromosome. The fluorescence in situ hybridization (FISH) pattern of two probes linked to sex suggested that the sex locus is physically located on the long arm of the Y chromosome. Fishes appear to be an excellent group of organisms for studying sex chromosome evolution and differentiation in vertebrates because they show considerable variability in the mechanisms and (or) patterns involved in sex determination.Key words: sex chromosomes, sex markers, cytogenetics, rainbow trout, fish.

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