scholarly journals The Comparative Analysis of the DNA Repeat Composition among Cannabis Sativa L., Humulus Lupulus L. And Humulus Japonicus Siebold & Zucc. With Heteromorphic Sex Chromosomes

2021 ◽  
Author(s):  
Julia V. Bocharkina ◽  
Oleg S. Alexandrov ◽  
Olga V. Razumova ◽  
Gennady I. Karlov
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Cannabis Sativa ◽  
Open Data ◽  
Humulus Lupulus ◽  
Sequencing Data ◽  
Male And Female ◽  
Dna Repeat ◽  
Heteromorphic Sex Chromosomes ◽  
Humulus Japonicus

Heteromorphic sex chromosomes are rarely found in plants. They were observed only in 47 species from phylogenetically distant families, suggesting that the evolution of sex chromosomes was independent in these species. It was shown that DNA repeat sequences are one of the major factors driving sex chromosomes evolution, and an accumulation or elimination of the repetitive DNA elements are closely linked with the formation of differences in the sex chromosomes. The goal of this study was to characterize the transposon composition in male and female plants of Cannabis sativa L., Humulus lupulus L. and Humulus japonicus Siebold & Zucc. For the first time, the male and female genomes of H. japonicus as well as male genomes of H. lupulus and C. sativa have been sequenced (there were no open data about them). The analysis of genome-wide sequencing data with using Repeatexplorer2 and author’s scripts was carried out. It was shown that accumulation of Ty3-gypsy may be associated with speciation in Cannabaceae family which is the opposite of the theory of speciation throw whole-genome duplication. Moreover, the sex-specific DNA repeat clusters in C. sativa and H. japonicus were found. The analysis also revealed that the concentration of Tekay, Retand and Ikeros repeats in the Y chromosome of C. sativa is lower than in the X chromosome and the Angela concentration is higher in the Y chromosome.

Identification of sex in hop (Humulus lupulus) using molecular markers

Genome ◽  
1997 ◽  
Vol 40 (3) ◽  
pp. 357-361 ◽  
Author(s):  
Andreas Polley ◽  
Martin W. Ganal ◽  
Elisabeth Seigner
Keyword(s):  
Molecular Markers ◽  
Y Chromosome ◽  
Dna Sequences ◽  
Sex Chromosome ◽  
Rapid Identification ◽  
Humulus Lupulus ◽  
Specific Product ◽  
Male And Female ◽  
Cultivated Plant ◽  
Male Specific

The rapid identification of sex in the dioecious hop (Humulus lupulus) is important for the breeding of this cultivated plant because only unfertilized flowers of the female plants are used as an ingredient in the production of beer. It is thought that a sex-chromosome mechanism controls the development of male or female plants. We have compared pools of male and female plants derived from a hop cross to identify molecular markers associated with the Y or male-specific chromosome. Of 900 functional RAPD primers, 32 revealed fragments specific for male plants that were absent in female plants of this cross. Subsequently, the 32 positive primers were tested on unrelated male and female plants. Three of these 32 primers were specific for the Y chromosome in all lines. The Y-specific product derived from one of these primers (OPJ9) was of low copy in hybridization experiments and predominantly present in male plants. Primers developed from the DNA sequence of this product provide a marker for rapid sex identification in crosses of hop by means of PCR.Key words: chromosomes, RAPD, sex-specific DNA sequences, plant breeding, Y chromosome.

scholarly journals Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers

2019 ◽  
Vol 116 (38) ◽  
pp. 19031-19036 ◽  
Author(s):  
Iulia Darolti ◽  
Alison E. Wright ◽  
Benjamin A. Sandkam ◽  
Jake Morris ◽  
Natasha I. Bloch ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Poecilia Reticulata ◽  
Sex Chromosome ◽  
Sequencing Data ◽  
Chromosome Differentiation ◽  
Y Chromosomes ◽  
Shared Ancestry ◽  
Suppressed Recombination

Once recombination is halted between the X and Y chromosomes, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about the variation in sex chromosome differentiation within clades. Here, we combined whole-genome and transcriptome sequencing data to characterize the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei, but also with Poecilia picta, which diverged roughly 20 million years ago. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata and P. wingei are largely homomorphic, with recombination in the former persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely nonrecombining and strikingly heteromorphic. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of functional chromosome-wide dosage compensation in this species, which has not been previously observed in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation.

Y chromosome specific markers and the evolution of dioecy in the genus Silene

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 141-147 ◽  
Author(s):  
Y Hi Zhang ◽  
Veronica S Stilio ◽  
Farah Rehman ◽  
Amy Avery ◽  
David Mulcahy ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Silene Latifolia ◽  
Dioecious Species ◽  
Sequence Characterized Amplified Region ◽  
Y Chromosomes ◽  
Heteromorphic Sex Chromosomes ◽  
Males And Females ◽  
Genus Silene ◽  
Evolution Of Dioecy

Sex determination in plants has been most thoroughly investigated in Silene latifolia, a dioecious species possessing heteromorphic sex chromosomes. We have identified several new Y chromosome linked RAPD markers and converted these to more reliable sequence characterized amplified region (SCAR) markers by cloning the RAPD fragments and developing longer primers. Of the primer pairs for seven SCARs, five amplify a single, unique fragment from the DNA of male S. latifolia. Two sets of primers also amplify additional fragments common to males and females. Homology between the X and Y chromosomes is sufficient to allow the amplification of fragments from females under less stringent PCR conditions. Five of the SCARs also distinguish between the sexes of closely related dioecious taxa of the section Elisanthe, but not between the sexes of distantly related dioecious species. These markers will be useful for continued investigations into the evolution of sex, phylogenetic relationships among taxa, and population dynamics of sex ratios in the genus Silene.Key words: Melandrium, RAPDs, sex chromosomes, SCARs.

scholarly journals Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers

2019 ◽  
Author(s):  
Iulia Darolti ◽  
Alison E. Wright ◽  
Benjamin A. Sandkam ◽  
Jake Morris ◽  
Natasha I. Bloch ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Poecilia Reticulata ◽  
Sex Chromosome ◽  
Sequencing Data ◽  
Chromosome Differentiation ◽  
Shared Ancestry ◽  
Sex Chromosome System ◽  
Suppressed Recombination

ABSTRACTOnce recombination is halted between the X and Y chromosome, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about variation in sex chromosome differentiation within clades. Here, we combined whole genome and transcriptome sequencing data to characterise the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei, but also with Poecilia picta, which diverged 30 mya. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata are largely homomorphic, with recombination persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely non-recombining and strikingly heteromorphic. ln addition to being highly divergent, the sex chromosome system in P. picta includes a neo-sex chromosome, the result of a fusion between the ancestral sex chromosome and part of chromosome 7. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of complete dosage compensation in this species, the first such documented case in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation.

RAPD markers encoding retrotransposable elements are linked to the male sex in Cannabis sativa L.

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 931-936 ◽  
Author(s):  
Koichi Sakamoto ◽  
Tomoko Abe ◽  
Tomoki Matsuyama ◽  
Shigeo Yoshida ◽  
Nobuko Ohmido ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Y Chromosome ◽  
Dna Sequences ◽  
Blot Analysis ◽  
Cannabis Sativa ◽  
Random Amplified Polymorphic Dna ◽  
Male And Female ◽  
Retrotransposable Elements

Male-associated DNA sequences were analyzed in Cannabis sativa L. (hemp), a dioecious plant with heteromorphic sex chromosomes. DNA was isolated from male and female plants and subjected to random amplified polymorphic DNA analysis. Of 120 primers, 17 yielded 400 to 1500-bp fragments detectable in male, but not female, plants. These fragments were cloned and used as probes in gel-blot analysis of genomic DNA. When male and female DNA was hybridized with 2 of these male-specific fragments, MADC(male-associated DNA sequences in C. sativa)3 and MADC4, particularly intense bands specific to male plants were detected in addition to bands common to both sexes. The MADC3 and MADC4 sequences were shown to encode gag/pol polyproteins of copia-like retrotransposons. Fluorescence in situ hybridization with MADC3 and MADC4 as probes revealed a number of intense signals on the Y chromosome as well as dispersed signals on all chromosomes. The gel-blot analysis and fluorescence in situ hybridization results presented here support the hypothesis that accumulation of retrotransposable elements on the Y chromosome might be 1 cause of heteromorphism of sex chromosomes.Key words: Cannabis sativa, FISH, RAPD, retrotransposon, sex chromosome.

On sex determination in the Turkish desert woodlouse Hemilepistus elongatus (Crustacea, Isopoda, Oniscidea): searching for sex chromosomes and for sex-specific differences in simple DNA repeats

Genome ◽  
1996 ◽  
Vol 39 (4) ◽  
pp. 818-821 ◽  
Author(s):  
G. Röder ◽  
K. E. Linsenmair ◽  
I. Nanda ◽  
M. Schmid
Keyword(s):  
Chromosome Number ◽  
Sex Determination ◽  
Sex Chromosomes ◽  
Genomic Dna ◽  
Constitutive Heterochromatin ◽  
Dna Repeats ◽  
Male And Female ◽  
General Morphology ◽  
C Banding ◽  
Heteromorphic Sex Chromosomes

The karyotype of male and female Hemilepistus elongatus was investigated by means of C-banding. The diploid chromosome number in both sexes is 2n = 50. By scrutinizing general morphology and localization of the constitutive heterochromatin, no heteromorphic sex chromosomes were found. All chromosome pairs in males are well paired during diakinesis. Hybridization of genomic DNA with (GACA)4 and (GATA)4 oligonucleotides revealed no sex-specific patterns. Key words : karyotype, C-banding, sex determination, simple DNA-repeats, Isopoda.

scholarly journals Toxic Y chromosome: increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome

2020 ◽  
Author(s):  
Alison H. Nguyen ◽  
Doris Bachtrog
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Young Male ◽  
Heterochromatin Formation ◽  
Young Males ◽  
Repeat Content ◽  
Y Chromosomes ◽  
Heteromorphic Sex Chromosomes ◽  
Heterogametic Sex ◽  
Effects Of Aging

Sex‐specific differences in lifespan are prevalent across the tree of life and influenced by heteromorphic sex chromosomes. In species with XY sex chromosomes, females often outlive males. Males and females can differ in their overall repeat content due to the repetitive Y chromosome, and repeats on the Y might lower survival of the heterogametic sex (toxic Y effect). Here, we take advantage of the well‐assembled young Y chromosome of Drosophila miranda to study the sex‐specific dynamics of chromatin structure and repeat expression during aging in male and female flies. Male D. miranda have about twice as much repetitive DNA compared to females, and live shorter than females. Heterochromatin is crucial for silencing of repetitive elements, yet old D. miranda flies lose H3K9me3 modifications in their pericentromere, with heterochromatin loss being more severe during aging in males than females. Satellite DNA becomes de‐repressed more rapidly in old vs. young male flies relative to females. In contrast to what is observed in D. melanogaster, we find that transposable elements (TEs) are expressed at higher levels in male D. miranda throughout their life. We show that epigenetic silencing via heterochromatin formation is ineffective on the large TE‐ rich neo‐Y chromosome, resulting in up‐regulation of Y‐linked TEs already in young males. This is consistent with an interaction between the age of the Y chromosome and the genomic effects of aging. Our data support growing evidence that “toxic Y chromosomes” can diminish male fitness and a reduction in heterochromatin can contribute to sex‐specific aging.

scholarly journals Single-cell RNA-seq reveals distinct dynamic behavior of sex chromosomes during early human embryogenesis

2018 ◽  
Author(s):  
Qing Zhou ◽  
Taifu Wang ◽  
Lizhi Leng ◽  
Wei Zheng ◽  
Jinrong Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Protein Translation ◽  
Preimplantation Embryos ◽  
Sequencing Data ◽  
Male And Female ◽  
Trophectoderm Cells ◽  
Human Embryogenesis

AbstractBackgroundSeveral animal and human studies have demonstrated that sex affects kinetics and metabolism during early embryo development. However, the mechanism governing these differences at the molecular level is unknown, warranting a systematic profiling of gene expression in males and females during embryogenesis.FindingsWe performed comprehensive analyses of gene expression comparing male and female embryos using available single-cell RNA-sequencing data of 1607 individual cells from 99 human preimplantation embryos, covering development stages from 4-cell to late blastocyst (E2 to E7). Consistent chromosome-wide transcription of autosomes was observed, while sex chromosomes showed significant differences after embryonic genome activation (EGA). Differentially expressed genes (DE genes) in male and female embryos mainly involved in the cell cycle, protein translation and metabolism. The Y chromosome was initially activated by pioneer genes, RPS4Y1 and DDX3Y, while the two X chromosomes in female were widely activated after EGA. Expression of X-linked genes in female significantly declined at the late blastocyst stage, especially in trophectoderm cells, revealing a rapid process of dosage compensation.ConclusionsWe observed imbalanced expression from sex chromosomes in male and female embryos during EGA, with dosage compensation occurring first in female trophectoderm cells. Studying the effect of sex differences during human embryogenesis, as well as understanding the mechanism of X chromosome inactivation and its correlation with early miscarriage, will provide a basis for advancing assisted reproductive technology (ART) and thereby improve the treatment of infertility and possibly enhance reproductive health.

scholarly journals Construction of Papaya Male and Female BAC Libraries and Application in Physical Mapping of the Sex Chromosomes

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Andrea R. Gschwend ◽  
Qingyi Yu ◽  
Paul Moore ◽  
Christopher Saski ◽  
Cuixia Chen ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Restriction Enzyme ◽  
Sex Chromosomes ◽  
Physical Map ◽  
Bac Library ◽  
Specific Region ◽  
Average Insert Size ◽  
Insert Size ◽  
Male And Female ◽  
Bac Libraries

Papaya is a major fruit crop in the tropics and has recently evolved sex chromosomes. Towards sequencing the papaya sex chromosomes, two bacterial artificial chromosome (BAC) libraries were constructed from papaya male and female genomic DNA. The female BAC library was constructed using restriction enzymeBstY I and consists of 36,864 clones with an average insert size of 104 kb, providing 10.3x genome equivalents. The male BAC library was constructed using restriction enzymeEcoR I and consists of 55,296 clones with an average insert size of 101 kb, providing 15.0x genome equivalents. The male BAC library was used in constructing the physical map of the male-specific region of the male Y chromosome (MSY) and in filling gaps and extending the physical map of the hermaphrodite-specific region of the Yhchromosome (HSY) and the X chromosome physical map. The female BAC library was used to extend the X physical map gap. The MSY, HSY, and X physical maps offer a unique opportunity to study chromosomal rearrangements, Y chromosome degeneration, and dosage compensation of the papaya nascent sex chromosomes.

scholarly journals Impact of deleterious mutations, sexually antagonistic selection and mode of recombination suppression on transitions between male and female heterogamety

2018 ◽  
Author(s):  
Paul A. Saunders ◽  
Samuel Neuenschwander ◽  
Nicolas Perrin
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Deleterious Mutations ◽  
Mutation Load ◽  
Recombination Suppression ◽  
Male And Female ◽  
Antagonistic Selection ◽  
Y Chromosomes ◽  
Chromosome Mutation ◽  
Sexually Antagonistic Selection

AbstractDeleterious mutations accumulating on non-recombining Y chromosomes can drive XY to XY turnovers, but are thought to prevent XY to ZW turnovers, because the latter require fixation of the ancestral Y. Using individual-based simulations, we explored whether and how a dominant W allele can spread in a young XY system that gradually accumulates deleterious mutations. We also investigated how sexually antagonistic (SA) polymorphism on the ancestral sex chromosomes, and the mechanism controlling X-Y recombination suppression affect these transitions. In contrast with XY to XY turnovers, XY to ZW turnovers cannot be favored by Y chromosome mutation load. If the arrest of X-Y recombination depends on genotypic sex, transitions are strongly hindered by deleterious mutations, and totally suppressed by very small SA cost, because deleterious mutations and female-detrimental SA alleles would have to fix with the Y. If, however, the arrest of X-Y recombination depends on phenotypic sex, X and Y recombine in XY ZW females, allowing for the purge of Y-linked deleterious mutations and loss of the SA polymorphism, causing XY to ZW turnovers to occur at a neutral rate. We generalize our results to other types of turnovers (e.g., triggered by non-dominant sex-determining mutations) and discuss their empirical relevance.

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