Isolation of Y Chromosome-Specific Sequences From Silene latifolia and Mapping of Male Sex-Determining Genes Using Representational Difference Analysis

The genomic subtraction method representational difference analysis (RDA) was used to identify male-specific restriction fragments in the dioecious plant Silene latifolia. Male-specific restriction fragments are linked to the male sex chromosome (the Y chromosome). Four RDA-derived male-specific restriction fragments were used to identify polymorphisms in a collection of X-ray-generated mutant plants with either hermaphroditic or asexual flowers. Some of the mutants have cytologically detectable deletions in the Y chromosome that were correlated with loss of male-specific restriction fragments. One RDA-derived probe detected a restriction fragment present in all mutants, indicating that each has retained Y chromosomal DNA. The other three probes detected genomic fragments that were linked in a region deleted in some hermaphroditic and some asexual mutants. Based on the mutant phenotypes and the correlation of cytologically visible deletions with loss of male-specific restriction fragments, these markers were assigned to positions on the Y chromosome close to the carpel suppression locus. This RDA mapping also revealed a Y-linked locus, not previously described, which is responsible for early stamen development.

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Isolation of X and Y Chromosome-Specific DNA Markers From a Liverwort, Marchantia polymorpha, by Representational Difference Analysis

Genetics ◽

10.1093/genetics/159.3.981 ◽

2001 ◽

Vol 159 (3) ◽

pp. 981-985

Author(s):

Masaki Fujisawa ◽

Kiwako Hayashi ◽

Tomohisa Nishio ◽

Tomoyuki Bando ◽

Sachiko Okada ◽

...

Keyword(s):

Y Chromosome ◽

Sex Chromosomes ◽

Dna Markers ◽

Representational Difference Analysis ◽

Marchantia Polymorpha ◽

Dna Fragments ◽

Difference Analysis ◽

Y Chromosomes ◽

Female Specific ◽

Male Specific

Abstract The liverwort Marchantia polymorpha has X and Y chromosomes in the respective female and male haploids. Here we report the successful exploitation of representational difference analyses to isolate DNA markers for the sex chromosomes. Two female-specific and six male-specific DNA fragments were genetically confirmed to originate from the X and Y chromosomes, respectively.

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NmeSI Restriction-Modification System Identified by Representational Difference Analysis of a HypervirulentNeisseria meningitidis Strain

Infection and Immunity ◽

10.1128/iai.69.3.1816-1820.2001 ◽

2001 ◽

Vol 69 (3) ◽

pp. 1816-1820 ◽

Cited By ~ 18

Author(s):

Aldert Bart ◽

Yvonne Pannekoek ◽

Jacob Dankert ◽

Arie van der Ende

Keyword(s):

Open Reading Frames ◽

Representational Difference Analysis ◽

Chromosomal Dna ◽

Modification System ◽

Difference Analysis ◽

Restriction Modification System ◽

Methyltransferase Gene ◽

Specific Restriction ◽

Restriction Modification ◽

Reading Frames

ABSTRACT Neisseria meningitidis is a gram-negative bacterium that may cause meningitis, sepsis, or both. The increase in the incidence of meningococcal disease in various countries in the past 2 decades is mainly due the genotypically related lineage III meningococci. The chromosomal DNA differences between lineage III strains and non-lineage III strains were identified using representational difference analysis. Thus, a 1.8-kb locus that is specific for lineage III meningococci was identified. The locus contains three open reading frames encoding the NmeSI restriction-modification system. The methyltransferase gene was cloned and expressed in Escherichia coli. Site AGTACT was found to be modified by the enzyme. In conclusion, lineage III strains differ from endemic strains by the presence of a specific restriction-modification system. This restriction-modification system may contribute to the clonal and hypervirulent character of lineage III strains by influencing horizontal gene transfer and transcription.

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The detection of female cell activity in male sex chromosome chimeric Rideau Arcott sheep, using the Xist gene product as a marker

SURG Journal ◽

10.21083/surg.v1i2.414 ◽

2008 ◽

Vol 1 (2) ◽

pp. 20-25

Author(s):

Okimi Peters ◽

W. Allan King

Keyword(s):

Y Chromosome ◽

Sex Chromosome ◽

Cell Activity ◽

Xist Gene ◽

Specific Gene ◽

Xist Expression ◽

Female Cell ◽

Male Sex ◽

Polymerase Chain ◽

Xy Female

The detection of the SRY (Sex-determining region on the Y chromosome) gene is a popular method used for the identification of freemartins (XX/XY female chimeras). This method relies on the fact that the SRY gene is a Y chromosome specific gene and is thus normally only present in males therefore detecting its presence in a female indicates the presence of male cells (XY cells) within the female. This concept can be extrapolated to the male counterparts of freemartins with regards to the Xist gene. This gene is normally only widely expressed in females and can be used as a marker for identifying females. Therefore, detecting Xist gene expression in males (in tissues other than the testes, as the Xist gene is expressed exclusively in the testes of males) may indicate that these males contain transcriptionally competent female cells and thus necessarily labels them as sex-chromosome chimeras. In the present study four previously identified male sex chromosome chimeras were screened for the expression of the Xist gene using reverse transcription Polymerase Chain Reaction (PCR), and it was detected in three of the four chimeras. Xist expression was not detected in one of the chimeras because the proportion of female cells in its blood is significantly low and thus it is likely that the blood sample used in the study did not possess female cells. None-the-less it was concluded that the detection of Xist expression in male sex chromosome chimeras can be used as an indication of the presence and transcriptional competence of female cells within them.

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

Genome ◽

10.1139/g97-048 ◽

1997 ◽

Vol 40 (3) ◽

pp. 357-361 ◽

Cited By ~ 42

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.

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The Y chromosome-specific STS marker MS2 and its peripheral regions on the Y chromosome of the dioecious plant Silene latifolia

Genome ◽

10.1139/g08-005 ◽

2008 ◽

Vol 51 (4) ◽

pp. 251-260 ◽

Cited By ~ 8

Author(s):

Kotaro Ishii ◽

Ryuji Sugiyama ◽

Megumi Onuki ◽

Yusuke Kazama ◽

Sachihiro Matsunaga ◽

...

Keyword(s):

Y Chromosome ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Early Stage ◽

Silene Latifolia ◽

Segmental Duplications ◽

Average Insert Size ◽

Sts Marker ◽

Bac Clone ◽

Peripheral Regions

Sex determination in Silene latifolia uses the XX/XY system. The recent evolution of dioecy in S. latifolia provides a unique opportunity to study the early stages of Y chromosome evolution. However, the current Y chromosome map still contains many large gaps with no available markers. In this study, a sequence tagged site (STS) marker, MS2, was isolated and mapped to the same locus as L8 on the Y chromosome. To investigate the peripheral regions of MS2, a bacterial artificial chromosome (BAC) library was constructed from a male plant, and the BAC clone containing MS2 (MS2-9d12F) was isolated from 32 640 clones with an average insert size of 115 kb. A 109-kb insert of the BAC clone was analyzed. BLASTX analysis showed 11 sequences similar to some known proteins, most of which are retrotransposon-like elements. The ORF Finder predicted 9 ORFs within MS2-9d12F. RT-PCR analyses revealed that only 4 of the 9 predicted ORFs are expressed in both male and female plants. These 4 ORFs are candidates for genes having counterparts on both the X and Y chromosomes. Dot-matrix plot analysis and a BLASTN search revealed LTR-like sequences close to the retrotransposon-like elements and high similarity to 3 known genomic sequences of S. latifolia. These results suggest an accumulation of retrotransposons and segmental duplications in peripheral regions of MS2 during the early stage of sex chromosome evolution.

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Sex determination in mice: Y and chromosome 17 interactions

Development ◽

10.1242/dev.101.supplement.25 ◽

1987 ◽

Vol 101 (Supplement) ◽

pp. 25-32

Author(s):

Robert P. Erickson ◽

Edward J. Durbin ◽

Laura L. Tres

Keyword(s):

Sex Determination ◽

Y Chromosome ◽

Dna Sequences ◽

Sex Differentiation ◽

Specific Antigen ◽

Inbred Strains ◽

Chromosome 17 ◽

Male Sex ◽

Male Specific ◽

Type Chromosome

Mice provide material for studies of Y-chromosomal and autosomal sequences involved in sex determination. Eicher and coworkers have identified four subregions in the mouse Y chromosome, one of which corresponds to the Sxr fragment. This fragment demonstrates that only a small portion of the Y is necessary for male sex determination. The mouse Y chromosome also shows variants: the BALB/cWt Y chromosome, which causes nondisjunction of the Y in some germ cells leading to XO and XYY cells and resulting in many infertile true hermaphrodites; the YDom, a wild-type chromosome which can result in sex reversal on a C57BL/6J background; and Y-chromosomal variants detected with Y-derived genomic DNA clones among inbred strains. Two different autosomal loci affecting sex differentiation have been identified in the mouse by Eicher and coworkers. The first of these has not been mapped to a particular chromosome and has been designated Tda-1 (Testis-determining autosomal-1). This is the locus in C57BL/6J mice at which animals must be homozygous in order to develop as true hermaphrodites or sex-reversed animals in the presence of YDom. The other locus has been identified on proximal chromosome 17. This locus also caused hermaphrodites on the C57BL/6J background and it is most easily interpreted as a locus deleted in 7hp. It is located in a region on chromosome 17 containing other genes or DNA sequences that may be related to sex determination. These include both the Hye (histocompatibility Y expression) locus that affects the amount of male-specific antigen detected by serological and cell-mediated assays and a concentration of Bkm sequences. Despite the Y and chromosomal 17 localizations of Bkm sequences, there is no evidence that transcripts from these are involved in sex determination: RNA hybridizing to sense and anti-sense Bkm clones can be detected in day-14 fetal gonads of both sexes.

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A Selective Sweep Associated With a Recent Gene Transposition in Drosophila miranda

Genetics ◽

10.1093/genetics/156.4.1753 ◽

2000 ◽

Vol 156 (4) ◽

pp. 1753-1763 ◽

Cited By ~ 3

Author(s):

Soojin Yi ◽

Brian Charlesworth

Keyword(s):

Y Chromosome ◽

X Chromosome ◽

Sequence Variation ◽

Selective Sweep ◽

Sex Chromosome ◽

Selective Advantage ◽

Chromosome Fusion ◽

Gene Transposition ◽

Sex Chromosome System ◽

Male Specific

Abstract In Drosophila miranda, a chromosome fusion between the Y chromosome and the autosome corresponding to Muller’s element C has created a new sex chromosome system. The chromosome attached to the ancestral Y chromosome is transmitted paternally and hence is not exposed to crossing over. This chromosome, conventionally called the neo-Y, and the homologous neo-X chromosome display many properties of evolving sex chromosomes. We report here the transposition of the exuperantia1 (exu1) locus from a neo-sex chromosome to the ancestral X chromosome of D. miranda. Exu1 is known to have several critical developmental functions, including a male-specific role in spermatogenesis. The ancestral location of exu1 is conserved in the sibling species of D. miranda, as well as in a more distantly related species. The transposition of exu1 can be interpreted as an adaptive fixation, driven by a selective advantage conferred by its effect on dosage compensation. This explanation is supported by the pattern of within-species sequence variation at exu1 and the nearby exu2 locus. The implications of this phenomenon for genome evolution are discussed.

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An accumulation of tandem DNA repeats on the Y chromosome in Silene latifolia during early stages of sex chromosome evolution

Chromosoma ◽

10.1007/s00412-006-0065-5 ◽

2006 ◽

Vol 115 (5) ◽

pp. 376-382 ◽

Cited By ~ 63

Author(s):

Roman Hobza ◽

Martina Lengerova ◽

Julia Svoboda ◽

Hana Kubekova ◽

Eduard Kejnovsky ◽

...

Keyword(s):

Y Chromosome ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Silene Latifolia ◽

Dna Repeats ◽

Sex Chromosome Evolution ◽

Early Stages

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Divergence and Remarkable Diversity of the Y Chromosome in Guppies

Molecular Biology and Evolution ◽

10.1093/molbev/msaa257 ◽

2020 ◽

Author(s):

Pedro Almeida ◽

Benjamin A Sandkam ◽

Jake Morris ◽

Iulia Darolti ◽

Felix Breden ◽

...

Keyword(s):

Y Chromosome ◽

Sex Chromosomes ◽

Sex Chromosome ◽

Haplotype Diversity ◽

Low Frequency ◽

Color Variation ◽

Recombination Suppression ◽

Specific Sequence ◽

Y Chromosome Evolution ◽

Male Specific

Abstract The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary in predator and food abundance in three replicate watersheds. Based on our population-specific genome assemblies, we first confirmed and extended earlier reports of two strata on the guppy sex chromosomes. Stratum I shows significant accumulation of male-specific sequence, consistent with Y divergence, and predates the colonization of Trinidad. In contrast, Stratum II shows divergence from the X, but no Y-specific sequence, and this divergence is greater in three replicate upstream populations compared with their downstream pair. Despite longstanding assumptions that sex chromosome recombination suppression is achieved through inversions, we find no evidence of inversions associated with either Stratum I or Stratum II. Instead, we observe a remarkable diversity in Y chromosome haplotypes within each population, even in the ancestral Stratum I. This diversity is likely due to gradual mechanisms of recombination suppression, which, unlike an inversion, allow for the maintenance of multiple haplotypes. In addition, we show that this Y diversity is dominated by low-frequency haplotypes segregating in the population, suggesting a link between haplotype diversity and female preference for rare Y-linked color variation. Our results reveal the complex interplay between recombination suppression and Y chromosome divergence at the earliest stages of sex chromosome divergence.

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An Ac -like Transposable Element Family With Transcriptionally Active Y-Linked Copies in the White Campion, Silene latifolia

Genetics ◽

10.1093/genetics/165.2.799 ◽

2003 ◽

Vol 165 (2) ◽

pp. 799-807

Author(s):

Ellen J Pritham ◽

Y Hi Zhang ◽

Cédric Feschotte ◽

Rick V Kesseli

Keyword(s):

Transposable Element ◽

Y Chromosome ◽

Genomic Library ◽

Open Reading Frames ◽

Silene Latifolia ◽

Hat Superfamily ◽

Alternatively Spliced ◽

Potential Activity ◽

Male Specific ◽

Related Proteins

Abstract An RFLP genomic subtraction was used to isolate male-specific sequences in the species Silene latifolia. One isolated fragment, SLP2, shares similarity to a portion of the Activator (Ac) transposase from Zea mays and to related proteins from other plant species. Southern blot analysis of male and female S. latifolia genomic DNA shows that SLP2 belongs to a low-copy-number repeat family with two Y-linked copies. Screening of a S. latifolia male genomic library using SLP2 as a probe led to the isolation of five clones, which were partially sequenced. One clone contains two large open reading frames that can be joined into a sequence encoding a putative protein of 682 amino acids by removing a short intron. Database searches and phylogenetic analysis show that this protein belongs to the hAT superfamily of transposases, closest to Tag2 (Arabidopsis thaliana), and contains all of the defined domains critical for the activity of these transposases. PCR with genomic and cDNA templates from S. latifolia male, female, and hermaphrodite individuals revealed that one of the Y-linked copies is transcriptionally active and alternatively spliced. This is the first report of a transcriptionally active transposable element (TE) family in S. latifolia and the first DNA transposon residing on a plant Y chromosome. The potential activity and regulation of this TE family and its use for Y chromosome gene discovery is discussed.

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