scholarly journals A selective sweep in or near the Silene latifolia X-linked gene SlssX

2008 ◽  
Vol 90 (1) ◽  
pp. 85-95 ◽  
Author(s):  
D. A. FILATOV
Keyword(s):  
High Frequency ◽  
Selective Sweep ◽  
Selective Advantage ◽  
Silene Latifolia ◽  
Gene Encoding ◽  
Linked Gene ◽  
Compensatory Evolution ◽  
Y Chromosomes ◽  
Strong Homology ◽  
Recent Origin

SummaryThe most prominent feature of Y chromosomes is that they do not recombine and are usually genetically degenerate, containing only a few genes. White campion Silene latifolia has evolved sex chromosomes relatively recently, probably within the last 10–15 million years. Perhaps due to its recent origin, the Y chromosome in this species has not completely degenerated and most isolated X-linked genes have intact Y-linked homologues. A gene encoding a protein with strong homology to spermidine synthases, Slss, is the exception to this rule, as the Y-linked copy of this gene has apparently lost its function. Here I report evidence for a recent selective sweep in the X-linked copy of this gene (SlssX) that could reflect compensatory evolution in an X-linked gene that has lost a functional Y-linked homologue. The spread and fixation of an advantageous mutation in SlssX has resulted in a dramatic loss of genetic diversity and an excess of high-frequency derived polymorphisms in this gene. As the sweep has not affected the closely linked DD44X gene, the selective advantage of the mutation that has driven the sweep in the SlssX gene might have been less than 1%.

scholarly journals Sequence Variation and Haplotype Structure at the HumanHFELocus

Genetics ◽  
2002 ◽  
Vol 161 (4) ◽  
pp. 1609-1623 ◽  
Author(s):  
Christopher Toomajian ◽  
Martin Kreitman
Keyword(s):  
High Frequency ◽  
Nucleotide Diversity ◽  
Sequence Variation ◽  
Hla Class I ◽  
Selective Advantage ◽  
European Ancestry ◽  
Iron Regulation ◽  
Intragenic Recombination ◽  
Nucleotide Variability ◽  
Show Evidence

AbstractThe HFE locus encodes an HLA class-I-type protein important in iron regulation and segregates replacement mutations that give rise to the most common form of genetic hemochromatosis. The high frequency of one disease-associated mutation, C282Y, and the nature of this disease have led some to suggest a selective advantage for this mutation. To investigate the context in which this mutation arose and gain a better understanding of HFE genetic variation, we surveyed nucleotide variability in 11.2 kb encompassing the HFE locus and experimentally determined haplotypes. We fully resequenced 60 chromosomes of African, Asian, or European ancestry as well as one chimpanzee, revealing 41 variable sites and a nucleotide diversity of 0.08%. This indicates that linkage to the HLA region has not substantially increased the level of HFE variation. Although several haplotypes are shared between populations, one haplotype predominates in Asia but is nearly absent elsewhere, causing higher than average genetic differentiation among the three major populations. Our samples show evidence of intragenic recombination, so the scarcity of recombination events within the C282Y allele class is consistent with selection increasing the frequency of a young allele. Otherwise, the pattern of variability in this region does not clearly indicate the action of positive selection at this or linked loci.

scholarly journals The Effect of Deleterious Alleles on Adaptation in Asexual Populations

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 395-411 ◽  
Author(s):  
Toby Johnson ◽  
Nick H Barton
Keyword(s):  
Selective Sweep ◽  
Deleterious Mutation ◽  
Short Interval ◽  
Selective Advantage ◽  
Asexual Population ◽  
Restrictive Assumption ◽  
Deleterious Alleles ◽  
Fixation Probabilities ◽  
Asexual Populations ◽  
Beneficial Allele

Abstract We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles.

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.

scholarly journals An estimate of heterosis in Drosophila melanogaster

1971 ◽  
Vol 18 (1) ◽  
pp. 97-105 ◽  
Author(s):  
J. A. Sved
Keyword(s):  
Drosophila Melanogaster ◽  
High Frequency ◽  
Marker Chromosome ◽  
Selective Advantage ◽  
Wild Type ◽  
Set Up

SUMMARYTwenty-five population cages of D. melanogaster were set up, each containing a different wild-type second chromosome and the marker chromosome Cy. In all but one case where contamination apparently occurred, the Cy chromosome persisted in the population at high frequency, showing a selective advantage of Cy/ + heterozygotes over wild-type homozygotes. Overall, the results indicate that homozygosity of the entire second chromosome causes a depression in fitness of the order of 85%.

scholarly journals Inactivation of KsgA, a 16S rRNA Methyltransferase, Causes Vigorous Emergence of Mutants with High-Level Kasugamycin Resistance

2008 ◽  
Vol 53 (1) ◽  
pp. 193-201 ◽  
Author(s):  
Kozo Ochi ◽  
Ji-Yun Kim ◽  
Yukinori Tanaka ◽  
Guojun Wang ◽  
Kenta Masuda ◽  
...  
Keyword(s):  
16S Rrna ◽  
High Frequency ◽  
Resistance Mutations ◽  
Gene Encoding ◽  
Adenosylmethionine Decarboxylase ◽  
Ribosomal Function ◽  
High Level ◽  
Antibiotic Resistance Mutations ◽  
Modest Level ◽  
Level Resistance

ABSTRACT The methyltransferases RsmG and KsgA methylate the nucleotides G535 (RsmG) and A1518 and A1519 (KsgA) in 16S rRNA, and inactivation of the proteins by introducing mutations results in acquisition of low-level resistance to streptomycin and kasugamycin, respectively. In a Bacillus subtilis strain harboring a single rrn operon (rrnO), we found that spontaneous ksgA mutations conferring a modest level of resistance to kasugamycin occur at a high frequency of 10−6. More importantly, we also found that once cells acquire the ksgA mutations, they produce high-level kasugamycin resistance at an extraordinarily high frequency (100-fold greater frequency than that observed in the ksgA + strain), a phenomenon previously reported for rsmG mutants. This was not the case for other antibiotic resistance mutations (Tspr and Rifr), indicating that the high frequency of emergence of a mutation for high-level kasugamycin resistance in the genetic background of ksgA is not due simply to increased persistence of the ksgA strain. Comparative genome sequencing showed that a mutation in the speD gene encoding S-adenosylmethionine decarboxylase is responsible for the observed high-level kasugamycin resistance. ksgA speD double mutants showed a markedly reduced level of intracellular spermidine, underlying the mechanism of high-level resistance. A growth competition assay indicated that, unlike rsmG mutation, the ksgA mutation is disadvantageous for overall growth fitness. This study clarified the similarities and differences between ksgA mutation and rsmG mutation, both of which share a common characteristic—failure to methylate the bases of 16S rRNA. Coexistence of the ksgA mutation and the rsmG mutation allowed cell viability. We propose that the ksgA mutation, together with the rsmG mutation, may provide a novel clue to uncover a still-unknown mechanism of mutation and ribosomal function.

HIGH FREQUENCY OF 3:1 TETRAD RATIOS FOR THE PDX-1 LOCUS OF NEUROSPORA CRASSA

1969 ◽  
Vol 11 (1) ◽  
pp. 60-64 ◽  
Author(s):  
A. Radford ◽  
S. F. H. Threlkeld
Keyword(s):  
Neurospora Crassa ◽  
Gene Conversion ◽  
High Frequency ◽  
High Ratio ◽  
The Other ◽  
Linked Gene

Nine crosses, involving three alleles, were used in a study of recombination at the pdx-1 locus of Neurospora. In two of the crosses, an unusually high ratio of apparent gene conversion was observed, Two asci of the aberrant type were analyzed by means of prototrophs from backcrosses. In one case the ascus was confirmed as an example of genuine gene conversion. In the other, however, the original scoring of the ascus was found to be due to the presence of a closely linked gene capable of modifying the expression of the two conditional pdx-1 mutants used in the study.

scholarly journals Rapid Y degeneration and dosage compensation in plant sex chromosomes

2015 ◽  
Vol 112 (42) ◽  
pp. 13021-13026 ◽  
Author(s):  
Alexander S. T. Papadopulos ◽  
Michael Chester ◽  
Kate Ridout ◽  
Dmitry A. Filatov
Keyword(s):  
Sex Chromosomes ◽  
Large Scale ◽  
De Novo ◽  
Silene Latifolia ◽  
Stop Codons ◽  
Y Chromosomes ◽  
Evolutionary Trajectories ◽  
Plant Sex Chromosomes ◽  
Two Kingdoms ◽  
Y Degeneration

The nonrecombining regions of animal Y chromosomes are known to undergo genetic degeneration, but previous work has failed to reveal large-scale gene degeneration on plant Y chromosomes. Here, we uncover rapid and extensive degeneration of Y-linked genes in a plant species, Silene latifolia, that evolved sex chromosomes de novo in the last 10 million years. Previous transcriptome-based studies of this species missed unexpressed, degenerate Y-linked genes. To identify sex-linked genes, regardless of their expression, we sequenced male and female genomes of S. latifolia and integrated the genomic contigs with a high-density genetic map. This revealed that 45% of Y-linked genes are not expressed, and 23% are interrupted by premature stop codons. This contrasts with X-linked genes, in which only 1.3% of genes contained stop codons and 4.3% of genes were not expressed in males. Loss of functional Y-linked genes is partly compensated for by gene-specific up-regulation of X-linked genes. Our results demonstrate that the rate of genetic degeneration of Y-linked genes in S. latifolia is as fast as in animals, and that the evolutionary trajectories of sex chromosomes are similar in the two kingdoms.

scholarly journals Three tightly linked genes encoding human type I keratins: conservation of sequence in the 5'-untranslated leader and 5'-upstream regions of coexpressed keratin genes.

1986 ◽  
Vol 6 (2) ◽  
pp. 539-548 ◽  
Author(s):  
A RayChaudhury ◽  
D Marchuk ◽  
M Lindhurst ◽  
E Fuchs
Keyword(s):  
Molecular Mechanisms ◽  
Type I ◽  
Differential Splicing ◽  
Gene Encoding ◽  
Linked Gene ◽  
Human Dna ◽  
Human Epidermal Cells ◽  
Genes Encoding ◽  
Positive Hybridization ◽  
Endonuclease Mapping

We have isolated and subcloned three separate segments of human DNA which share strong sequence homology with a previously sequenced gene encoding a type I keratin, K14 (50 kilodaltons). Restriction endonuclease mapping has demonstrated that these three genes are tightly linked chromosomally, whereas the K14 gene appears to be separate. As judged by positive hybridization-translation and Northern blot analyses, the central linked gene encodes a keratin, K17, which is expressed in abundance with K14 and two other type I keratins in cultured human epidermal cells. None of these other epidermal keratin mRNAs appears to be generated from the K17 gene through differential splicing of its transcript. The sequence of the K17 gene reveals striking homologies not only with the coding portions and intron positions of the K14 gene, but also with its 5'-noncoding and 5'-upstream sequences. These similarities may provide an important clue in elucidating the molecular mechanisms underlying the coexpression of the two genes.

LTR retrotransposons in the dioecious plant Silene latifolia

Genome ◽  
2002 ◽  
Vol 45 (4) ◽  
pp. 745-751 ◽  
Author(s):  
Sachihiro Matsunaga ◽  
Fumi Yagisawa ◽  
Maki Yamamoto ◽  
Wakana Uchida ◽  
Shunsuke Nakao ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Evolutionary Dynamics ◽  
Sex Chromosome ◽  
Silene Latifolia ◽  
Ltr Retrotransposons ◽  
Dioecious Plant ◽  
Dioecious Species ◽  
Y Chromosomes ◽  
Genus Silene ◽  
Silene Species

Conserved domains of two types of LTR retrotransposons, Ty1–copia- and Ty3–gypsy-like retrotransposons, were isolated from the dioecious plant Silene latifolia, whose sex is determined by X and Y chromosomes. Southern hybridization analyses using these retrotransposons as probes resulted in identical patterns from male and female genomes. Fluorescence in situ hybridization indicated that these retrotransposons do not accumulate specifically in the sex chromosomes. These results suggest that recombination between the sex chromosomes of S. latifolia has not been severely reduced. Conserved reverse transcriptase regions of Ty1–copia-like retrotransposons were isolated from 13 different Silene species and classified into two major families. Their categorization suggests that parallel divergence of the Ty1–copia-like retrotransposons occurred during the differentiation of Silene species. Most functional retrotransposons from three dioecious species, S. latifolia, S. dioica, and S. diclinis, fell into two clusters. The evolutionary dynamics of retrotransposons implies that, in the genus Silene, dioecious species evolved recently from gynodioecious species.Key words: retrotransposon, dioecious plant, sex chromosome.

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.

Sign in / Sign up

Export Citation Format

Share Document