Masculinization of the X-chromosome in aphid soma and gonads

Males and females share essentially the same genome but differ in their optimal values for many phenotypic traits, which can result in intra-locus conflict between the sexes. Aphids display XX/X0 sex chromosomes and combine unusual X chromosome inheritance with cyclical parthenogenesis. Theoretical and empirical works support the hypothesis that the large excess of male-biased genes observed on the aphid X chromosome compared to autosomes has evolved in response to sexual conflicts, by restricting the product of a sexually antagonistic allele to the sex it benefits. However, whether such masculinization of the X affects all tissues (as expected if it evolved in response to sexual conflicts) or reflects tissue specificities (which would contradict the sexual conflict hypothesis) remains an open question. To address it, we measured gene expression in different somatic and gonadic tissues of males, sexual females and parthenogenetic females of the pea aphid. We observed a masculinization of the X at the tissue-level, with male-biased genes being 2.5 to 3.5 more frequent on the X than expected. We also tested the hypothesis that gene duplication can facilitate the attenuation of conflicts by allowing gene copies to neo- or sub-functionalize and reach sex-specific optima. As predicted, X-linked copies of duplicated genes having their other copies on autosomes were more frequently male-biased (40.5% of the genes) than duplicated autosomal genes (6.6%) or X-linked single-copy genes (32.5%). These results highlight a peculiar pattern of expression of X-linked genes in aphids at the tissue level and provides further support for sex-biased expression as a mechanism to attenuate intra-locus sexual conflicts.

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Mapping the SRY gene in Microtus cabrerae: a vole species with multiple SRY copies in males and females

Genome ◽

10.1139/g02-007 ◽

2002 ◽

Vol 45 (3) ◽

pp. 600-603 ◽

Cited By ~ 16

Author(s):

Rosa Fernández ◽

María José L Barragán ◽

Mónica Bullejos ◽

Juan Alberto Marchal ◽

Sergio Martínez ◽

...

Keyword(s):

Y Chromosome ◽

X Chromosome ◽

Heterochromatic Region ◽

Pericentromeric Region ◽

Specific Gene ◽

Sry Gene ◽

Microtus Cabrerae ◽

Gene Copies ◽

Vole Species ◽

Males And Females

The SRY gene is a single-copy, male-specific gene, located on the Y chromosome in most mammals. However, recently we have described the presence of multiple polymorphic copies of this gene in both males and females of the vole species Microtus cabrerae. Here, we present the chromosomal localization of SRY gene copies in this species by fluorescent in situ hybridization (FISH). This technique localized these gene copies in the short arm, and hence in the euchromatic region, of the Y chromosome. Furthermore, several copies of the SRY gene are located on the X chromosome. These copies are spread along the entire heterochromatic region of the X chromosome, occupying the whole short arm, the centromeric region, and the pericentromeric region of the long arm.Key words: FISH mapping, Micotus cabrerae, SRY gene, X chromosome, Y chromosome.

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Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome

Genome Biology and Evolution ◽

10.1093/gbe/evaa161 ◽

2020 ◽

Vol 12 (11) ◽

pp. 1953-1960

Author(s):

Andrey A Yurchenko ◽

Hans Recknagel ◽

Kathryn R Elmer

Keyword(s):

Linkage Map ◽

Single Copy ◽

Phenotypic Traits ◽

Sequencing Data ◽

High Coverage ◽

Squamate Reptiles ◽

Common Lizard ◽

Zootoca Vivipara ◽

The Common ◽

Chromosome Level

Abstract Squamate reptiles exhibit high variation in their phenotypic traits and geographical distributions and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46-Gb genome assembly has a scaffold N50 of 11.52 Mb with N50 contig size of 220.4 kb and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total, 19,829 gene models were annotated to the genome using a combination of ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles.

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Intragenomic and intraspecific heterogeneity in rrs may surpass interspecific variability in a natural population of Veillonella

Microbiology ◽

10.1099/mic.0.038224-0 ◽

2010 ◽

Vol 156 (7) ◽

pp. 2080-2091 ◽

Cited By ~ 28

Author(s):

Anne-Laure Michon ◽

Fabien Aujoulat ◽

Laurent Roudière ◽

Olivier Soulier ◽

Isabelle Zorgniotti ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Diversity ◽

Natural Populations ◽

Variable Region ◽

Housekeeping Gene ◽

Single Copy ◽

Population Based ◽

Rrna Gene ◽

Gene Copies

As well as intraspecific heterogeneity, intragenomic heterogeneity between 16S rRNA gene copies has been described for a range of bacteria. Due to the wide use of 16S rRNA gene sequence analysis for taxonomy, identification and metagenomics, evaluating the extent of these heterogeneities in natural populations is an essential prerequisite. We investigated inter- and intragenomic 16S rRNA gene heterogeneity of the variable region V3 in a population of 149 clinical isolates of Veillonella spp. of human origin and in 13 type or reference Veillonella strains using PCR-temporal temperature gel electrophoresis (TTGE). 16S rRNA gene diversity was high in the studied population, as 45 different banding patterns were observed. Intragenomic heterogeneity was demonstrated for 110 (74 %) isolates and 8 (61.5 %) type or reference strains displaying two or three different gene copies. Polymorphic nucleotide positions accounted for 0.5–2.5 % of the sequence and were scattered in helices H16 and H17 of the rRNA molecule. Some of them changed the secondary structure of H17. Phylotaxonomic structure of the population based on the single-copy housekeeping gene rpoB was compared with TTGE patterns. The intragenomic V3 heterogeneity, as well as recombination events between strains or isolates of different rpoB clades, impaired the 16S rRNA-based identification for some Veillonella species. Such approaches should be conducted in other bacterial populations to optimize the interpretation of 16S rRNA gene sequences in taxonomy and/or diversity studies.

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An N-Ethyl-N-Nitrosourea Mutagenesis Screen for Epigenetic Mutations in the Mouse

Genetics ◽

10.1093/genetics/164.4.1481 ◽

2003 ◽

Vol 164 (4) ◽

pp. 1481-1494

Author(s):

Ivona Percec ◽

Joanne L Thorvaldsen ◽

Robert M Plenge ◽

Christopher J Krapp ◽

Joseph H Nadeau ◽

...

Keyword(s):

Genomic Imprinting ◽

X Chromosome ◽

X Inactivation ◽

Monoallelic Expression ◽

Chromosome 15 ◽

Chromosome 5 ◽

Chromosome 10 ◽

Mutagenesis Screen ◽

Distal Chromosome ◽

Males And Females

Abstract The mammalian epigenetic phenomena of X inactivation and genomic imprinting are incompletely understood. X inactivation equalizes X-linked expression between males and females by silencing genes on one X chromosome during female embryogenesis. Genomic imprinting functionally distinguishes the parental genomes, resulting in parent-specific monoallelic expression of particular genes. N-ethyl-N-nitrosourea (ENU) mutagenesis was used in the mouse to screen for mutations in novel factors involved in X inactivation. Previously, we reported mutant pedigrees identified through this screen that segregate aberrant X-inactivation phenotypes and we mapped the mutation in one pedigree to chromosome 15. We now have mapped two additional mutations to the distal chromosome 5 and the proximal chromosome 10 in a second pedigree and show that each of the mutations is sufficient to induce the mutant phenotype. We further show that the roles of these factors are specific to embryonic X inactivation as neither genomic imprinting of multiple genes nor imprinted X inactivation is perturbed. Finally, we used mice bearing selected X-linked alleles that regulate X chromosome choice to demonstrate that the phenotypes of all three mutations are consistent with models in which the mutations have affected molecules involved specifically in the choice or the initiation of X inactivation.

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Analysis of the sex ratio in Bradysia matogrossensis (Diptera, Sciaridae)

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000100018 ◽

2000 ◽

Vol 23 (1) ◽

pp. 97-103 ◽

Cited By ~ 4

Author(s):

Lincoln S. Rocha ◽

André Luiz P. Perondini

Keyword(s):

Sex Ratio ◽

Sex Determination ◽

X Chromosome ◽

Control Mechanism ◽

Sex Ratios ◽

Laboratory Strain ◽

Chromosome Elimination ◽

Common Control ◽

Males And Females ◽

Successive Generations

In sciarid flies, the control of sex determination and of the progeny sex ratio is exercised by the parental females, and is based on differential X-chromosome elimination in the initial stages of embryogenesis. In some species, the females produce unisexual progenies (monogenic females) while in others, the progenies consist of males and females (digenic females). The sex ratio of bisexual progenies is variable, and departs considerably from 1:1. Bradysia matogrossensis shows both monogenic and digenic reproduction. In a recently established laboratory strain of this species, 15% of the females were digenic, 10% produced only females, 13% produced only males, and 62% produced progenies with one predominant sex (33% predominantly of female and 29% predominantly male progenies). These progeny sex ratios were maintained in successive generations. Females from female-skewed progenies yielded female- and male-producing daughters in a 1:1 ratio. In contrast, daughters of females from male-skewed progenies produce bisexual or male-skewed progenies. The X-chromosome of B. matogrossensis shows no inversion or other gross aberration. These results suggest that the control of the progeny sex ratio (or differential X-chromosome elimination) involves more than one locus or, at least, more than one pair of alleles. The data also suggest that, in sciarid flies, monogeny and digeny may share a common control mechanism.

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Mapping quantitative trait loci for body weight on the X chromosome in mice. I. Analysis of a reciprocal F2 population

Genetics Research ◽

10.1017/s0016672397002917 ◽

1997 ◽

Vol 70 (2) ◽

pp. 117-124 ◽

Cited By ~ 21

Author(s):

KELLIE A. RANCE ◽

WILLIAM G. HILL ◽

PETER D. KEIGHTLEY

Keyword(s):

Body Weight ◽

Quantitative Trait Loci ◽

X Chromosome ◽

Quantitative Trait ◽

Selection Line ◽

Fat Percentage ◽

Analytical Technique ◽

F2 Population ◽

Trait Loci ◽

Males And Females

Evidence of a large sex-linked effect accounting for 25% of the divergence between mouse lines selected for body weight has been described previously. A marker-based study was undertaken to determine the number and map positions of the putative X-linked quantitative trait loci (QTLs). An F2 population was generated from a reciprocal F1 between an inbred low line derived from the low selection line and the high selection line. To enable inference of marker-associated QTL effects on the X chromosome, an analytical technique was developed based on the multiple regression method of Haley and Knott. The analysis of data on 10 week weight indicated a single QTL of large effect situated at about 23 cM from the proximal end of the chromosome, with a peak LOD score of 24·4. The likelihood curve showed a single well-defined peak, and gave a 95% confidence interval for the QTL location of 8 cM. The estimates for the additive genotypic effects in males and females (half the differences between hemizygous males and between homozygous females) were 2·6 g in both cases, or 17% and 20% of the 10 week body weight in males and females respectively. Dominance effects in the females were found to be non-significant. No significant X-linked effect on carcass fat percentage was detected, but a single X-linked QTL appears to explain almost the entire X-linked body weight effect.

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An anonymous single copy X-chromosome clone DXS92, from Xq26–27, identifies two frequent RFLPs

Nucleic Acids Research ◽

10.1093/nar/13.20.7540 ◽

1985 ◽

Vol 13 (20) ◽

pp. 7540-7540 ◽

Cited By ~ 1

Author(s):

G. Davatelis ◽

M. Siniscalco ◽

P. Szabo

Keyword(s):

X Chromosome ◽

Single Copy

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Landscape of X chromosome inactivation across human tissues

Nature ◽

10.1038/nature24265 ◽

2017 ◽

Vol 550 (7675) ◽

pp. 244-248 ◽

Cited By ~ 245

Author(s):

Taru Tukiainen ◽

◽

Alexandra-Chloé Villani ◽

Angela Yen ◽

Manuel A. Rivas ◽

...

Keyword(s):

Gene Expression ◽

X Chromosome ◽

Mammalian Cells ◽

Phenotypic Diversity ◽

X Chromosome Inactivation ◽

Chromosome Inactivation ◽

Phenotypic Traits ◽

Human Tissues ◽

X Chromosomes ◽

Chromosomal Genes

Abstract X chromosome inactivation (XCI) silences transcription from one of the two X chromosomes in female mammalian cells to balance expression dosage between XX females and XY males. XCI is, however, incomplete in humans: up to one-third of X-chromosomal genes are expressed from both the active and inactive X chromosomes (Xa and Xi, respectively) in female cells, with the degree of ‘escape’ from inactivation varying between genes and individuals1,2. The extent to which XCI is shared between cells and tissues remains poorly characterized3,4, as does the degree to which incomplete XCI manifests as detectable sex differences in gene expression5 and phenotypic traits6. Here we describe a systematic survey of XCI, integrating over 5,500 transcriptomes from 449 individuals spanning 29 tissues from GTEx (v6p release) and 940 single-cell transcriptomes, combined with genomic sequence data. We show that XCI at 683 X-chromosomal genes is generally uniform across human tissues, but identify examples of heterogeneity between tissues, individuals and cells. We show that incomplete XCI affects at least 23% of X-chromosomal genes, identify seven genes that escape XCI with support from multiple lines of evidence and demonstrate that escape from XCI results in sex biases in gene expression, establishing incomplete XCI as a mechanism that is likely to introduce phenotypic diversity6,7. Overall, this updated catalogue of XCI across human tissues helps to increase our understanding of the extent and impact of the incompleteness in the maintenance of XCI.

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Macroevolutionary consequences of sexual conflict

Biology Letters ◽

10.1098/rsbl.2018.0186 ◽

2018 ◽

Vol 14 (6) ◽

pp. 20180186

Author(s):

Jo S. Hermansen ◽

Jostein Starrfelt ◽

Kjetil L. Voje ◽

Nils C. Stenseth

Keyword(s):

Sexual Selection ◽

Genetic Architecture ◽

Time Frame ◽

Sexual Conflicts ◽

Males And Females ◽

Selection For ◽

Evolutionary Consequences ◽

Future Work ◽

Shared Genetic

Intralocus sexual conflicts arise whenever the fitness optima for a trait expressed in both males and females differ between the sexes and shared genetic architecture constrains the sexes from evolving independently towards their respective optima. Such sexual conflicts are commonplace in nature, yet their long-term evolutionary consequences remain unexplored. Using a Bayesian phylogenetic comparative framework, we studied the macroevolutionary dynamics of intersexual trait integration in stalk-eyed flies (Diopsidae) spanning a time frame of more than 25 Myr. We report that increased intensity of sexual selection on male eyestalks is associated with reduced intersexual eyestalk integration, as well as sex-specific rates of eyestalk evolution. Despite this, lineages where males have been under strong sexual selection for millions of years still exhibit high levels of intersexual trait integration. This low level of decoupling between the sexes may indicate that exaggerated female eyestalks are in fact adaptive—or alternatively, that there are strong constraints on reducing trait integration between the sexes. Future work should seek to clarify the relative roles of constraints and selection in contributing to the varying levels of intersexual trait integration in stalk-eyed flies, and in this way clarify whether sexual conflicts can act as constraints on adaptive evolution even on macroevolutionary time scales.

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Quantitative Genetics of Drosophila Melanogaster. II. Heritabilities and Genetic Correlations between Sexes for Head and Thorax Traits.

Genetics ◽

10.1093/genetics/119.2.421 ◽

1988 ◽

Vol 119 (2) ◽

pp. 421-433

Author(s):

D E Cowley ◽

W R Atchley

Keyword(s):

Drosophila Melanogaster ◽

Sexual Dimorphism ◽

Genetic Analysis ◽

X Chromosome ◽

Dosage Compensation ◽

Imaginal Disc ◽

Genetic Correlations ◽

Body Parts ◽

Quantitative Genetic ◽

Males And Females

Abstract A quantitative genetic analysis is reported for traits on the head and thorax of adult fruit flies, Drosophila melanogaster. Females are larger than males, and the magnitude of sexual dimorphism is similar for traits derived from the same imaginal disc, but the level of sexual dimorphism varies widely across discs. The greatest difference between males and females occurs for the dimensions of the sclerotized mouthparts of the proboscis. Most of the traits studied are highly heritable with heritabilities ranging from 0.26 to 0.84 for males and 0.27 to 0.81 for females. In general, heritabilities are slightly higher for males, possibly reflecting the effect of dosage compensation on X-linked variance. The X chromosome contributes substantially to variance for many of these traits, and including results reported elsewhere, the variance for over two-thirds of the traits studied includes X-linked variance. The genetic correlations between sexes for the same trait are generally high and close to unity. Coupled with the small differences in the traits between sexes for heritabilities and phenotypic variances, these results suggest that selection would be very slow to change the level of sexual dimorphism in size of various body parts.

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