scholarly journals Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Henrik R. Hallingbäck ◽  
Pascal Pucholt ◽  
Pär K. Ingvarsson ◽  
Ann Christin Rönnberg-Wästljung ◽  
Sofia Berlin
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Chromosome 9 ◽  
Genome Wide Association ◽  
Salix Viminalis ◽  
Chromosome 15 ◽  
W Chromosome ◽  
Genome Wide ◽  
Heterogametic Sex

Abstract Background Sex chromosomes are in some species largely undifferentiated (homomorphic) with restricted sex determination regions. Homomorphic but different sex chromosomes are found in the closely related genera Populus and Salix indicating flexible sex determination systems, ideal for studies of processes involved in sex chromosome evolution. We have performed genome-wide association studies of sex and analysed sex chromosomes in a population of 265 wild collected Salix viminalis accessions and studied the sex determining locus. Results A total of 19,592 markers were used in association analyses using both Fisher’s exact tests and a single-marker mixed linear model, which resulted in 48 and 41 sex-associated (SA) markers respectively. Across all 48 SA markers, females were much more often heterozygous than males, which is expected if females were the heterogametic sex. The majority of the SA markers were, based on positions in the S. purpurea genome, located on chromosome 15, previously demonstrated to be the sex chromosome. Interestingly, when mapping the genotyping-by-sequencing sequence tag harbouring the two SA markers with the highest significance to the S. viminalis genomic scaffolds, five regions of very high similarity were found: three on a scaffold that represents a part of chromosome 15, one on a scaffold that represents a part of chromosome 9 and one on a scaffold not anchored to the genome. Based on segregation differences of the alleles at the two marker positions and on differences in PCR amplification between females and males we conclude that females had multiple copies of this DNA fragment (chromosome 9 and 15), whereas males only had one (chromosome 9). We therefore postulate that the female specific sequences have been copied from chromosome 9 and inserted on chromosome 15, subsequently developing into a hemizygous W chromosome linked region. Conclusions Our results support that sex determination in S. viminalis is controlled by one locus on chromosome 15. The segregation patterns observed at the SA markers furthermore confirm that S. viminalis females are the heterogametic sex. We also identified a translocation from chromosome 9 to the W chromosome.

scholarly journals The Diversity and Evolution of Sex Chromosomes in Frogs

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 483
Author(s):  
Wen-Juan Ma ◽  
Paris Veltsos
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Comparative Genomic ◽  
Ancestral State ◽  
Heteromorphic Sex Chromosomes ◽  
Genomic Studies ◽  
Evolutionary Trajectories ◽  
Heterogametic Sex

Frogs are ideal organisms for studying sex chromosome evolution because of their diversity in sex chromosome differentiation and sex-determination systems. We review 222 anuran frogs, spanning ~220 Myr of divergence, with characterized sex chromosomes, and discuss their evolution, phylogenetic distribution and transitions between homomorphic and heteromorphic states, as well as between sex-determination systems. Most (~75%) anurans have homomorphic sex chromosomes, with XY systems being three times more common than ZW systems. Most remaining anurans (~25%) have heteromorphic sex chromosomes, with XY and ZW systems almost equally represented. There are Y-autosome fusions in 11 species, and no W-/Z-/X-autosome fusions are known. The phylogeny represents at least 19 transitions between sex-determination systems and at least 16 cases of independent evolution of heteromorphic sex chromosomes from homomorphy, the likely ancestral state. Five lineages mostly have heteromorphic sex chromosomes, which might have evolved due to demographic and sexual selection attributes of those lineages. Males do not recombine over most of their genome, regardless of which is the heterogametic sex. Nevertheless, telomere-restricted recombination between ZW chromosomes has evolved at least once. More comparative genomic studies are needed to understand the evolutionary trajectories of sex chromosomes among frog lineages, especially in the ZW systems.

Unusual sex chromosome inheritance in mammals

1970 ◽  
Vol 259 (828) ◽  
pp. 15-36 ◽  
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
General Pattern ◽  
Male Meiosis ◽  
Present Knowledge ◽  
Microtus Arvalis ◽  
Present Contribution ◽  
Original Size ◽  
Heterogametic Sex

The male has proven to be the heterogametic sex in all mammals studied so far. As is well known, the males usually have the sex chromosomes XY and the females XX. In recent years, however, many exceptions from this general pattern have been discovered. With our present knowledge, the different sex chromosome mechanisms in mammals may be divided into five main groups, and the first of them into subgroups, as follows: (i) Species with XX/XY sex chromosomes: (a) X of original size (see below), Y small; (b) X large, Y small; (c) X large, Y large: (i) end-to-end association of X and Y at male meiosis, (ii) chiasma between X and Y at male meiosis. (ii) Species with XX/XY 1 Y 2 sex chromosomes. (iii) Species with X 1 X 1 X 2 X 2 /X 1 X 2 Y sex chromosomes. (iv) Species with complicated or unknown mechanisms for sex determination. (v) Species with mosaicism of the sex chromosomes, but apparently with an XX/XY mechanism for sex determination. The present contribution will mainly deal with unusual sex chromosome inheritance, that is the groups (ii), (iii) and (iv) above, but the other two groups will also be briefly discussed and examples will be given. Recently Raicu, Kirillova & Hamar (1969) described a new sex chromosome mechanism ( X 1 X 1 X 2 X 2 /X 1 X 2 Y 1 Y 2 ) in the vole Microtus arvalis , but this observation was not confirmed by Schmid (1969), who found an ordinary XX/XY mechanism with both X and Y readily identifiable and of ‘normal’ size, the X comprising 5.6% of ( n A + X) and Y being the smallest chromosome of the complement. Late DNA replication was demonstrated in the allocyclic X and in the Y. Also Wolf (1969) found normal sex chromosomes in this species with no multivalents at male meiosis.

scholarly journals Proto-sex locus in large yellow croaker provides insights into early evolution of the sex chromosome

2020 ◽  
Author(s):  
Zhiyong Wang ◽  
Shijun Xiao ◽  
Mingyi Cai ◽  
Zhaofang Han ◽  
Wanbo Li ◽  
...  
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Draft Genome ◽  
Sex Reversal ◽  
Large Yellow Croaker ◽  
Larimichthys Crocea ◽  
Suppressed Recombination ◽  
Heterogametic Sex ◽  
Sex Locus

AbstractAutosomal origins of heterogametic sex chromosomes have been inferred frequently from suppressed recombination and gene degeneration manifested in incompletely differentiated sex chromosomes. However, the initial transition of an autosome region to a proto-sex locus has been not explored in depth. By assembling and analyzing a chromosome-level draft genome, we found a recent (evolved 0.26 million years ago), highly homologous, and dmrt1 containing sex-determination locus with slightly reduced recombination in large yellow croaker (Larimichthys crocea), a teleost species with genetic sex determination (GSD) and with undifferentiated sex chromosomes. We observed genomic homology and polymorphic segregation of the proto-sex locus between sexes. Expression of dmrt1 showed a stepwise increase in the development of testis, but not in the ovary. We infer that the inception of the proto-sex locus involves a few divergences in nucleotide sequences and slight suppression of recombination in an autosome region. In androgen-induced sex reversal of genetic females, in addition to dmrt1, genes in the conserved dmrt1 cluster, and the rest of the sex determination network were activated. We provided evidence that broad functional links were shared by genetic sex determination and environmental sex reversal.

scholarly journals A derived ZW chromosome system in Amborella trichopoda, the sister species to all other extant flowering plants

2020 ◽  
Author(s):  
Jos Kafer ◽  
Adam Bewick ◽  
Amelie Andres-Robin ◽  
Garance Lapetoule ◽  
Alex Harkess ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Sex Determination ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Chromosome 9 ◽  
Male And Female ◽  
Recent Origin ◽  
Sex Chromosome System ◽  
Genetic And Environmental Factors ◽  
Evo Devo

Sex determination is poorly understood in plants. Amborella trichopoda is a well-known plant model for evo-devo studies, which is also dioecious (has male and female individuals), with an unknown sex determination mechanism. A. trichopoda is a sex switcher, which points to possible environmental factors that act on sex, but populations grown from seed under greenhouse conditions exhibit a 50:50 sex ratio, which indicates the operation of genetic factors. Here, we use a new method (SDpop) to identify sex-linked genes from genotyping data of male and female individuals sampled in the field, and find that A. trichopoda has a ZW sex-chromosome system. The sex-linked genes map to a 4 Mb sex-determining region on chromosome 9. The low extent of ZW divergence suggests these sex chromosomes are of recent origin, which is consistent with dioecy being derived character in the A. trichopoda lineage. Our work has uncovered clearly formed sex chromosomes in a species in which both genetic and environmental factors can influence sex.

scholarly journals Transition from environmental to partial genetic sex determination in Daphnia through the evolution of a female-determining incipient W-chromosome

2016 ◽  
Author(s):  
Céline M.O. Reisser ◽  
Dominique Fasel ◽  
Evelin Hürlimann ◽  
Marinela Dukič ◽  
Cathy Haag-Liautard ◽  
...  
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Sex Differentiation ◽  
Genomic Region ◽  
Additional Restriction ◽  
W Chromosome ◽  
Recombination Suppression ◽  
Evolutionary Transitions ◽  
Dominant Female

AbstractSex chromosomes can evolve during the evolution of genetic sex determination (GSD) from environmental sex determination (ESD). Despite theoretical attention, early mechanisms involved in the transition from ESD to GSD have yet to be studied in nature. No mixed ESD-GSD animal species have been reported, except for some species of Daphnia, small freshwater crustaceans in which sex is usually determined solely by the environment, but in which a dominant female sex-determining locus is present in some populations. This locus follows Mendelian single-locus inheritance, but has otherwise not been characterized genetically. We now show that the sex-determining genomic region maps to the same low-recombining peri-centromeric region of linkage group 3 (LG3) in three highly divergent populations of D. magna, and spans 3.6 Mb. Despite low levels of recombination, the associated region contains signs of historical recombination, suggesting a role for selection acting on several genes thereby maintaining linkage disequilibrium among the 36 associated SNPs. The region carries numerous genes involved in sex differentiation in other taxa, including transformer2 and sox9. Taken together, the region determining the NMP phenotype shows characteristics of a sex-related supergene, suggesting that LG3 is potentially an incipient W chromosome despite the lack of significant additional restriction of recombination between Z and W. The occurrence of the female-determining locus in a pre-existing low recombining region illustrates one possible form of recombination suppression in sex chromosomes. D. magna is a promising model for studying the evolutionary transitions from ESD to GSD and early sex chromosome evolution.

scholarly journals Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes

2019 ◽  
Vol 9 (10) ◽  
pp. 3467-3476 ◽  
Author(s):  
Paul M. Hime ◽  
Jeffrey T. Briggler ◽  
Joshua S. Reece ◽  
David W. Weisrock
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Model Organisms ◽  
Reduced Representation ◽  
Non Invasive ◽  
Female Heterogamety ◽  
Genome Wide ◽  
Great Utility ◽  
Genomic Regions

Systems of genetic sex determination and the homology of sex chromosomes in different taxa vary greatly across vertebrates. Much progress remains to be made in understanding systems of genetic sex determination in non-model organisms, especially those with homomorphic sex chromosomes and/or large genomes. We used reduced representation genome sequencing to investigate genetic sex determination systems in the salamander family Cryptobranchidae (genera Cryptobranchus and Andrias), which typifies both of these inherent difficulties. We tested hypotheses of male- or female-heterogamety by sequencing hundreds of thousands of anonymous genomic regions in a panel of known-sex cryptobranchids and characterized patterns of presence/absence, inferred zygosity, and depth of coverage to identify sex-linked regions of these 56 gigabase genomes. Our results strongly support the hypothesis that all cryptobranchid species possess homologous systems of female heterogamety, despite maintenance of homomorphic sex chromosomes over nearly 60 million years. Additionally, we report a robust, non-invasive genetic assay for sex diagnosis in Cryptobranchus and Andrias which may have great utility for conservation efforts with these endangered salamanders. Co-amplification of these W-linked markers in both cryptobranchid genera provides evidence for long-term sex chromosome stasis in one of the most divergent salamander lineages. These findings inform hypotheses about the ancestral mode of sex determination in salamanders, but suggest that comparative data from other salamander families are needed. Our results further demonstrate that massive genomes are not necessarily a barrier to effective genome-wide sequencing and that the resulting data can be highly informative about sex determination systems in taxa with homomorphic sex chromosomes.

scholarly journals Miniscule differences between the sex chromosomes in the giant genome of a salamander, Ambystoma mexicanum

2018 ◽  
Author(s):  
Melissa C. Keinath ◽  
Nataliya Timoshevskaya ◽  
Vladimir A. Timoshevskiy ◽  
S. Randal Voss ◽  
Jeramiah J. Smith
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
New Technologies ◽  
Sex Chromosome ◽  
Morphological Differentiation ◽  
Ambystoma Mexicanum ◽  
Chromosome 9 ◽  
Strong Candidate ◽  
Determining Factor ◽  
Specific Sequences

ABSTRACTIn the Mexican axolotl (Ambystoma mexicanum) sex is known to be determined by a single Mendelian factor, yet the sex chromosomes of this model salamander do not exhibit morphological differentiation that is typical of many vertebrate taxa that possess a single sex-determining locus. Differentiated sex chromosomes are thought to evolve rapidly in the context of a Mendelian sex-determining gene and, therefore, undifferentiated chromosomes provide an exceptional opportunity to reconstruct early events in sex chromosome evolution. Whole chromosome sequencing, whole genome resequencing (48 individuals from a backcross of axolotl and tiger salamander) and in situ hybridization were used to identify a homomorphic chromosome that carries an A. mexicanum sex determining factor and identify sequences that are present only on the W chromosome. Altogether, these sequences cover ~300 kb, or roughly 1/100,000th of the ~32 Gb genome. Notably, these W-specific sequences also contain a recently duplicated copy of the ATRX gene: a known component of mammalian sex-determining pathways. This gene (designated ATRW) is one of the few functional (non-repetitive) genes in the chromosomal segment and maps to the tip of chromosome 9 near the marker E24C3, which was previously found to be linked to the sex-determining locus. These analyses provide highly predictive markers for diagnosing sex in A. mexicanum and identify ATRW as a strong candidate for the primary sex determining locus or alternately a strong candidate for a recently acquired, sexually antagonistic gene.AUTHOR SUMMARYSex chromosomes are thought to follow fairly stereotypical evolutionary trajectories that result in differentiation of sex-specific chromosomes. In the salamander A. mexicanum (the axolotl), sex is determined by a single Mendelian locus, yet the sex chromosomes are essentially undifferentiated, suggesting that these sex chromosomes have recently acquired a sex locus and are in the early stages of differentiating. Although Mendelian sex determination was first reported for the axolotl more than 70 years ago, no sex-specific sequences have been identified for this important model species. Here, we apply new technologies and approaches to identify and validate a tiny region of female-specific DNA within the gigantic genome of the axolotl (1/100,000th of the genome). This region contains a limited number of genes, including a duplicate copy of the ATRX gene which, has been previously shown to contribute to mammalian sex determination. Our analyses suggest that this gene, which we refer to as ATRW, evolved from a recent duplication and presents a strong candidate for the primary sex determining factor of the axolotl, or alternately a recently evolved sexually antagonistic gene.

scholarly journals Male-specific restriction of recombination frequency in the sex chromosomes of the medaka, Oryzias latipes

1999 ◽  
Vol 73 (3) ◽  
pp. 225-231 ◽  
Author(s):  
MASARU MATSUDA ◽  
SAEMI SOTOYAMA ◽  
SATOSHI HAMAGUCHI ◽  
MITSURU SAKAIZUMI
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Recombination Frequency ◽  
Oryzias Latipes ◽  
Body Colour ◽  
Specific Restriction ◽  
Xx Males ◽  
Heterogametic Sex ◽  
Male Specific

In the medaka, Oryzias latipes, the mechanism of sex determination (XX/XY) can be revealed by genetic crosses using a body-colour gene, though it does not have cytologically recognizable sex chromosomes. The recombination restriction of sex chromosomes in heterogametic (XY) males has been demonstrated. To elucidate whether the recombination is prevented by the heterogamety of the sex chromosomes or by maleness, we examined the recombination frequencies among three loci located on the sex chromosomes (r, SL1 and SL2) in heterogametic males (XY), homogametic males (XX and YY), homogametic females (XX) and heterogametic females (XY). The recombination frequencies between r–SL1 and SL1–SL2 were as follows: 0, 0 (XY males); 0, 1·5 (XX males); 1·6% (YY males; 1·2%, 14·4% (XY females); 0·8%, 21·8% (XX females). These results indicate that the recombination restriction of the sex chromosomes in heterogametic males does not result from heterogametic sex chromosomes, but from maleness. Such sex-chromosome- specific recombination restriction in heterogametic sex may have triggered the differentiation of sex chromosomes in vertebrates.

scholarly journals Bisection of the X chromosome disrupts the initiation of chromosome silencing during meiosis in Caenorhabditis elegans

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yisrael Rappaport ◽  
Hanna Achache ◽  
Roni Falk ◽  
Omer Murik ◽  
Oren Ram ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Rna Polymerase Ii ◽  
X Chromosome ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Transcription Analysis ◽  
X Chromosomes ◽  
Unique Character ◽  
Active Transcription ◽  
Heterogametic Sex

AbstractDuring meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans nematodes with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments are enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome are upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.

Sign in / Sign up

Export Citation Format

Share Document