scholarly journals New Insights into Mammalian Sex Chromosome Structure and Evolution from High-quality Bovine X and Y Chromosome Sequences

2019 ◽  
Author(s):  
Ruijie Liu ◽  
Wai Yee Low ◽  
Rick Tearle ◽  
Sergey Koren ◽  
Jay Ghurye ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Immune Modulation ◽  
Sex Chromosome ◽  
Inflammatory Responses ◽  
Structure Evolution ◽  
Pseudoautosomal Region ◽  
Evolutionary Divergence ◽  
High Quality ◽  
Global Regulators ◽  
Y Chromosomes

Abstract Background Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The PAR is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes is still poorly understood because few species have high quality sex chromosome assemblies. Results Here we report the first bovine sex chromosome assemblies that include the complete pseudoautosomal region (PAR) spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. We show that the ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary divergence times. Conclusions A bovidae-specific expansion of members of the lipocalin gene family in the PAR may reflect immune-modulation and anti-inflammatory responses that contribute to parasite resistance in ruminants. Comparison of the X-d regions of Y chromosomes across species reveal five conserved X-Y gametologs, which are global regulators of gene activity, and may have a fundamental role in mammalian sexual dimorphism.

scholarly journals New Insights into Mammalian Sex Chromosome Structure and Evolution from High-quality Bovine X and Y Chromosome Sequences

2019 ◽  
Author(s):  
Ruijie Liu ◽  
Wai Yee Low ◽  
Rick Tearle ◽  
Sergey Koren ◽  
Jay Ghurye ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Immune Modulation ◽  
Sex Chromosome ◽  
Inflammatory Responses ◽  
Structure Evolution ◽  
Pseudoautosomal Region ◽  
Evolutionary Divergence ◽  
High Quality ◽  
Global Regulators ◽  
Y Chromosomes

Abstract Background Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The PAR is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes is still poorly understood because few species have high quality sex chromosome assemblies. Results Here we report the first bovine sex chromosome assemblies that include the complete pseudoautosomal region (PAR) spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. We show that the ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary divergence times. Conclusions A bovidae-specific expansion of members of the lipocalin gene family in the PAR may reflect immune-modulation and anti-inflammatory responses that contribute to parasite resistance in ruminants. Comparison of the X-d regions of Y chromosomes across species reveal five conserved X-Y gametologs, which are global regulators of gene activity, and may have a fundamental role in mammalian sexual dimorphism.

scholarly journals New Insights into Mammalian Sex Chromosome Structure and Evolution from High-quality Bovine X and Y Chromosome Sequences

2019 ◽  
Author(s):  
Ruijie Liu ◽  
Wai Yee Low ◽  
Rick Tearle ◽  
Sergey Koren ◽  
Jay Ghurye ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Immune Modulation ◽  
Sex Chromosome ◽  
Inflammatory Responses ◽  
Structure Evolution ◽  
Pseudoautosomal Region ◽  
Evolutionary Divergence ◽  
High Quality ◽  
Global Regulators ◽  
Y Chromosomes

Abstract Background Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The PAR is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes is still poorly understood because few species have high quality sex chromosome assemblies. Results Here we report the first bovine sex chromosome assemblies that include the complete pseudoautosomal region (PAR) spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. We show that the ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary divergence times. Conclusions A bovidae-specific expansion of members of the lipocalin gene family in the PAR may reflect immune-modulation and anti-inflammatory responses that contribute to parasite resistance in ruminants. Comparison of the X-d regions of Y chromosomes across species reveal five conserved X-Y gametologs, which are global regulators of gene activity, and may have a fundamental role in mammalian sexual dimorphism.

scholarly journals New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Ruijie Liu ◽  
Wai Yee Low ◽  
Rick Tearle ◽  
Sergey Koren ◽  
Jay Ghurye ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Immune Modulation ◽  
Sex Chromosome ◽  
Inflammatory Responses ◽  
Structure Evolution ◽  
Pseudoautosomal Region ◽  
Evolutionary Divergence ◽  
Chromosome X ◽  
High Quality ◽  
Y Chromosomes

Abstract Background Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The pseudoautosomal region (PAR) is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes, particularly the Y chromsome, is still poorly understood because few species have high quality sex chromosome assemblies. Results Here we report the first bovine sex chromosome assemblies that include the complete PAR spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. The PAR comprises 31 genes, including genes that are missing from the X chromosome in current cattle, sheep and goat reference genomes. Twenty-nine PAR genes are single-copy genes and two are multi-copy gene families, OBP, which has 3 copies and BDA20, which has 4 copies. The Y chromosome X-d1, 2a and 2b regions contain 11, 2 and 2 gametologs, respectively. Conclusions The ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary divergence times. A bovidae-specific expansion of members of the lipocalin gene family in the PAR reported here, may affect immune-modulation and anti-inflammatory responses in ruminants. Comparison of the X-d regions of Y chromosomes across species revealed that five of the X-Y gametologs, which are known to be global regulators of gene activity and candidate sexual dimorphism genes, are conserved.

scholarly journals Gene-level, but not chromosome-wide, divergence between a very young house fly proto-Y chromosome and its homologous proto-X chromosome

2020 ◽  
Author(s):  
Jae Hak Son ◽  
Richard P. Meisel
Keyword(s):  
Gene Expression ◽  
Y Chromosome ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
House Fly ◽  
Evolutionary Divergence ◽  
Y Chromosomes ◽  
Mitochondrial Functions ◽  
Xx Males ◽  
Y Chromosome Evolution

AbstractX and Y chromosomes are usually derived from a pair of homologous autosomes, which then diverge from each other over time. Although Y-specific features have been characterized in sex chromosomes of various ages, the earliest stages of Y chromosome evolution remain elusive. In particular, we do not know whether early stages of Y chromosome evolution consist of changes to individual genes or happen via chromosome-scale divergence from the X. To address this question, we quantified divergence between young proto-X and proto-Y chromosomes in the house fly, Musca domestica. We compared proto-sex chromosome sequence and gene expression between genotypic (XY) and sex-reversed (XX) males. We find evidence for sequence divergence between genes on the proto-X and proto-Y, including five genes with mitochondrial functions. There is also an excess of genes with divergent expression between the proto-X and proto-Y, but the number of genes is small. This suggests that individual proto-Y genes, but not the entire proto-Y chromosome, have diverged from the proto-X. We identified one gene, encoding an axonemal dynein assembly factor (which functions in sperm motility), that has higher expression in XY males than XX males because of a disproportionate contribution of the proto-Y allele to gene expression. The up-regulation of the proto-Y allele may be favored in males because of this gene’s function in spermatogenesis. The evolutionary divergence between proto-X and proto-Y copies of this gene, as well as the mitochondrial genes, is consistent with selection in males affecting the evolution of individual genes during early Y chromosome evolution.

scholarly journals Gene-Level, but Not Chromosome-Wide, Divergence between a Very Young House Fly Proto-Y Chromosome and Its Homologous Proto-X Chromosome

2020 ◽  
Author(s):  
Jae Hak Son ◽  
Richard P Meisel
Keyword(s):  
Gene Expression ◽  
Y Chromosome ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
House Fly ◽  
Evolutionary Divergence ◽  
Y Chromosomes ◽  
Mitochondrial Functions ◽  
Xx Males ◽  
Y Chromosome Evolution

Abstract X and Y chromosomes are usually derived from a pair of homologous autosomes, which then diverge from each other over time. Although Y-specific features have been characterized in sex chromosomes of various ages, the earliest stages of Y chromosome evolution remain elusive. In particular, we do not know whether early stages of Y chromosome evolution consist of changes to individual genes or happen via chromosome-scale divergence from the X. To address this question, we quantified divergence between young proto-X and proto-Y chromosomes in the house fly, Musca domestica. We compared proto-sex chromosome sequence and gene expression between genotypic (XY) and sex-reversed (XX) males. We find evidence for sequence divergence between genes on the proto-X and proto-Y, including five genes with mitochondrial functions. There is also an excess of genes with divergent expression between the proto-X and proto-Y, but the number of genes is small. This suggests that individual proto-Y genes, but not the entire proto-Y chromosome, have diverged from the proto-X. We identified one gene, encoding an axonemal dynein assembly factor (which functions in sperm motility), that has higher expression in XY males than XX males because of a disproportionate contribution of the proto-Y allele to gene expression. The upregulation of the proto-Y allele may be favored in males because of this gene’s function in spermatogenesis. The evolutionary divergence between proto-X and proto-Y copies of this gene, as well as the mitochondrial genes, is consistent with selection in males affecting the evolution of individual genes during early Y chromosome evolution.

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.

The Continuum of Psychosis and Its Genetic Origins

1990 ◽  
Vol 156 (6) ◽  
pp. 788-797 ◽  
Author(s):  
T. J. Crow
Keyword(s):  
Sex Chromosome ◽  
Homo Sapiens ◽  
Polymorphic Marker ◽  
Cerebral Dominance ◽  
Homo Erectus ◽  
Evolutionary Development ◽  
Pseudoautosomal Region ◽  
Sibling Pairs ◽  
Homo Habilis ◽  
Y Chromosomes

Attempts to draw a line of genetic demarcation between schizophrenic and affective illnesses have failed. It must be assumed that these diseases are genetically related. A post-mortem study has demonstrated that enlargement of the temporal horn of the lateral ventricle in schizophrenia but not in Alzheimer-type dementia is selective to the left side of the brain. This suggests that the gene for psychosis is the ‘cerebral dominance gene‘, the factor that determines the asymmetrical development of the human brain. That the psychosis gene is located in the pseudoautosomal region of the sex chromosomes is consistent with observations that sibling pairs with schizophrenia are more often than would be expected of the same sex and share alleles of a polymorphic marker at the short-arm telomeres of the X and Y chromosomes above chance expectation. That the cerebral dominance gene also is pseudoautosomal is suggested by the pattern of verbal and performance deficits associated with sex-chromosome aneuploidies. The psychoses may thus represent aberrations of a late evolutionary development underlying the recent and rapid increase in brain weight in the transition fromAustralopithecusthroughHomo habilisandHomo erectustoHomo sapiens.

scholarly journals Meiotic Behavior of Achiasmate Sex Chromosomes in the African Pygmy Mouse Mus mattheyi Offers New Insights into the Evolution of Sex Chromosome Pairing and Segregation in Mammals

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1434
Author(s):  
Ana Gil-Fernández ◽  
Marta Ribagorda ◽  
Marta Martín-Ruiz ◽  
Pablo López-Jiménez ◽  
Tamara Laguna ◽  
...  
Keyword(s):  
Dna Repair ◽  
Y Chromosome ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Mammalian Species ◽  
Evolutionary Process ◽  
Small Region ◽  
Pseudoautosomal Region ◽  
Evolution Of Sex ◽  
African Pygmy Mouse

X and Y chromosomes in mammals are different in size and gene content due to an evolutionary process of differentiation and degeneration of the Y chromosome. Nevertheless, these chromosomes usually share a small region of homology, the pseudoautosomal region (PAR), which allows them to perform a partial synapsis and undergo reciprocal recombination during meiosis, which ensures their segregation. However, in some mammalian species the PAR has been lost, which challenges the pairing and segregation of sex chromosomes in meiosis. The African pygmy mouse Mus mattheyi shows completely differentiated sex chromosomes, representing an uncommon evolutionary situation among mouse species. We have performed a detailed analysis of the location of proteins involved in synaptonemal complex assembly (SYCP3), recombination (RPA, RAD51 and MLH1) and sex chromosome inactivation (γH2AX) in this species. We found that neither synapsis nor chiasmata are found between sex chromosomes and their pairing is notably delayed compared to autosomes. Interestingly, the Y chromosome only incorporates RPA and RAD51 in a reduced fraction of spermatocytes, indicating a particular DNA repair dynamic on this chromosome. The analysis of segregation revealed that sex chromosomes are associated until metaphase-I just by a chromatin contact. Unexpectedly, both sex chromosomes remain labelled with γH2AX during first meiotic division. This chromatin contact is probably enough to maintain sex chromosome association up to anaphase-I and, therefore, could be relevant to ensure their reductional segregation. The results presented suggest that the regulation of both DNA repair and epigenetic modifications in the sex chromosomes can have a great impact on the divergence of sex chromosomes and their proper transmission, widening our understanding on the relationship between meiosis and the evolution of sex chromosomes in mammals.

Polymorphism and differentiation of rainbow trout Y chromosomes

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1105-1113 ◽  
Author(s):  
Alicia Felip ◽  
Atushi Fujiwara ◽  
William P Young ◽  
Paul A Wheeler ◽  
Marc Noakes ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Y Chromosome ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Morphological Differentiation ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Y Chromosomes ◽  
Cytogenetic Analyses ◽  
Clonal Lines ◽  
Sex Locus

Most fish species show little morphological differentiation in the sex chromosomes. We have coupled molecular and cytogenetic analyses to characterize the male-determining region of the rainbow trout (Oncorhynchus mykiss) Y chromosome. Four genetically diverse male clonal lines of this species were used for genetic and physical mapping of regions in the vicinity of the sex locus. Five markers were genetically mapped to the Y chromosome in these male lines, indicating that the sex locus was located on the same linkage group in each of the lines. We also confirmed the presence of a Y chromosome morphological polymorphism among these lines, with the Y chromosomes from two of the lines having the more common heteromorphic Y chromosome and two of the lines having Y chromosomes morphologically similar to the X chromosome. The fluorescence in situ hybridization (FISH) pattern of two probes linked to sex suggested that the sex locus is physically located on the long arm of the Y chromosome. Fishes appear to be an excellent group of organisms for studying sex chromosome evolution and differentiation in vertebrates because they show considerable variability in the mechanisms and (or) patterns involved in sex determination.Key words: sex chromosomes, sex markers, cytogenetics, rainbow trout, fish.

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.

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