Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels

Repetitive DNAs and differentiation of the ZZ/ZW sex chromosome system in the combtail fish Belontia hasselti (Perciformes: Osphronemidae)

BACKGROUND

Java combtail fish Belontia hasselti (Cuvier, 1831), a member of the Osphronemidae family, inhabits lakes and rivers throughout Southeast Asia and Sri Lanka. Previous cytogenetic research revealed it possesses a diploid chromosome number of 48 chromosomes with a female-heterogametic ZZ/ZW sex chromosome system, where the W chromosome is distinguishable as the only metacentric element in the complement. Female-heterogametic sex chromosome systems seem to be otherwise surprisingly rare in the highly diverse order Perciformes and, therefore, B. hasselti provides an important comparative model to evolutionary studies in this teleost lineage. To examine the level of sex chromosome differentiation in B. hasselti and the contribution of repetitive DNAs to this process we combined bioinformatic analyses with chromosomal mapping of selected repetitive DNA classes, and comparative genomic hybridization.

RESULTS

By providing the first satellitome study in Perciformes, we herein identified 13 satellite DNA monomers in B. hasselti, suggesting a very low diversity of satDNA in this fish species. Using fluorescence in situ hybridization, we revealed detectable clusters on chromosomes only for four satellite DNA monomers. Together with the two mapped microsatellite motifs, the repeats primarily accumulated on autosomes, with no distinct clusters located on the sex chromosomes. Comparative genomic hybridization showed no region with accumulated female-specific or enriched repeats on the W chromosome. Telomeric repeats terminated all chromosomes, and no additional interstitial sites were detected.

CONCLUSION

These data collectively indicate a low degree of sex chromosome differentiation in B. hasselti despite their considerable heteromorphy. Possible mechanisms that may underlie this pattern are discussed.

Y chromosome introgression between deeply divergent primate species

Hybridization and introgression are widespread in nature, with important implications for adaptation and speciation. Since heterogametic hybrids often have lower fitness than homogametic individuals, a phenomenon known as Haldane's rule, loci inherited strictly through the heterogametic sex rarely introgress. We focus on the Y-chromosomal history of guenons, African primates that hybridized extensively in the past. Although our inferences suggest that Haldane's rule generally applies, we uncover a Y chromosome introgression event between two species ca. six million years after their initial divergence. Using simulations, we show that selection likely drove the introgressing Y chromosome to fixation from a low initial frequency. We identify non-synonymous substitutions on the novel Y chromosome as candidate targets of selection, and explore meiotic drive as an alternative mechanism. Our results provide a rare example of Y chromosome introgression, showing that the ability to produce fertile heterogametic hybrids likely persisted for six million years in guenons.

Sex Chromosome Evolution: Hallmarks and Question Marks

Sex chromosomes are widespread in species with separate sexes. They have evolved many times independently and display a truly remarkable diversity. New sequencing technologies and methodological developments have allowed the field of molecular evolution to explore this diversity in a large number of model and nonmodel organisms, broadening our vision on the mechanisms involved in their evolution. Diverse studies have allowed us to better capture the common evolutionary routes that shape sex chromosomes; however, we still mostly fail to explain why sex chromosomes are so diverse. We review over half a century of theoretical and empirical work on sex chromosome evolution and highlight pending questions on their origins, turnovers, rearrangements, degeneration, dosage compensation, gene content, and rates of evolution. We also report recent theoretical progress on our understanding of the ultimate reasons for sex chromosomes' existence.

Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content

Reference genomes of cattle and sheep have lacked contiguous assemblies of the sex-determining Y chromosome. Here, we assemble complete and gapless telomere to telomere (T2T) Y chromosomes for these species. We find that the pseudo-autosomal regions are similar in length, but the total chromosome size is substantially different, with the cattle Y more than twice the length of the sheep Y. The length disparity is accounted for by expanded ampliconic region in cattle. The genic amplification in cattle contrasts with pseudogenization in sheep suggesting opposite evolutionary mechanisms since their divergence 19MYA. The centromeres also differ dramatically despite the close relationship between these species at the overall genome sequence level. These Y chromosomes have been added to the current reference assemblies in GenBank opening new opportunities for the study of evolution and variation while supporting efforts to improve sustainability in these important livestock species that generally use sire-driven genetic improvement strategies.

The complete sequence and comparative analysis of ape sex chromosomes

Apes possess two sex chromosomes-the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked to infertility1. The X chromosome is vital for reproduction and cognition2. Variation in mating patterns and brain function among apes suggests corresponding differences in their sex chromosomes. However, owing to their repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (bonobo (Pan paniscus), chimpanzee (Pan troglodytes), western lowland gorilla (Gorilla gorilla gorilla), Bornean orangutan (Pongo pygmaeus) and Sumatran orangutan (Pongo abelii)) and a lesser ape (the siamang gibbon (Symphalangus syndactylus)), and untangled the intricacies of their evolution. Compared with the X chromosomes, the ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements-owing to the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements and satellites. Many Y chromosome genes expand in multi-copy families and some evolve under purifying selection. Thus, the Y chromosome exhibits dynamic evolution, whereas the X chromosome is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of more than 100 individual great apes. These reference assemblies are expected to inform human evolution and conservation genetics of non-human apes, all of which are endangered species.

The first complete T2T Assemblies of Cattle and Sheep Y-Chromosomes uncover remarkable divergence in structure and gene content

Reference genomes of cattle and sheep have lacked contiguous assemblies of the sex-determining Y chromosome. We assembled complete and gapless telomere to telomere (T2T) Y chromosomes for these species. The pseudo-autosomal regions were similar in length, but the total chromosome size was substantially different, with the cattle Y more than twice the length of the sheep Y. The length disparity was accounted for by expanded ampliconic region in cattle. The genic amplification in cattle contrasts with pseudogenization in sheep suggesting opposite evolutionary mechanisms since their divergence 18MYA. The centromeres also differed dramatically despite the close relationship between these species at the overall genome sequence level. These Y chromosome have been added to the current reference assemblies in GenBank opening new opportunities for the study of evolution and variation while supporting efforts to improve sustainability in these important livestock species that generally use sire-driven genetic improvement strategies.

Transcript Isoform Diversity of Y Chromosome Ampliconic Genes of Great Apes Uncovered Using Long Reads and Telomere-to-Telomere Reference Genome Assemblies

Y chromosomes of great apes harbor Ampliconic Genes (YAGs)-multi-copy gene families (BPY2, CDY, DAZ, HSFY, PRY, RBMY, TSPY, VCY, and XKRY) that encode proteins important for spermatogenesis. Previous work assembled YAG transcripts based on their targeted sequencing but not using reference genome assemblies, potentially resulting in an incomplete transcript repertoire. Here we used the recently produced gapless telomere-to-telomere (T2T) Y chromosome assemblies of great ape species (bonobo, chimpanzee, human, gorilla, Bornean orangutan, and Sumatran orangutan) and analyzed RNA data from whole-testis samples for the same species. We generated hybrid transcriptome assemblies by combining targeted long reads (Pacific Biosciences), untargeted long reads (Pacific Biosciences) and untargeted short reads (Illumina)and mapping them to the T2T reference genomes. Compared to the results from the reference-free approach, average transcript length was more than two times higher, and the total number of transcripts decreased three times, improving the quality of the assembled transcriptome. The reference-based transcriptome assemblies allowed us to differentiate transcripts originating from different Y chromosome gene copies and from their non-Y chromosome homologs. We identified two sources of transcriptome diversity-alternative splicing and gene duplication with subsequent diversification of gene copies. For each gene family, we detected transcribed pseudogenes along with protein-coding gene copies. We revealed previously unannotated gene copies of YAGs as compared to currently available NCBI annotations, as well as novel isoforms for annotated gene copies. This analysis paves the way for better understanding Y chromosome gene functions, which is important given their role in spermatogenesis.

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

Apes possess two sex chromosomes-the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and cognition. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosome structure and evolution. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the state-of-the-art experimental and computational methods developed for the telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies completely resolved ampliconic, palindromic, and satellite sequences, including the entire centromeres, allowing us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the X, ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions and palindromes (which are shared more broadly among species on the X) and from the abundance of transposable elements and satellites (which have a lower representation on the X). Our analysis of Y chromosome genes revealed lineage-specific expansions of multi-copy gene families and signatures of purifying selection. In summary, the Y exhibits dynamic evolution, while the X is more stable. Finally, mapping short-read sequencing data from >100 great ape individuals revealed the patterns of diversity and selection on their sex chromosomes, demonstrating the utility of these reference assemblies for studies of great ape evolution. These complete sex chromosome assemblies are expected to further inform conservation genetics of nonhuman apes, all of which are endangered species.

Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes

Y chromosomal ampliconic genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been studied in great apes; however, the diversity of splicing variants remains unexplored. Here, we deciphered the sequences of polyadenylated transcripts of all nine YAG families (BPY2, CDY, DAZ, HSFY, PRY, RBMY, TSPY, VCY, and XKRY) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan). To achieve this, we enriched YAG transcripts with capture probe hybridization and sequenced them with long (Pacific Biosciences) reads. Our analysis of this data set resulted in several findings. First, we observed evolutionarily conserved alternative splicing patterns for most YAG families except for BPY2 and PRY. Second, our results suggest that BPY2 transcripts and proteins originate from separate genomic regions in bonobo versus human, which is possibly facilitated by acquiring new promoters. Third, our analysis indicates that the PRY gene family, having the highest representation of noncoding transcripts, has been undergoing pseudogenization. Fourth, we have not detected signatures of selection in the five YAG families shared among great apes, even though we identified many species-specific protein-coding transcripts. Fifth, we predicted consensus disorder regions across most gene families and species, which could be used for future investigations of male infertility. Overall, our work illuminates the YAG isoform landscape and provides a genomic resource for future functional studies focusing on infertility phenotypes in humans and critically endangered great apes.

Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes

Y-chromosomal Ampliconic Genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been recently studied in great apes, however, the diversity of splicing variants remains unexplored. Here we deciphered the sequences of polyadenylated transcripts of all nine YAG families (BPY2, CDY, DAZ, HSFY, PRY, RBMY, TSPY, VCY, and XKRY) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan). To achieve this, we enriched YAG transcripts with capture-probe hybridization and sequenced them with long (Pacific Biosciences) reads. Our analysis of this dataset resulted in several findings. First, we uncovered a high diversity of YAG transcripts across great apes. Second, we observed evolutionarily conserved alternative splicing patterns for most YAG families except for BPY2 and PRY. Our results suggest that BPY2 transcripts and predicted proteins in several great ape species (bonobo and the two orangutans) have independent evolutionary origins and are not homologous to human reference transcripts and proteins. In contrast, our results suggest that the PRY gene family, having the highest representation of transcripts without open reading frames, has been undergoing pseudogenization. Third, even though we have identified many species-specific protein-coding YAG transcripts, we have not detected any signatures of positive selection. Overall, our work illuminates the YAG isoform landscape and its evolutionary history, and provides a genomic resource for future functional studies focusing on infertility phenotypes in humans and critically endangered great apes.

Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups

Structural rearrangements like copy number variations in the male-specific Y chromosome have been associated with male fertility phenotypes in human and mouse but have been sparsely studied in other mammalian species. Here, we designed digital droplet PCR assays for 7 horse male-specific Y chromosome multicopy genes and SRY and evaluated their absolute copy numbers in 209 normal male horses of 22 breeds, 73 XY horses with disorders of sex development and/or infertility, 5 Przewalski's horses and 2 kulans. This established baseline copy number for these genes in horses. The TSPY gene showed the highest copy number and was the most copy number variable between individuals and breeds. SRY was a single-copy gene in most horses but had 2-3 copies in some indigenous breeds. Since SRY is flanked by 2 copies of RBMY, their copy number variations were interrelated and may lead to SRY-negative XY disorders of sex development. The Przewalski's horse and kulan had 1 copy of SRY and RBMY. TSPY and ETSTY2 showed significant copy number variations between cryptorchid and normal males (P < 0.05). No significant copy number variations were observed in subfertile/infertile males. Notably, copy number of TSPY and ETSTY5 differed between successive male generations and between cloned horses, indicating germline and somatic mechanisms for copy number variations. We observed no correlation between male-specific Y chromosome gene copy number variations and male-specific Y chromosome haplotypes. We conclude that the ampliconic male-specific Y chromosome reference assembly has deficiencies and further studies with an improved male-specific Y chromosome assembly are needed to determine selective constraints over horse male-specific Y chromosome gene copy number and their relation to stallion reproduction and male biology.

The contribution of sex chromosome conflict to disrupted spermatogenesis in hybrid house mice

Incompatibilities on the sex chromosomes are important in the evolution of hybrid male sterility, but the evolutionary forces underlying this phenomenon are unclear. House mice (Mus musculus) lineages have provided powerful models for understanding the genetic basis of hybrid male sterility. X chromosome-autosome interactions cause strong incompatibilities in M. musculus F1 hybrids, but variation in sterility phenotypes suggests a more complex genetic basis. In addition, XY chromosome conflict has resulted in rapid expansions of ampliconic genes with dosage-dependent expression that is essential to spermatogenesis. Here, we evaluated the contribution of XY lineage mismatch to male fertility and stage-specific gene expression in hybrid mice. We performed backcrosses between two house mouse subspecies to generate reciprocal Y-introgression strains and used these strains to test the effects of XY mismatch in hybrids. Our transcriptome analyses of sorted spermatid cells revealed widespread overexpression of the X chromosome in sterile F1 hybrids independent of Y chromosome subspecies origin. Thus, postmeiotic overexpression of the X chromosome in sterile F1 mouse hybrids is likely a downstream consequence of disrupted meiotic X-inactivation rather than XY gene copy number imbalance. Y chromosome introgression did result in subfertility phenotypes and disrupted expression of several autosomal genes in mice with an otherwise nonhybrid genomic background, suggesting that Y-linked incompatibilities contribute to reproductive barriers, but likely not as a direct consequence of XY conflict. Collectively, these findings suggest that rapid sex chromosome gene family evolution driven by genomic conflict has not resulted in strong male reproductive barriers between these subspecies of house mice.

Copy number variation of ZNF280BY across eight sheep breeds and its association with testicular size of Hu sheep

ZNF280BY, a bovid-specific Y chromosome gene, was firstly found to be highly expressed in bovine testis, indicating it may play important roles in testicular development and male fertility. In this study, we firstly cloned the full-length cDNA of ovine ZNF280BY containing 1993 bp, and with a 1632 bp open reading frame. ZNF280BY was predominantly expressed in the testis, and its expression level was significantly higher in large testis than in small testis in Hu sheep at 6 months of age. In addition, the expression level of ZNF280BY significantly increased during testicular development, showing the highest expression level at 12 months of age. ZNF280BY showed copy number variation (CNV) in 723 rams from eight sheep breeds, ranging from 17 to 514 copies, with a median copy number of 188. Pearson correlation analysis showed that the CNV of ZNF280BY was negatively correlated with testis size in Hu sheep. Furthermore, its mRNA expression level in testis had no significant correlation with the CNV but was significantly correlated with testis size. This study concluded that the expression of ZNF280BY was closely related to testicular development, and the CNV of ZNF280BY could be used as an important genetic marker to evaluate the ram reproductive capacity at an early stage in Hu sheep.

Detecting signatures of selection on gene expression

A substantial amount of phenotypic diversity results from changes in gene expression levels and patterns. Understanding how the transcriptome evolves is therefore a key priority in identifying mechanisms of adaptive change. However, in contrast to powerful models of sequence evolution, we lack a consensus model of gene expression evolution. Furthermore, recent work has shown that many of the comparative approaches used to study gene expression are subject to biases that can lead to false signatures of selection. Here we first outline the main approaches for describing expression evolution and their inherent biases. Next, we bridge the gap between the fields of phylogenetic comparative methods and transcriptomics to reinforce the main pitfalls of inferring selection on expression patterns and use simulation studies to show that shifts in tissue composition can heavily bias inferences of selection. We close by highlighting the multi-dimensional nature of transcriptional variation and identifying major unanswered questions in disentangling how selection acts on the transcriptome.

Multi-Copy Gene Family Evolution on the Avian W Chromosome

The sex chromosomes often follow unusual evolutionary trajectories. In particular, the sex-limited chromosomes frequently exhibit a small but unusual gene content in numerous species, where many genes have undergone massive gene amplification. The reasons for this remain elusive with a number of recent studies implicating meiotic drive, sperm competition, genetic drift, and gene conversion in the expansion of gene families. However, our understanding is primarily based on Y chromosome studies as few studies have systematically tested for copy number variation on W chromosomes. Here, we conduct a comprehensive investigation into the abundance, variability, and evolution of ampliconic genes on the avian W. First, we quantified gene copy number and variability across the duck W chromosome. We find a limited number of gene families as well as conservation in W-linked gene copy number across duck breeds, indicating that gene amplification may not be such a general feature of sex chromosome evolution as Y studies would initially suggest. Next, we investigated the evolution of HINTW, a prominent ampliconic gene family hypothesized to play a role in female reproduction and oogenesis. In particular, we investigated the factors driving the expansion of HINTW using contrasts between modern chicken and duck breeds selected for different female-specific selection regimes and their wild ancestors. Although we find the potential for selection related to fecundity in explaining small-scale gene amplification of HINTW in the chicken, purifying selection seems to be the dominant mode of evolution in the duck. Together, this challenges the assumption that HINTW is key for female fecundity across the avian phylogeny.

Dynamic evolution of great ape Y chromosomes

The male-specific Y chromosome harbors genes important for sperm production. Because Y is repetitive, its DNA sequence was deciphered for only a few species, and its evolution remains elusive. Here we compared the Y chromosomes of great apes (human, chimpanzee, bonobo, gorilla, and orangutan) and found that many of their repetitive sequences and multicopy genes were likely already present in their common ancestor. Y repeats had increased intrachromosomal contacts, which might facilitate preservation of genes and gene regulatory elements. Chimpanzee and bonobo, experiencing high sperm competition, underwent many DNA changes and gene losses on the Y. Our research is significant for understanding the role of the Y chromosome in reproduction of nonhuman great apes, all of which are endangered.

The mammalian male-specific Y chromosome plays a critical role in sex determination and male fertility. However, because of its repetitive and haploid nature, it is frequently absent from genome assemblies and remains enigmatic. The Y chromosomes of great apes represent a particular puzzle: their gene content is more similar between human and gorilla than between human and chimpanzee, even though human and chimpanzee share a more recent common ancestor. To solve this puzzle, here we constructed a dataset including Ys from all extant great ape genera. We generated assemblies of bonobo and orangutan Ys from short and long sequencing reads and aligned them with the publicly available human, chimpanzee, and gorilla Y assemblies. Analyzing this dataset, we found that the genus Pan, which includes chimpanzee and bonobo, experienced accelerated substitution rates. Pan also exhibited elevated gene death rates. These observations are consistent with high levels of sperm competition in Pan. Furthermore, we inferred that the great ape common ancestor already possessed multicopy sequences homologous to most human and chimpanzee palindromes. Nonetheless, each species also acquired distinct ampliconic sequences. We also detected increased chromatin contacts between and within palindromes (from Hi-C data), likely facilitating gene conversion and structural rearrangements. Our results highlight the dynamic mode of Y chromosome evolution and open avenues for studies of male-specific dispersal in endangered great ape species.