skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


This content will become publicly available on February 7, 2026

Title: The Silene latifolia genome and its giant Y chromosome
In many species with sex chromosomes, the Y is a tiny chromosome. However, the dioecious plantSilene latifoliahas a giant ~550-megabase Y chromosome, which has remained unsequenced so far. We used a long- and short-read hybrid approach to obtain a high-quality male genome. Comparative analysis of the sex chromosomes with their homologs in outgroups showed that the Y is highly rearranged and degenerated. Recombination suppression between X and Y extended in several steps and triggered a massive accumulation of repeats on the Y as well as in the nonrecombining pericentromeric region of the X, leading to giant sex chromosomes. Using sex phenotype mutants, we identified candidate sex-determining genes on the Y in locations consistent with their favoring recombination suppression events 11 and 5 million years ago.  more » « less
Award ID(s):
2048407
PAR ID:
10652678
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more » ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; « less
Publisher / Repository:
American Association for the Advancement of Science
Date Published:
Journal Name:
Science
Volume:
387
Issue:
6734
ISSN:
0036-8075
Page Range / eLocation ID:
630 to 636
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; (, Genome Biology and Evolution)
    Schaack, Sarah (Ed.)
    Abstract Sex chromosomes diverge after the establishment of recombination suppression, resulting in differential sex-linkage of genes involved in genetic sex determination and dimorphic traits. This process produces systems of male or female heterogamety wherein the Y and W chromosomes are only present in one sex and are often highly degenerated. Sex-limited Y and W chromosomes contain valuable information about the evolutionary transition from autosomes to sex chromosomes, yet detailed characterizations of the structure, composition, and gene content of sex-limited chromosomes are lacking for many species. In this study, we characterize the female-specific W chromosome of the prairie rattlesnake (Crotalus viridis) and evaluate how recombination suppression and other processes have shaped sex chromosome evolution in ZW snakes. Our analyses indicate that the rattlesnake W chromosome is over 80% repetitive and that an abundance of GC-rich mdg4 elements has driven an overall high degree of GC-richness despite a lack of recombination. The W chromosome is also highly enriched for repeat sequences derived from endogenous retroviruses and likely acts as a “refugium” for these and other retroelements. We annotated 219 putatively functional W-linked genes across at least two evolutionary strata identified based on estimates of sequence divergence between Z and W gametologs. The youngest of these strata is relatively gene-rich, however gene expression across strata suggests retained gene function amidst a greater degree of degeneration following ancient recombination suppression. Functional annotation of W-linked genes indicates a specialization of the W chromosome for reproductive and developmental function since recombination suppression from the Z chromosome. 
    more » « less
  2. ; ; ; ; ; ; ; (, bioRxiv)
    The relatively young and repeated evolutionary origins of dioecy (separate sexes) in flowering plants enable investigation of molecular dynamics occurring at the earliest stages of sex chromosome evolution. With two independently young origins of dioecy in the genus,Asparagusis a model taxon for studying genetic sex-determination and sex chromosome evolution. Dioecy first evolved inAsparagus~3-4 million years ago (Ma) in the ancestor of a now widespread Eurasian clade that includes garden asparagus (Asparagus officinalis), while the second origin occurred in a smaller, geographically restricted, Mediterranean Basin clade includingAsparagus horridus. The XY sex chromosomes and sex-determination genes in garden asparagus have been well characterized, but the genetics underlying dioecy in the Mediterranean Basin clade are unknown. We generated new haplotype-resolved reference genomes for garden asparagus andA. horridus, to elucidate the sex chromosomes ofA. horridusand explore how dioecy evolved between these two closely related lineages. Analysis of theA. horridusgenome revealed an independently evolved XY system derived from different ancestral autosomes (chromosome 3) with different sex-determining genes than documented for garden asparagus (on chromosome 1). We estimate that proto-XY chromosomes evolved around 1-2 Ma in the Mediterranean Basin clade, following an ~2.1-megabase inversion between the ancestral pair. Recombination suppression and LTR retrotransposon accumulation drove the establishment and expansion of the Y-linked sex-determination region (Y-SDR) that now reaches ~9.6-megabases inA. horridus. The new garden asparagus genome revealed a Y-SDR that spans ~1.9-megabases with ten hemizygous genes. Our results evoke hemizygosity as the most probable mechanism responsible for the origin of proto-XY recombination suppression in the Eurasian clade, and that neofunctionalization of one duplicated gene (SOFF) drove the origin of dioecy. These findings support previous inference based on phylogeographic analysis revealing two recent origins of dioecy inAsparagus. Moreover, this work implicates alternative molecular mechanisms for two separate shifts to dioecy in a model taxon important for investigating young sex chromosome evolution. 
    more » « less
  3. ; ; (, Molecular Biology and Evolution)
    Wittkopp, Patricia (Ed.)
    Abstract Allele-specific gene expression evolves rapidly on heteromorphic sex chromosomes. Over time, the accumulation of mutations on the Y chromosome leads to widespread loss of gametolog expression, relative to the X chromosome. It remains unclear if expression evolution on degrading Y chromosomes is primarily driven by mutations that accumulate through processes of selective interference, or if positive selection can also favor the down-regulation of coding regions on the Y chromosome that contain deleterious mutations. Identifying the relative rates of cis-regulatory sequence evolution across Y chromosomes has been challenging due to the limited number of reference assemblies. The threespine stickleback (Gasterosteus aculeatus) Y chromosome is an excellent model to identify how regulatory mutations accumulate on Y chromosomes due to its intermediate state of divergence from the X chromosome. A large number of Y-linked gametologs still exist across 3 differently aged evolutionary strata to test these hypotheses. We found that putative enhancer regions on the Y chromosome exhibited elevated substitution rates and decreased polymorphism when compared to nonfunctional sites, like intergenic regions and synonymous sites. This suggests that many cis-regulatory regions are under positive selection on the Y chromosome. This divergence was correlated with X-biased gametolog expression, indicating the loss of expression from the Y chromosome may be favored by selection. Our findings provide evidence that Y-linked cis-regulatory regions exhibit signs of positive selection quickly after the suppression of recombination and allow comparisons with recent theoretical models that suggest the rapid divergence of regulatory regions may be favored to mask deleterious mutations on the Y chromosome. 
    more » « less
  4. ; ; ; ; ; ; ; ; ; ; et al (, Nature)
    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. 
    more » « less
  5. ; ; ; (, PLOS Genetics)
    Meiklejohn, Colin (Ed.)
    Sex chromosomes often evolve unique patterns of gene expression during spermatogenesis. In many species, sex-linked genes are downregulated during meiosis in response to asynapsis of the heterogametic sex chromosome pair (meiotic sex chromosome inactivation; MSCI). This process has evolved convergently across many taxa with independently derived sex chromosomes. Our understanding how quickly MSCI can evolve and whether it is connected to the degree of sequence degeneration remains limited. Teleost fish are a noteworthy group to investigate MSCI because sex chromosomes have evolved repeatedly across species, often over short evolutionary timescales. Here, we investigate whether MSCI occurs in the threespine stickleback fish (Gasterosteus aculeatus), which have an X and Y chromosome that evolved less than 26 million years ago. Using single-cell RNA-seq, we found that the X and Y chromosomes do not have a signature of MSCI, maintaining gene expression across meiosis. Using immunofluorescence, we also show the threespine stickleback do not form a condensed sex body around the X and Y, a feature of MSCI in many species. We did not see patterns of gene content evolution documented in other species with MSCI. Y-linked ampliconic gene families were expressed across multiple stages of spermatogenesis, rather than being restricted to post-meiotic stages, like in mammals. Our work shows MSCI does not occur in the threespine stickleback fish and has not shaped the evolution of the Y chromosome. In addition, the absence of MSCI in the threespine stickleback suggests this process may not be a conserved feature of teleost fish, despite overall sequence degeneration and structural evolution of the Y chromosome, and argues for additional investigation in other species. We also observed testis-dependent differences in coding and expression evolution for X-linked genes, revealing evidence of testis specific faster-X effect and gene-by-gene dosage compensation. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email