Evolutionary Genomics of Unconventional Sex Chromosomes in Frogs

Project Information

FrogWY

Grant agreement ID: 101039501

DOI

10.3030/101039501

EC signature date 16 November 2022

Start date 1 May 2023

End date 30 April 2028

Funded under

• European Research Council (ERC)

Total cost

€ 1 499 950,00

EU contribution

€ 1 499 950,00

Coordinated by

VRIJE UNIVERSITEIT BRUSSEL
Belgium

Periodic Reporting for period 1 - FrogWY (Evolutionary Genomics of Unconventional Sex Chromosomes in Frogs)

Reporting period: 2023-05-01 to 2025-10-31

Summary of the context and overall objectives of the project

Most familiar animals from humans to fruit flies, rely on deeply entrenched, “old” sex chromosomes (X/Y in mammals, Z/W in birds). Yet in many reptiles, fish, amphibians and flowering plants, sex chromosomes are young, change rapidly, and often swap sex chromosomes entirely. We still don’t understand why some lineages lock in a single sex chromosome for millions of years, while others reinvent sex determination over and over. This knowledge gap matters because the way sex is determined affects everything from population dynamics and species survival to how animals adapt to changing environments. Frogs are a perfect window into this mystery. Many frog species carry only slightly differentiated sex chromosomes, within male-heterogametic (XY), or female-heterogametic (ZW) systems, or between the XY and ZW systems in short evolutionary bursts. By investigating these early-stage evolution of sex chromosomes, we can discover the hidden principles that govern their birth, lifespan, death, and renewal. The three project objectives are:
1.Uncover alternative mechanism for recombination arrest: In most textbook examples, sex chromosomes stop recombining across their entire length under the sexually antagonistic selection. We will test whether, in various robber frogs with both XY and ZW systems, this recombination arrest happens in XY males and ZW females along the sex chromosome length but the chromosome ends, offering an alternative mechanism for how sex-linked regions form.
2. Reveal the drivers of sex-determination switches: Using genetic and comparative genomic analyses, we will pinpoint the evolutionary forces and genetic mechanism driving the sex-chromosome turnover in frogs with both homomorphic and heteromorphic sex chromosomes.
3. Understand the evolutionary dynamics of giant sex chromosomes: Some frog species carry enormously enlarged Y or W chromosomes packed with repetitive sequences. We will assemble these chromosomes in high resolution to uncover how they form, how their gene content differs between male- and female-linked regions, and whether and how dosage compensation mechanisms evolve and function.
By shining light on alternative pathways for sex-chromosome formation and turnover, this research will expand our fundamental understanding of genome and sex chromosome evolution.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

1. Evolution and molecular basis of extreme heterochiasmy in frogs
Extreme heterochiasmy, where recombination is largely confined to telomeric regions in males but distributed evenly across the female genome, occurs in both XY and ZZ systems across multiple frog lineages. To unravel its molecular underpinnings, we imaged female meiosis I for the first time in early‑stage ovaries of the common frog (Rana temporaria, XY system) and the toad (Bufo bufo, ZW system). By directly comparing male and female meiotic dynamics in both systems, we revealed striking sex‑specific behaviors of homologous chromosomes. In parallel, we profiled expression of key meiosis-related genes across five wild populations of R. temporaria, identifying clear male‑ versus female‑biased and sex‑specific expression patterns. Together, these results illuminate the core molecular machinery that drives sex‑specific crossover landscapes in frogs.
2. Drivers of sex‑chromosome turnover in true frogs and robber frogs
Frogs have repeatedly switched between XY and ZW systems over evolutionary time, yet the genetic forces behind these turnovers remained elusive. We sequenced DNA and RNA from multiple European Ranidae (true frog) species and 19 Caribbean Eleutherodactylus (robber frog) species to map sex‑determining regions and quantify levels of chromosome differentiation. By building a custom library of frog transposable elements (TEs), we aim to uncover patterns of TE accumulation that closely parallel episodes of sex‑chromosome turnover, suggesting that these mobile elements may catalyze rearrangements and the relocation of master sex‑determining genes in both lineages.
3. Chromosome‑level assemblies reveal the diversity of Y and W chromosomes in Robber frogs
Caribbean robber frogs exhibit a remarkable spectrum of sex‑chromosome differentiation—from homomorphic to highly heteromorphic, and from XY to ZW systems in roughly equal measure. In collaboration with the Wellcome Sanger Institute, we generated chromosome‑level genome assemblies for 15 Eleutherodactylus species. Firstly, for E. flavescens from the Dominican Republic, we combined male and female DNA‑ and RNA‑seq data to pinpoint its sex chromosome and delineate sex‑linked regions for the first time in this clade. These high‑quality assemblies now provide a foundational resource for comparative analyses of sex‑chromosome evolution.
4. Non‑canonical recombination suppression in European common frogs
Using pooled DNA sequencing of a wild Rana temporaria population, we identified three discrete stages of divergence between the X and Y chromosomes: localized differentiation at the sex‑determining gene Dmrt1; extension of divergence into subtelomeric regions, despite minimal overall gene loss; Regions showing no detectable divergence, reflecting occasional X–Y recombination via sex‑reversed XY females. We also showed a single origin of Dmrt1 evolvolution in various Y chromosomes in this species. These findings substantiate a “telomere‑restricted” model of recombination suppression and reveal a non‑canonical path by which sex chromosomes recombination is induced by extreme heterochiasmy and sex reversal. This work significantly broadens our understanding of how sex‑determining systems evolve and maintain genetic integrity in the face of dynamic recombination landscapes.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

1. Towards the detection of molecular basis of sexual dimorphism in meiosis machinery
If successful, this will enable the direct comparison of male vs. female recombination landscapes at the molecular basis, unlocking new insights into sexual dimorphism in recombination landscape.

2. Setting up molecular function tool CRISPR–Cas9 in Rana temporaria
Opens the door to functional tests of candidate sex-determination and other interesting genes.

3. Creating a robust sex-chromosome detection pipeline
Delivered an end-to-end Snakemake workflow that integrates read-coverage ratios, SNP-density, FST metrics, genome-wide association, and sex-specific k-mer analyses to pinpoint sex-linked regions.
Impact: Streamlines discovery in both homomorphic and heteromorphic systems across any organism with whole-genome data.

4. Empirical evidence for telomere-restricted recombination in association with dynamics of sex chromosome evolution
In a pool-seq study of a wild Rana temporaria population, we identified three discrete levels of X–Y divergence with minimal Y degeneration, all anchored around the sex-determining gene Dmrt1. Our anlaysis showed the single origin of Dmrt1 sex-determining region, and confirms a novel mechanism in driving sex chromosome differentiation and dynamics, that extends the canonical model of sex-chromosome evolution.

image of an Eleutherodactylus frog with their clutch eggs