Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko DOI Creative Commons
Marion Talbi, George F. Turner, Milan Malinsky

et al.

Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 26, 2024

Abstract Variation of recombination rate along the genome is crucial importance to rapid adaptation and organismal diversification. Many unknowns remain regarding how why landscapes evolve in nature. Here, we reconstruct maps based on linkage disequilibrium use subsampling simulations derive a new measure landscape evolution: Population Recombination Divergence Index (PRDI). Using PRDI, show that fine-scale differ substantially between two cichlid fish ecotypes Astatotilapia calliptera diverged only ~2,500 generations ago. Perhaps surprisingly, differences are not driven by divergence terms allele frequency (FST) nucleotide diversity (Δ(π)): although there some association, observe positive PRDI regions where FST Δ(π) zero. We found stronger association evolution 47 large haplotype blocks polymorphic Lake Masoko, cover 21% genome, appear include multiple inversions. Among blocks, strong clear degree heterozygosity, consistent with suppression heterozygotes. Overall, our work provides holistic view changes population during early stages speciation gene flow.

Language: Английский

Patterns of recombination in snakes reveal a tug-of-war between PRDM9 and promoter-like features DOI
Carla Hoge, Marc de Manuel, Mohamed Mahgoub

et al.

Science, Journal Year: 2024, Volume and Issue: 383(6685)

Published: Feb. 22, 2024

In some mammals, notably humans, recombination occurs almost exclusively where the protein PRDM9 binds, whereas in vertebrates lacking an intact

Language: Английский

Citations

23
Understanding the Genetic Basis of Variation in Meiotic Recombination: Past, Present, and Future DOI Creative Commons
Susan E. Johnston

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(7)

Published: July 1, 2024

Meiotic recombination is a fundamental feature of sexually reproducing species. It often required for proper chromosome segregation and plays important role in adaptation the maintenance genetic diversity. The molecular mechanisms are remarkably conserved across eukaryotes, yet meiotic genes proteins show substantial variation their sequence function, even between closely related Furthermore, rate distribution shows huge diversity within chromosomes, individuals, sexes, populations, This has implications many evolutionary processes, how why this evolved not well understood. A key step understanding trait evolution to determine its basis-that is, number, effect sizes, loci underpinning variation. In perspective, I discuss past current knowledge on basis distribution, explore implications, present open questions future research.

Language: Английский

Citations

17
PRDM9 drives the location and rapid evolution of recombination hotspots in salmonid fish DOI Creative Commons
Marie Raynaud, Paola Sanna, Julien Joseph

et al.

PLoS Biology, Journal Year: 2025, Volume and Issue: 23(1), P. e3002950 - e3002950

Published: Jan. 6, 2025

In many eukaryotes, meiotic recombination occurs preferentially at discrete sites, called hotspots. various lineages, hotspots are located in regions with promoter-like features and evolutionarily stable. Conversely, some mammals, driven by PRDM9 that targets away from promoters. Paradoxically, induces the self-destruction of its this triggers an ultra-fast evolution mammalian is ancestral to all animals, suggesting a critical importance for program, but has been lost lineages surprisingly little effect on meiosis success. However, it unclear whether function described mammals shared other species. To investigate this, we analyzed landscape several salmonids, genome which harbors one full-length truncated paralogs. We identified initiation sites Oncorhynchus mykiss mapping DNA double-strand breaks (DSBs). found DSBs clustered positioned promoters, enriched H3K4me3 H3K36me3 location depended genotype Prdm9 . observed high level polymorphism zinc finger domain , indicating diversification positive selection. Moreover, population-scaled maps O kisutch Salmo salar revealed rapid turnover caused target motif erosion. Our results imply conserved across vertebrates peculiar evolutionary runaway active hundred million years.

Language: Английский

Citations

2
Divergence and conservation of the meiotic recombination machinery DOI
Meret Arter, Scott Keeney

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 25(5), P. 309 - 325

Published: Nov. 30, 2023

Language: Английский

Citations

30
Meiotic DNA breaks drive multifaceted mutagenesis in the human germ line DOI
Robert Hinch, Peter Donnelly, Anjali Gupta Hinch

et al.

Science, Journal Year: 2023, Volume and Issue: 382(6674)

Published: Nov. 30, 2023

Meiotic recombination commences with hundreds of programmed DNA breaks; however, the degree to which they are accurately repaired remains poorly understood. We report that meiotic break repair is eightfold more mutagenic for single-base substitutions than was previously understood, leading de novo mutation in one four sperm and 12 eggs. Its impact on indels structural variants even higher, 100- 1300-fold increases rates per break. uncovered new mutational signatures footprints relative sites, implicate unexpected biochemical processes error-prone mechanisms, including translesion synthesis end joining repair. provide evidence these mechanisms drive mutagenesis human germ lines lead disruption genes genome wide.

Language: Английский

Citations

27
High prevalence of PRDM9-independent recombination hotspots in placental mammals DOI Creative Commons
Julien Joseph, Djivan Prentout, Alexandre Laverré

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(23)

Published: May 29, 2024

In many mammals, recombination events are concentrated in hotspots directed by a sequence-specific DNA-binding protein named PRDM9. Intriguingly, PRDM9 has been lost several times vertebrates, and notably among it pseudogenized the ancestor of canids. absence PRDM9, tend to occur promoter-like features such as CpG islands. It thus proposed that one role could be direct away from PRDM9-independent hotspots. However, ability assessed only handful species, clear picture how much occurs outside PRDM9-directed mammals is still lacking. this study, we derived an estimator past activity based on signatures GC-biased gene conversion substitution patterns. We quantified 52 species boreoeutherian mammals. observe wide range rates at these loci: (such mice, humans, some felids, or cetaceans) show deficit recombination, while majority display peak recombination. Our results demonstrate can coexist their coexistence appears rule rather than exception. Additionally, location relatively more stable hotspots, but nevertheless evolve slowly concert with DNA hypomethylation.

Language: Английский

Citations

11
Bridging the gap between the evolutionary dynamics and the molecular mechanisms of meiosis: A model based exploration of the PRDM9 intra-genomic Red Queen DOI Creative Commons
Alice Genestier, Laurent Duret, Nicolas Lartillot

et al.

PLoS Genetics, Journal Year: 2024, Volume and Issue: 20(5), P. e1011274 - e1011274

Published: May 20, 2024

Molecular dissection of meiotic recombination in mammals, combined with population-genetic and comparative studies, have revealed a complex evolutionary dynamic characterized by short-lived hotspots. Hotspots are chromosome positions containing DNA sequences where the protein PRDM9 can bind cause crossing-over. To explain these fast dynamic, so-called intra-genomic Red Queen model has been proposed, based on interplay between two antagonistic forces: biased gene conversion, mediated double-strand breaks, resulting hotspot extinction (the conversion paradox), followed positive selection favoring mutant alleles recognizing new sequence motifs. Although this predicts many empirical observations, exact causes acting is still not well understood. In direction, experiment mouse hybrids suggested that, addition to targeting double strand another role during meiosis. Specifically, symmetric binding (simultaneous at same site both homologues) would facilitate homology search and, as result, pairing homologues. discovered hybrids, second function could also be involved observed within populations. address point, here, we present theoretical integrating current knowledge about molecular PRDM9. Our modeling work gives important insights into selective forces driving turnover reduced symmetrical caused loss high affinity sites induces net eliciting targets. The offers influence dosage PRDM9, which paradoxically result negative entering population, their eviction thus reducing standing variation locus.

Language: Английский

Citations

6
PRDM9 drives the location and rapid evolution of recombination hotspots in salmonids DOI Creative Commons
Marie Raynaud, Paola Sanna, Julien Joseph

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 7, 2024

Abstract In many eukaryotes, meiotic recombination occurs preferentially at discrete sites, called hotspots. various lineages, hotspots are located in regions with promoter-like features and evolutionarily stable. Conversely, some mammals, driven by PRDM9 that targets away from promoters. Paradoxically, induces the self-destruction of its this triggers an ultra-fast evolution mammalian is ancestral to all animals, suggesting a critical importance for program, but has been lost lineages surprisingly little effect on meiosis success. However, it unclear whether function described mammals shared other species. To investigate this, we analyzed landscape several salmonids, genome which harbors one full-length truncated paralogs. We identified initiation sites Oncorhynchus mykiss mapping DNA double-strand breaks (DSBs). found DSBs clustered positioned promoters, enriched H3K4me3 H3K4me36 marks location depended genotype Prdm9 . observed high level polymorphism zinc finger domain , not Moreover, population-scaled maps O. kisutch Salmo salar revealed rapid turnover caused target motif erosion. Our results imply conserved across vertebrates peculiar evolutionary runaway active hundred million years.

Language: Английский

Citations

5
The GC-content at the 5′ ends of human protein-coding genes is undergoing mutational decay DOI Creative Commons
Yi Qiu,

Yoon Mo Kang,

Christopher Korfmann

et al.

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: Aug. 13, 2024

Abstract Background In vertebrates, most protein-coding genes have a peak of GC-content near their 5′ transcriptional start site (TSS). This feature promotes both the efficient nuclear export and translation mRNAs. Despite importance for RNA metabolism, its general features, origin, maintenance remain mysterious. We investigate evolutionary forces shaping at (TSS) through comparative genomic analysis nucleotide substitution rates between different species by examining human de novo mutations. Results Our data suggests that GC-peaks TSSs were present in last common ancestor amniotes, likely vertebrates. observe apes rodents, where recombination is directed away from PRDM9, end gene currently undergoing mutational decay. canids, which lack PRDM9 perform TSSs, increasing. show these patterns extend into open reading frame, thus impacting synonymous codon position choices. Conclusions results indicate dynamics this GC-peak amniotes largely shaped historic recombination. Since decay towards mutation rate equilibrium default state non-functional DNA, observed decrease rodents indicates not being maintained selection on those species.

Language: Английский

Citations

5
Patterns of recombination in snakes reveal a tug of war between PRDM9 and promoter-like features DOI Creative Commons
Carla Hoge, Marc de Manuel, Mohamed Mahgoub

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 11, 2023

In vertebrates, there are two known mechanisms by which meiotic recombination is directed to the genome: in humans, mice, and other mammals, occurs almost exclusively where protein PRDM9 binds, while species lacking an intact

Language: Английский

Citations

9