The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate DOI Open Access
Mathieu Hénault, Souhir Marsit, Guillaume Charron

и другие.

Опубликована: Фев. 2, 2024

Transposable elements (TEs) are major contributors to structural genomic variation by creating interspersed duplications of themselves. In return, variants (SVs) can affect the distribution TE copies and shape their load. One long-standing hypothesis states that hybridization could trigger mobilization thus increase load in hybrids. We previously tested this performing a large-scale evolution experiment mutation accumulation (MA) on multiple hybrid genotypes within between wild populations yeasts Saccharomyces paradoxus cerevisiae . Using aggregate measures with short-read sequencing, we found no evidence for MA lines. Here, resolve genomes lines long-read phasing assembly precisely characterize role SVs shaping landscape. Highly contiguous phased assemblies 127 revealed SV types like polyploidy, aneuploidy loss heterozygosity have large impacts characterized 18 de novo insertions, indicating transposition only has minor landscape Because scarcity provided insufficient resolution confidently dissect rate hybrids, adapted an vivo assay measure rates various S. backgrounds. not increased hybridization, but modulated many genotype-specific factors including initial load, sequence mitochondrial DNA inheritance. Our results show scales at which is shaped genomes, being highly impacted dynamics finely rates.

Язык: Английский

The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate DOI Creative Commons
Mathieu Hénault, Souhir Marsit, Guillaume Charron

и другие.

eLife, Год журнала: 2024, Номер 12

Опубликована: Фев. 27, 2024

Transposable elements (TEs) are major contributors to structural genomic variation by creating interspersed duplications of themselves. In return, variants (SVs) can affect the distribution TE copies and shape their load. One long-standing hypothesis states that hybridization could trigger mobilization thus increase load in hybrids. We previously tested this (Hénault et al., 2020) performing a large-scale evolution experiment mutation accumulation (MA) on multiple hybrid genotypes within between wild populations yeasts Saccharomyces paradoxus cerevisiae . Using aggregate measures with short-read sequencing, we found no evidence for MA lines. Here, resolve genomes lines long-read phasing assembly precisely characterize role SVs shaping landscape. Highly contiguous phased assemblies 127 revealed SV types like polyploidy, aneuploidy, loss heterozygosity have large impacts characterized 18 de novo insertions, indicating transposition only has minor landscape Because scarcity provided insufficient resolution confidently dissect rate hybrids, adapted an vivo assay measure rates various S. backgrounds. not increased hybridization, but modulated many genotype-specific factors including initial load, sequence variants, mitochondrial DNA inheritance. Our results show scales at which is shaped genomes, being highly impacted dynamics finely rates.

Язык: Английский

Процитировано

2
Strain-specific evolution and host-specific regulation of transposable elements in the model plant symbiont Rhizophagus irregularis DOI Creative Commons
Jordana Inácio Nascimento Oliveira, Nicolas Corradi

G3 Genes Genomes Genetics, Год журнала: 2024, Номер 14(5)

Опубликована: Март 20, 2024

Abstract Transposable elements (TEs) are repetitive DNA that can create genome structure and regulation variability. The of Rhizophagus irregularis, a widely studied arbuscular mycorrhizal fungus (AMF), comprises ∼50% sequences include TEs. Despite their abundance, two-thirds TEs remain unclassified, among AMF life stages remains unknown. Here, we aimed to improve our understanding TE diversity in this model species by curating repeat datasets obtained from chromosome-level assemblies investigating expression across multiple conditions. Our analyses uncovered new superfamilies families symbiont revealed significant differences how these evolve both within between R. irregularis strains. With curated annotation, also found the number upregulated colonized roots is 4 times higher than extraradical mycelium, overall differs depending on plant host. This work provides fine-scale view evolution symbionts highlights transcriptional dynamism specificity during host–microbe interactions. We provide Hidden Markov Model profiles domains for future manual curation uncharacterized (https://github.com/jordana-olive/TE-manual-curation/tree/main).

Язык: Английский

Процитировано

2
The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate DOI Creative Commons
Mathieu Hénault, Souhir Marsit, Guillaume Charron

и другие.

eLife, Год журнала: 2023, Номер 12

Опубликована: Авг. 21, 2023

Transposable elements (TEs) are major contributors to structural genomic variation by creating interspersed duplications of themselves. In return, variants (SVs) can affect the distribution TE copies and shape their load. One long-standing hypothesis states that hybridization could trigger mobilization thus increase load in hybrids. We previously tested this (Hénault et al., 2020) performing a large-scale evolution experiment mutation accumulation (MA) on multiple hybrid genotypes within between wild populations yeasts Saccharomyces paradoxus cerevisiae. Using aggregate measures with short-read sequencing, we found no evidence for MA lines. Here, resolve genomes lines long-read phasing assembly precisely characterize role SVs shaping landscape. Highly contiguous phased assemblies 127 revealed SV types like polyploidy, aneuploidy, loss heterozygosity have large impacts characterized 18 de novo insertions, indicating transposition only has minor landscape Because scarcity provided insufficient resolution confidently dissect rate hybrids, adapted an vivo assay measure rates various S. backgrounds. not increased hybridization, but modulated many genotype-specific factors including initial load, sequence variants, mitochondrial DNA inheritance. Our results show scales at which is shaped genomes, being highly impacted dynamics finely rates.

Язык: Английский

Процитировано

5
Transposable elements impact the population divergence of rice blast fungus Magnaporthe oryzae DOI Creative Commons
Lian‐Yu Lin, Ting Sun,

Jiayuan Guo

и другие.

mBio, Год журнала: 2024, Номер 15(5)

Опубликована: Март 27, 2024

ABSTRACT Dynamic transposition of transposable elements (TEs) in fungal pathogens has significant impact on genome stability, gene expression, and virulence to the host. In Magnaporthe oryzae , plasticity resulting from TE insertion is a major driving force leading rapid evolution diversification this fungus. Despite their importance M. population divergence, our understanding TEs context remains limited. Here, we conducted genome-wide analysis dynamics 11 most abundant families populations. Our results show that these have specifically expanded recently isolated rice populations, with presence/absence polymorphism insertions highly concordant divergence Geng/ Japonica Xian/ Indica cultivars. Notably, genes targeted by clade-specific showed expression patterns are involved pathogenic process, suggesting transcriptional regulation genes. study provides comprehensive populations demonstrates crucial role recent bursts adaptive rice-infecting lineage. IMPORTANCE causal agent destructive blast disease, which caused massive loss yield annually worldwide. The fungus diverged into distinct clades during adaptation toward two subspecies, . Although was well established, mechanisms underlying how promote remain largely unknown. study, reported shape differentially regulating between -infecting revealed insertion-mediated adaption led infecting different subspecies.

Язык: Английский

Процитировано

1
Starships: a new frontier for fungal biology DOI
Andrew J. Urquhart, Aaron A. Vogan, Emile Gluck‐Thaler

и другие.

Trends in Genetics, Год журнала: 2024, Номер unknown

Опубликована: Сен. 1, 2024

Язык: Английский

Процитировано

1
Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen DOI Creative Commons
Leen Abraham, Ursula Oggenfuss, Daniel Croll

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Март 29, 2023

Abstract Rapid adaptive evolution is driven by strong selection pressure acting on standing genetic variation within populations. How generated species and how such influences phenotypic trait expression often not well understood though. Here, we focused recent activity of transposable elements (TEs) using deep population genomics transcriptomics analyses a fungal plant pathogen with highly active content TEs in the genome. Zymoseptoria tritici causes one most damaging diseases wheat, adaptation to host environment being facilitated TE-associated mutations. We obtained genomic RNA-sequencing data from 146 isolates collected single wheat field. established genome-wide map TE insertion polymorphisms analyzing insertions among individuals. quantified locus-specific transcription individual revealed considerable across loci. About 20% all copies show genome implying that defenses as repressive epigenetic marks repeat-induced are ineffective at preventing proliferation A quarter associated neighboring genes providing broad potential influence expression. indeed found likely responsible for virulence secondary metabolite production. Our study emphasizes TE-derived segregate even populations broadly underpin species.

Язык: Английский

Процитировано

3
Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen DOI Creative Commons
Leen Abraham, Daniel Croll

BMC Biology, Год журнала: 2023, Номер 21(1)

Опубликована: Ноя. 20, 2023

Abstract Background In agricultural ecosystems, outbreaks of diseases are frequent and pose a significant threat to food security. A successful pathogen undergoes complex well-timed sequence regulatory changes avoid detection by the host immune system; hence, well-tuned gene regulation is essential for survival. However, extent which polymorphisms in population provide an adaptive advantage poorly understood. Results We used Zymoseptoria tritici , one most important pathogens wheat, generate genome-wide map polymorphism governing expression. investigated transcription levels 146 strains grown under nutrient starvation performed expression quantitative trait loci (eQTL) mapping. identified cis -eQTLs 65.3% all genes majority eQTL within 2kb upstream downstream start site (TSS). also show that different elements contributes disproportionally variation. Investigating categories, we found enrichment variants predicted be fungal pathogenesis but with comparatively low effect size, suggesting separate layer involving epigenetics. previously reported trait-associated SNPs populations frequently -regulatory neighboring implications architecture. Conclusions Overall, our study provides extensive evidence single segregate large-scale variation likely fuel rapid adaptation resistant hosts environmental change.

Язык: Английский

Процитировано

3
Recent reactivation of a pathogenicity-associated transposable element triggers major chromosomal rearrangements in a fungal wheat pathogen DOI Creative Commons
Thomas Badet, Alice Feurtey, Daniel Croll

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Март 29, 2023

Summary Transposable elements (TEs) are key drivers of genomic variation contributing to recent adaptation in most species. Yet, the evolutionary origins and insertion dynamics within species remain poorly understood. We recapitulate spread pathogenicity-associated Styx element across five that last diverged ∼11,000 years ago. show likely originated Zymoseptoria fungal pathogen genus underwent multiple independent reactivation events. Using a global 900-genome panel wheat Z. tritici, we assess copy number identify renewed transposition activity Oceania South America. can mobilize create additional copies four-generation pedigree. Importantly, find new not affected by defenses revealing loss control against element. preferentially located recombination breakpoints triggered types large chromosomal rearrangements. Taken together, establish origin, diversification, highly active TE with major consequences for integrity expression disease.

Язык: Английский

Процитировано

2
The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate DOI Creative Commons
Mathieu Hénault, Souhir Marsit, Guillaume Charron

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Май 9, 2023

Abstract Transposable elements (TEs) are major contributors to structural genomic variation by creating interspersed duplications of themselves. In return, variants (SVs) can affect the distribution TE copies and shape their load. One long-standing hypothesis states that hybridization could trigger mobilization thus increase load in hybrids. We previously tested this performing a large-scale evolution experiment mutation accumulation (MA) on multiple hybrid genotypes within between wild populations yeasts Saccharomyces paradoxus cerevisiae . Using aggregate measures with short-read sequencing, we found no evidence for MA lines. Here, resolve genomes lines long-read phasing assembly precisely characterize role SVs shaping landscape. Highly contiguous phased assemblies 127 revealed SV types like polyploidy, aneuploidy loss heterozygosity have large impacts characterized 18 de novo insertions, indicating transposition only has minor landscape Because scarcity provided insufficient resolution confidently dissect rate hybrids, adapted an vivo assay measure rates various S. backgrounds. not increased hybridization, but modulated many genotype-specific factors including initial load, sequence mitochondrial DNA inheritance. Our results show scales at which is shaped genomes, being highly impacted dynamics finely rates.

Язык: Английский

Процитировано

2
Replicators, genes, and the C-value enigma: High-quality genome assembly of barley provides direct evidence that self-replicating DNA forms ‘cooperative’ associations with genes in arms races DOI Creative Commons
M. Timothy Rabanus‐Wallace, Thomas Wicker, Nils Stein

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Окт. 2, 2023

Abstract The C-value enigma—the apparent disjunction between the complexity of organisms and sizes their genomes—could be in part resolved if it were definitively shown that tolerance self-copying DNA elements incurred an occasional selective advantage. We leverage power latest genome assembly exceptionally repetitive well-studied cereal crop barley ( Hordeum vulgare L.) to explicitly test hypothesis population genes have been repeatedly replicated by action replication-inducing sequences has undergone selection, favouring involved co-evolutionary arms races (such as implicated pathogen resistance). This was achieved algorithmically identifying 1,999 genomic stretches are locally rich long repeated units. In these loci, we identified 554 geanes, belonging 42 gene families. These families strongly overlap with a set resistance other likely evolutionary ‘arms-race’ compiled independently from literature. By statistically demonstrating selection systematically influenced composition replicator-associated at genome-wide scale provide evidence repeat-inducing is adaptive strategy may contribute enigmatically inflated C-values, invite more detailed research on how particular become prone duplication, organism’s To this end, examined surrounding several candidate families, find pattern disperse-and-expand dynamics, but where unit itself varies sites expansion. suggests effectively form opportunistic relationships elements. mention implications for agriculture.

Язык: Английский

Процитировано

2