Recurrent chromosome destabilization through repeat-mediated rearrangements in a fungal pathogen

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

Published: July 15, 2023

Abstract Genomic instability caused by chromosomal rearrangements has severe consequences for organismal fitness and progression of cancerous cell lines. The triggers destabilized chromosomes remain poorly understood but are often assumed to be associated with fragile sites. Here, we retrace a runaway degeneration process observed in fungal pathogen using telomere-to-telomere assemblies across an experimental pedigree. We show that the same sites triggered reproducible, large-scale through non-allelic recombination. Across four-generation pedigree, were accompanied non-disjunction events aneuploid progeny carry up four copies. identify specific transposable element as most likely trigger repeated degeneration. is higher virulence undergone burst increasing copy numbers genome. Chromosome sequences also targeted genome defense mechanism active on duplicated sequences, which may contribute decay. Our work identifies exact sequence initiating chromosome perpetuating degenerative cycles. Dissecting proximate causes leading run-away expands our understanding evolution beyond cancer

Language: Английский

---

Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen

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

Published: July 16, 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.

Language: Английский

---

Evolutionary dynamics of the LTR-retrotransposon crapaud in the Podospora anserina species complex and the interaction with repeat-induced point mutations

Mobile DNA, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 13, 2024

Abstract Background The genome of the filamentous ascomycete Podospora anserina shows a relatively high abundance retrotransposons compared to other interspersed repeats. LTR-retrotransposon family crapaud is particularly abundant in genome, and consists multiple diverged sequence variations specifically localized 5’ half both long terminal repeats (LTRs). P. part recently species-complex, which makes system ideal classify based on observed LTR variation study evolutionary dynamics, such as diversification bursts elements over recent time. Results We developed similarity network approach seven genomes representing species complex into 14 subfamilies. This method does not utilize consensus sequence, but instead it connects any copies that share enough set coverage. Based phylogenetic analyses, we found likely diversified ancestor have had activity at different time points for Furthermore, while hypothesized evolution subfamilies could been direct effect escaping defense repeat induced point mutations, this be case. Conclusions Our contributes development methods transposable fungi, also highlights intricate patterns retrotransposon short timescales under mutational load caused by nucleotide-altering defense.

Language: Английский

---

The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate

Published: Feb. 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.

Language: Английский

---

A recent and rapid genome expansion driven by the amplification of transposable elements in the Neotropical annual killifish Austrolebias charrua

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: March 26, 2024

Abstract Background. Neotropical annual killifish are able to survive in seasonal ponds due their ability undergo embryonic diapauses the dry season and grow, reproduce die span of a few months during rainy season. The genus group Austrolebias is endemic South American basins shows remarkable speciation genetic plasticity. charrua co-exists with another killifish, Cynopoecilus melanotaenia , from which it diverged about 25 million years ago. Despite similar life histories, both species show important differences genome size. It interest explore genomic structure these as basis for understanding evolution unique adaptations. Results. We have sequenced genomes A. C. determined that they structural between them. While has undergone an evolutionarily recent massive expansion, size (3Gb) triples most characterized teleosts, melaotaenia retained 1Gb. expansion occurred amplification repetitive elements, recently LINE class elements. characterize detail contribution elements at level superfamilies, well analyze relationship coding genes . also examine selection pressures on gene sequences identify functions under positive or purifying selection, compare data derived other species. Conclusions. Our study adds crucial element fish history. variability plasticity accompanied by genome-wide By comparing findings species, we bursts specific superfamilies retrotransposons DNA transposons being prevalent recent. In addition, potentially implicated adaptive traits because interaction mobile display evidence selection. These candidates functional studies aimed unraveling annualism this teleosts.

Language: Английский

---