A high-quality reference genome for the fission yeastSchizosaccharomyces osmophilus DOI Creative Commons
Guo‐Song Jia, Wen Cai Zhang, Yue Liang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Dec. 9, 2022

Abstract Fission yeasts are an ancient group of fungal species that diverged from each other tens to hundreds million years ago. Among them is the preeminent model organism Schizosaccharomyces pombe , which has significantly contributed our understandings molecular mechanisms underlying fundamental cellular processes. The availability genomes S. and three fission yeast japonicus octosporus cryophilus enabled cross-species comparisons provide insights into evolution genes, pathways, genomes. Here, we performed genome sequencing on type strain recently identified osmophilus obtained a complete mitochondrial nuclear assembly with gaps only at rRNA gene arrays. A total 5098 protein-coding genes were annotated orthologs for more than 95% identified. Genome-based phylogenetic analysis showed most closely related these two around 16 To demonstrate utility this reference genome, conducted comparative analyses centromeres, telomeres, transposons, mating-type region, Cbp1 family proteins, These revealed conservation repeat arrangements sequence motifs in centromere cores, telomeric sequences composed types repeats, delineated relationships among Tf1/sushi retrotransposons, characterized evolutionary origins trajectories domesticated transposases, discovered signs interspecific transfer selfish elements.

Language: Английский

A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus DOI Creative Commons
Guo‐Song Jia, Wen Cai Zhang, Yue Liang

et al.

G3 Genes Genomes Genetics, Journal Year: 2023, Volume and Issue: 13(4)

Published: Feb. 7, 2023

Fission yeasts are an ancient group of fungal species that diverged from each other tens to hundreds million years ago. Among them is the preeminent model organism Schizosaccharomyces pombe, which has significantly contributed our understandings molecular mechanisms underlying fundamental cellular processes. The availability genomes S. pombe and 3 fission yeast japonicus, octosporus, cryophilus enabled cross-species comparisons provide insights into evolution genes, pathways, genomes. Here, we performed genome sequencing on type strain recently identified osmophilus obtained a complete mitochondrial nuclear assembly with gaps only at rRNA gene arrays. A total 5,098 protein-coding genes were annotated orthologs for more than 95% identified. Genome-based phylogenetic analysis showed most closely related octosporus these 2 around 16 To demonstrate utility this reference genome, conducted comparative analyses centromeres, telomeres, transposons, mating-type region, Cbp1 family proteins, These revealed conservation repeat arrangements sequence motifs in centromere cores, telomeric sequences composed types repeats, delineated relationships among Tf1/sushi retrotransposons, characterized evolutionary origins trajectories domesticated transposases, discovered signs interspecific transfer selfish elements.

Language: Английский

Citations

16
Transposon removal Reveals Their Adaptive Fitness Contribution DOI Creative Commons

Susanne Cranz-Mileva,

Eve Reilly,

Noor Chalhoub

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(2)

Published: Jan. 20, 2024

Abstract Transposable elements are molecular parasites that persist in their host genome by generating new copies to outpace natural selection. exert a large influence on evolution, some cases providing adaptive changes. Here we measure the fitness effect of transposable element insertions fission yeast Schizosaccharomyces pombe type strain removing all its only native family, long terminal repeat retrotransposon Tf2. We show Tf2 provide positive contribution host. ablation results changes regulation mitochondrial gene and, consistently, sensitive growth conditions. propose influences directed manner dynamically rewiring transcriptional response metabolic stress.

Language: Английский

Citations

4
Physiological novelties for salinity tolerance created by transgressive effects and cryptic gene functionsunlocked by alien introgression from Oryza rufipogon to Oryza sativa DOI Creative Commons
Swarupa Nanda Mandal, Ai Kitazumi,

Coenraad R. van Beek

et al.

Current Plant Biology, Journal Year: 2025, Volume and Issue: unknown, P. 100477 - 100477

Published: April 1, 2025

Language: Английский

Citations

0
Accumulation and ineffective silencing of transposable elements on an avian W Chromosome DOI Creative Commons
Vera Warmuth, Matthias H. Weissensteiner, Jochen B. W. Wolf

et al.

Genome Research, Journal Year: 2022, Volume and Issue: 32(4), P. 671 - 681

Published: Feb. 11, 2022

One of the defining features transposable elements (TEs) is their ability to move new locations in host genome. To minimize potentially deleterious effects de novo TE insertions, hosts have evolved several mechanisms control activity, including recombination-mediated removal and epigenetic silencing; however, increasing evidence suggests that silencing TEs often incomplete. The crow family experienced a recent radiation LTR retrotransposons (LTRs), offering an opportunity gain insight into regulatory young, still active TEs. We quantified abundance TE-derived transcripts across tissues 15 Eurasian crows ( Corvus corone ) spp. raised under common garden conditions find for ineffective suppression on female-specific W Chromosome. Using RNA-seq data, we show ∼9.5% all transcribed had considerably greater (average, 16-fold) transcript female >85% these female-biased originated After accounting differences density among chromosomal classes, W-linked were significantly more highly expressed than residing other chromosomes, consistent with former. Together, our results suggest Chromosome acts as source transcriptionally TEs, possible negative fitness consequences birds analogous Drosophila (an X/Y system), which overexpression Y-linked associated male-specific aging loss (“toxic Y”).

Language: Английский

Citations

18
Homoplastic versus xenoplastic evolution: exploring the emergence of key intrinsic and extrinsic traits in the montane genus Soldanella (Primulaceae) DOI Creative Commons
Ivan Rurik, Andrea Melichárková,

Eliška Gbúrová Štubová

et al.

The Plant Journal, Journal Year: 2024, Volume and Issue: 118(3), P. 753 - 765

Published: Jan. 13, 2024

SUMMARY Specific ecological conditions in the high mountain environment exert a selective pressure that often leads to convergent trait evolution. Reticulations induced by incomplete lineage sorting and introgression can lead discordant patterns among gene species trees (hemiplasy/xenoplasy), providing false illusion traits under study are homoplastic. Using phylogenetic networks, we explored effect of exchange on evolution Soldanella , genus profoundly influenced historical introgression. At least three features evolved independently multiple times: single‐flowered dwarf phenotype, dysploid cytotype, generalism. The present analyses also indicated recurring occurrence stoloniferous growth might have been prompted an event between ancestral still extant species, although its emergence via cannot be completely ruled out. Phylogenetic regression suggested independent larger genomes snowbells is most likely result interplay hybridization events euploid taxa hostile environments at range margins genus. key intrinsic extrinsic has significantly impacted not only but recent events.

Language: Английский

Citations

3
Rates and spectra of de novo structural mutations inChlamydomonas reinhardtii DOI Creative Commons
Eugenio López‐Cortegano, Rory J. Craig, Jobran Chebib

et al.

Genome Research, Journal Year: 2022, Volume and Issue: 33(1), P. 45 - 60

Published: Dec. 12, 2022

Genetic variation originates from several types of spontaneous mutation, including single-nucleotide substitutions, short insertions and deletions (indels), larger structural changes. Structural mutations (SMs) drive genome evolution are thought to play major roles in evolutionary adaptation, speciation, genetic disease, cancers. Sequencing mutation accumulation (MA) lines has provided estimates rates spectra indel many species, yet the rate new SMs is largely unknown. Here, we use long-read sequencing determine full spectrum MA derived two strains (CC-1952 CC-2931) green alga Chlamydomonas reinhardtii . The SM highly variable between lines, represent a substantial proportion all both 6%; CC-2931 12%). differ considerably strains, with almost inversions translocations occurring lines. This associated heterogeneity number type active transposable elements (TEs), which comprise proportions 22%; 38%). In CC-2931, Crypton previously undescribed DNA element have caused 71% chromosomal rearrangements, whereas CC-1952, Dualen LINE 87% duplications. Other SMs, notably large duplications likely products various double-strand break repair pathways. Our results show that diverse occur at rates, support prominent for TEs evolution.

Language: Английский

Citations

13
Evolutionary modes of wtf meiotic driver genes in Schizosaccharomyces pombe DOI Creative Commons
Yanhui Xu, Fang Suo, Xiaoran Zhang

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(10)

Published: Oct. 1, 2024

Abstract Killer meiotic drivers are a class of selfish genetic elements that bias inheritance in their favor by destroying progeny do not carry them. How killer evolve is well understood. In the fission yeast, Schizosaccharomyces pombe, largest gene family, known as wtf genes, driver family causes intraspecific hybrid sterility. Here, we investigate how genes using long-read–based genome assemblies 31 distinct S. pombe natural isolates, which encompass diversity pombe. Our analysis, involving nearly 1,000 these yields comprehensive portrayal genes. Leveraging single-nucleotide polymorphisms adjacent unique sequences, pinpoint gene-containing loci have recently undergone conversion events and infer ancestral state. These include revival pseudogenes, lending support to notion plays role preserving this from extinction. Moreover, our investigation reveals solo long terminal repeats retrotransposons, frequently found near can act recombination arms, influencing upstream regulatory sequences Additionally, exploration outer boundaries uncovers previously unrecognized type directly oriented flanking may facilitated early expansion findings enhance understanding mechanisms evolution family.

Language: Английский

Citations

2
Recent insights into the evolution of mutation rates in yeast DOI
Robert H. Melde, Kevin Bao, Nathaniel P. Sharp

et al.

Current Opinion in Genetics & Development, Journal Year: 2022, Volume and Issue: 76, P. 101953 - 101953

Published: July 11, 2022

Language: Английский

Citations

9
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

et al.

eLife, Journal Year: 2023, Volume and Issue: 12

Published: Aug. 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.

Language: Английский

Citations

5
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

et al.

eLife, Journal Year: 2024, Volume and Issue: 12

Published: Feb. 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.

Language: Английский

Citations

1