High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)

Chromosome Research, Journal Year: 2023, Volume and Issue: 31(1)

Published: Jan. 20, 2023

Abstract Karyotypes are generally conserved between closely related species and large chromosome rearrangements typically have negative fitness consequences in heterozygotes, potentially driving speciation. In the order Lepidoptera, most investigated ancestral karyotype gene synteny is often across deep divergence, although examples of extensive genome reshuffling recently been demonstrated. The genus Leptidea has an unusual level variation rearranged sex chromosomes, but extent restructuring rest so far unknown. To explore genomes wood white ( ) complex, we generated eight assemblies using a combination 10X linked reads HiC data, improved them linkage maps for two populations common L. sinapis with distinct karyotypes. Synteny analysis revealed amount rearrangements, both compared to species, where only one three Z chromosomes was all comparisons. Most explained by fissions fusions, while translocations appear relatively rare. We further detected several segregating rearrangement polymorphisms supporting highly dynamic evolution this clade. Fusion breakpoints were enriched LINEs LTR elements, which suggests that ectopic recombination might be important driver formation new chromosomes. Our results show count alone may conceal propose Lepidoptera still underestimated due lack taxonomic sampling.

Language: Английский

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Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: April 1, 2023

Abstract With >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, feature unique to in which two haploid nuclei reside same cell. A key example is Phakopsora pachyrhizi , causal agent Asian soybean disease, one world’s most economically damaging agricultural diseases. Despite P. ’s impact, exceptional size complexity its genome prevented generation an accurate assembly. Here, we sequence three independent genomes uncover up 1.25 Gb comprising haplotypes with transposable element (TE) content ~93%. We study incursion dominant these TEs show how they have various processes such as host range adaptation, stress responses genetic plasticity.

Language: Английский

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Heterologous survey of 130 DNA transposons in human cells highlights their functional divergence and expands the genome engineering toolbox

Cell, Journal Year: 2024, Volume and Issue: 187(14), P. 3741 - 3760.e30

Published: June 5, 2024

Language: Английский

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Constitutive Heterochromatin in Eukaryotic Genomes: A Mine of Transposable Elements

Cells, Journal Year: 2022, Volume and Issue: 11(5), P. 761 - 761

Published: Feb. 22, 2022

Transposable elements (TEs) are abundant components of constitutive heterochromatin the most diverse evolutionarily distant organisms. TEs enrichment in was originally described model organism Drosophila melanogaster, but it is now considered as a general feature this peculiar portion genomes. The phenomenon TE has been proposed to be consequence progressive accumulation transposable caused by both reduced recombination and lack functional genes heterochromatin. However, view does not take into account classical genetics studies recent evidence derived genomic analyses other species. In particular, seem any more Sequencing annotation melanogaster have shown that compartment contains hundreds transcriptionally active genes, generally larger size than euchromatic ones. Together, these occupy significant fraction territory Moreover, suggested drive formation recruiting HP1 repressive chromatin marks. addition, there several pieces might important for centromere telomere structure. Thus, may complexity relationship between heterochromatin, different forces could dynamic phenomenon. Among those forces, preferential transposition an factor. article, we present overview experimental findings showing cases transposon their positive evolutionary interactions with impact host

Language: Английский

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Transposons and non-coding regions drive the intrafamily differences of genome size in insects

iScience, Journal Year: 2022, Volume and Issue: 25(9), P. 104873 - 104873

Published: Aug. 4, 2022

Genome size (GS) can vary considerably between phylogenetically close species, but the landscape of GS changes in insects remain largely unclear. To better understand specific evolutionary factors that determine insects, we examined flow cytometry-based published data from 1,326 insect spanning 700 genera, 155 families, and 21 orders. Model fitting showed generally followed an Ornstein-Uhlenbeck adaptive model Insecta overall. Ancestral reconstruction indicated a likely 1,069 Mb, suggesting most clades appeared to undergo massive genome expansions or contractions. Quantification genomic components 56 species nine families four orders revealed proliferation transposable elements contributed high variation such as within Coleoptera. This study sheds lights on pattern provides understanding evolution.

Language: Английский

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Teleost genomic repeat landscapes in light of diversification rates and ecology

Mobile DNA, Journal Year: 2023, Volume and Issue: 14(1)

Published: Oct. 3, 2023

Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering major branches diverse lineage teleost fish. We investigated if TE correlates family level net diversification rates and found support for weak negative correlation. Further, demonstrated that proportion size, but not to short tandem repeats (STRs), which implies independent evolutionary paths. Marine freshwater fish had large differences STR content, extreme propagation detected genomes codfish Atlantic herring. Such high density STRs is likely increase mutational load, propose could be counterbalanced by fecundity as seen codfishes

Language: Английский

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Retrotransposon LINE-1 bodies in the cytoplasm of piRNA-deficient mouse spermatocytes: Ribonucleoproteins overcoming the integrated stress response

PLoS Genetics, Journal Year: 2023, Volume and Issue: 19(6), P. e1010797 - e1010797

Published: June 12, 2023

Transposable elements (TE) are mobile DNA sequences whose excessive proliferation endangers the host. Although animals have evolved robust TE-targeting defenses, including Piwi-interacting (pi)RNAs, retrotransposon LINE-1 (L1) still thrives in humans and mice. To gain insights into L1 endurance, we characterized Bodies (LBs) ORF1p complexes germ cells of piRNA-deficient Maelstrom null We report that interacts with TE RNAs, genic mRNAs, stress granule proteins, consistent earlier studies. also show associates CCR4-NOT deadenylation complex PRKRA, a Protein Kinase R factor. Despite interactions these negative regulators RNA expression, stability translation LB-localized mRNAs remain unchanged. scrutinize findings, studied effects PRKRA on cultured showed it elevates levels retrotransposition. These results suggest ORF1p-driven condensates promote propagation, without affecting metabolism endogenous RNAs.

Language: Английский

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Analysis of nucleotide sequences of bacterial retrointrons for the presence of homology to eukaryotic MGE

Visnik ukrains kogo tovaristva genetikiv i selekcioneriv, Journal Year: 2025, Volume and Issue: 22(1-2), P. 4 - 9

Published: Jan. 1, 2025

Aims. To analyze the sequences of bacterial retrointrons for presence homology to representatives various classes eukaryotic mobile genetic elements (MGE). Methods. Nucleotide group II introns were taken analysis from Database Bacterial Group Introns. The results search and identification MGE have been realized by CENSOR program. Results. In analyzed retrointrons, fragments both MGEs found in combinations: non-LTR; LTR; DNA; non-LTR+LTR; non-LTR+DNA; LTR+DNA; non-LTR+LTR+DNA. largest contains classes. Conclusions. can be not only ancestors non-LTR retroelements, but also carriers fragmentary nucleotide formation MGEs.

Language: Английский

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Epigenetics in evolution and adaptation to environmental challenges: pathways for disease prevention and treatment

Epigenomics, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 17

Published: Feb. 13, 2025

Adaptation to challenging environmental conditions is crucial for the survival/fitness of all organisms. Alongside genetic mutations that provide adaptive potential during challenges, epigenetic modifications offer dynamic, reversible, and rapid mechanisms regulating gene expression in response changes both evolution daily life, without altering DNA sequences or relying on accidental favorable mutations. The widespread conservation diverse – like methylation, histone modifications, RNA interference across species, including plants underscores their significance evolutionary biology. Remarkably, environmentally induced alterations are passed daughter cells inherited transgenerationally through germline cells, shaping offspring phenotypes while preserving memory. Throughout anthropoid evolution, have played roles in: i) suppressing transposable elements viral genomes intruding into host genome; ii) inactivating one X chromosomes female balance dosage; iii) imprinting ensure from parental allele; iv) functional alleles compensate dysfunctional ones; v) modulating epigenome transcriptome influence gut microbiome among other functions. Understanding interplay between factors processes may valuable insights developmental plasticity, dynamics, disease susceptibility.

Language: Английский

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Significant improvement of environmental DNA assay by targeting retrotransposon sequences characteristic toAnguillaeels

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 11, 2025

Abstract Environmental DNA (eDNA) analysis faces challenges regarding sensitivity and quantification accuracy, particularly in areas with low target species densities or during seasons when eDNA release decreases. Multi-copy markers such as mitochondrial genomic ribosomal (rDNA) have been widely used to address this issue. However, the copy number of per cell remains a potential bottleneck for sensitivity. In study, we aimed increase assays by using retrotransposons, which are abundant genome, novel markers. We developed an assay targeting UnaSINE1, short interspersed nucleotide element (SINE) characteristic Anguilla eels, compared its accuracy that established 16S rRNA marker. Our results demonstrated UnaSINE1 was detected at over 100 times marker both samples. river surveys, positive 32 81 samples, whereas 62 indicating use SINE remarkably reduced false negatives. Furthermore, biological technical replicates exhibited improved consistency variability quantification, leading more robust presence/absence determination quantitative results. Utilizing retrotransposon sequences requires additional effort sequence acquisition organization may limit taxonomic resolution genus level. approach significantly improves without increasing labor cost sampling PCR analysis, making it highly practical studies.

Language: Английский

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