GDBr: genomic signature interpretation tool for DNA double-strand break repair mechanisms

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(2)

Published: Jan. 11, 2025

Abstract Large genetic variants can be generated via homologous recombination (HR), such as polymerase theta-mediated end joining (TMEJ) or single-strand annealing (SSA). Given that these HR-based mechanisms leave specific genomic signatures, we developed GDBr, a signature interpretation tool for DNA double-strand break repair using high-quality genome assemblies. We applied GDBr to draft human pangenome reference. found 78.1% of non-repetitive insertions and deletions 11.0% complex substitutions contained signatures. Of these, interpreted 98.7% 1.3% the were TMEJ SSA, respectively, all TMEJ. Since population-level datasets are being dramatically accumulated, provide mechanistic insights into how formed. is available on GitHub at https://github.com/Chemical118/GDBr.

Language: Английский

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Positive correlations in susceptibility to a diverse panel of viruses across Drosophilidae host species

Evolution Letters, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 5, 2025

Our ability to predict the emergence of novel viruses relies on there being generalisable patterns in susceptibilities hosts infections. Studies investigating variation susceptibility among host species have consistently shown that closely related share similar a given virus. However, extent which such phylogenetic are correlated amongst diverse sets is unclear. Here, we investigate correlations Drosophilidae panel eleven different invertebrate viruses, comprising seven unique virus species, six families, and both RNA DNA viruses. The each pair tested was either positively across or did not show evidence correlation. No negative correlations, indicative evolutionary trade-offs were detected between any pairs. strength generally higher same family, consistent with infectivity. results suggest generalised can result positive even highly diverged while specialised interactions individual cause stepwise decrease correlation from within-species, within-family, across-family level.

Language: Английский

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Nested likelihood-ratio testing of the nonsynonymous:synonymous ratio suggests greater adaptation in the piRNA machinery of Drosophila melanogaster compared with Drosophila ananassae and Drosophila willistoni, two species with higher repeat content

G3 Genes Genomes Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 21, 2025

Abstract Numerous studies have revealed a signature of strong adaptive evolution in the piwi-interacting RNA (piRNA) machinery Drosophila melanogaster, but cause this pattern is not understood. Several hypotheses been proposed. One hypothesis that transposable element (TE) families and piRNA are co-evolving under an evolutionary arms race, perhaps due to antagonism by TEs against machinery. A related, though co-evolutionary, recurrent TE invasion drives adapt novel strategies. third ongoing fluctuation abundance leads adaptation must constantly adjust between sensitivity for detecting new elements specificity avoid cost off-target gene silencing. Rapid may also be driven independently TEs, instead from other functions such as role piRNAs suppressing sex-chromosome meiotic drive. We sought evaluate impact on D. melanogaster 2 species with higher repeat content—Drosophila ananassae willistoni. This comparison was achieved employing likelihood-based testing framework based McDonald–Kreitman test. show we can reject faster rate these species. propose high either recent influx occurred during range expansion or selection

Language: Английский

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Analysis of 30 chromosome-level Drosophila genome assemblies reveals dynamic evolution of centromeric satellite repeats

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 18, 2025

Abstract Background The Drosophila genus is ideal for studying genome evolution due to its relatively simple chromosome structure and small size, with rearrangements mainly restricted within arms, such as Muller elements. However, work on the rapidly evolving repetitive genomic regions, composed of transposons tandem repeats, have been hampered by lack genus-wide chromosome-level assemblies. Results Integrating long-read sequencing capture technology, here we produce annotate 30 assemblies genus. Based this dataset, reveal evolutionary dynamics across phylogeny, including identification regions that show comparatively high structural stability throughout evolution. Moreover, ananassae subgroup, uncover emergence new conformations rapid expansion novel satellite DNA sequence families, which form large continuous pericentromeric domains higher-order repeat structures are reminiscent those observed in human Arabidopsis genomes. Conclusions These present a valuable resource future research, power demonstrated our analysis In addition, based findings, propose subgroup an model system centromere structure.

Language: Английский

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Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data

PLoS Genetics, Journal Year: 2021, Volume and Issue: 17(2), P. e1009373 - e1009373

Published: Feb. 26, 2021

Whether hard sweeps or soft dominate adaptation has been a matter of much debate. Recently, we developed haplotype homozygosity statistics that (i) can detect both and with similar power (ii) classify the detected as soft. The application our method to population genomic data from natural Drosophila melanogaster (DGRP) allowed us rediscover three known cases at loci Ace, Cyp6g1, CHKov1 be driven by sweeps, additional candidate for recent strong sweeps. Surprisingly, all top 50 candidates showed patterns more consistent rather than Harris et al. 2018 criticized this work, suggesting statistics, including positive controls, are unlikely instead these easily explained complex neutral demographic models. They also claim non-sweeps likely Here, reanalyze DGRP using range admixture models reconfirm original published results majority in D. first true second, they do appear Furthermore, discuss ways take work forward given most employed such analyses necessarily too simple capture full complexity, while realistic inferred correctly because require large number free parameters.

Language: Английский

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The Worldwide Invasion ofDrosophila suzukiiIs Accompanied by a Large Increase of Transposable Element Load and a Small Number of Putatively Adaptive Insertions

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(10), P. 4252 - 4267

Published: May 21, 2021

Transposable elements (TEs) are ubiquitous and mobile repeated sequences. They major determinants of host fitness. Here, we characterized the TE content spotted wing fly Drosophila suzukii. Using a recently improved genome assembly, reconstructed sequences de novo found that TEs occupy 47% mostly located in gene-poor regions. The majority insertions segregate at low frequencies, indicating recent probably ongoing activity. To explore dynamics context biological invasions, studied variation abundance genomic data from 16 invasive six native populations D. We large increase load correlated with reduced Watterson estimate genetic diversity θw^ proxy effective population size. did not find any correlation between contents bioclimatic variables, minor effect environmentally induced A genome-wide association study revealed ca. 2,000 regions associated abundance. find, however, evidence such an enrichment for genes known to interact activity (e.g., transcription factor encoding or piRNA pathway). Finally, insertion frequencies 15 putatively adaptive insertions, them being likely invasion history species.

Language: Английский

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In-Depth Satellitome Analyses of 37 Drosophila Species Illuminate Repetitive DNA Evolution in the Drosophila Genus

Genome Biology and Evolution, Journal Year: 2022, Volume and Issue: 14(5)

Published: April 30, 2022

Abstract Satellite DNAs (SatDNA) are ubiquitously present in eukaryotic genomes and have been recently associated with several biological roles. Understanding the evolution significance of SatDNA requires an extensive comparison across multiple phylogenetic depths. We combined RepeatExplorer pipeline cytogenetic approaches to conduct a comprehensive identification analysis satellitome 37 species from genus Drosophila. identified 188 SatDNA-like families, 112 them being characterized for first time. Repeat within framework has revealed deeply divergent nature sequences Drosophila genus. The content varied 0.54% D. arizonae genome 38.8% albomicans genome, often following signal. Monomer size guanine–cytosine-content also showed extreme variation ranging 2–570 bp 9.1–71.4%, respectively. families shared among closely related species, consistent library hypothesis. However, we uncovered emergence species-specific through amplification unique or low abundant lineage. Finally, found that sizes Sophophora subgenus positively correlated transposable element content, whereas is SatDNA. This finding indicates could be driven by different categories repetitive elements each subgenus. Altogether, conducted most perspective generated largest catalog date, enabling future discoveries architecture.

Language: Английский

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Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus

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

Published: Nov. 13, 2023

Abstract The PIWI-interacting RNA (piRNA) pathway prevents endogenous genomic parasites, i.e. transposable elements, from damaging the genetic material of animal gonadal cells. Specific regions in genome, called piRNA clusters, are thought to define each species’ repertoire and therefore its capacity recognize silence specific transposon families. unistrand cluster flamenco ( flam ) is essential somatic compartment Drosophila ovary restrict Gypsy -family transposons infecting neighbouring germ Disruption results de-repression sterility, yet it remains unknown whether this silencing mechanism present more widely. Here, we systematically characterise 119 species identify five additional -like clusters separated by up 45 million years evolution. Small RNA-sequencing validated these as bona-fide expressed cells ovary, where they selectively target family. Together, our study provides compelling evidence a widely conserved that co-evolved with virus-like transposons.

Language: Английский

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Genomes of historical specimens reveal multiple invasions of LTR retrotransposons in Drosophila melanogaster during the 19th century

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(15)

Published: April 2, 2024

Transposable element invasions have a profound impact on the evolution of genomes and phenotypes. It is thus an important open question how often such TE occur. To address this question, we utilize historical specimens, sampled about 200 y ago. We found that LTR retrotransposons Blood, Opus, 412 spread in Drosophila melanogaster 19th century. These constitute second waves, as degraded fragments were for all three TEs. The composition Opus 412, but not shows pronounced geographic heterogeneity, likely due to founder effects during invasions. Finally, identified species from simulans complex origin show total, seven families invaded D. last 200y, thereby increasing genome size by up 1.2Mbp. suggest high rate was triggered human activity. Based analysis strains specimens at different times, provide detailed timeline invasions, making first organism where invasion history TEs two centuries could be inferred.

Language: Английский

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The Drosophila melanogaster Y-linked gene, WDY, is required for sperm to swim in the female reproductive tract

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: Jan. 12, 2024

Abstract Unique patterns of inheritance and selection on Y chromosomes have led to the evolution specialized gene functions. We report CRISPR mutants in Drosophila Y-linked gene, WDY , which is required for male fertility. demonstrate that sperm tails beat approximately half as fast those wild-type mutant do not propel themselves within ejaculatory duct or female reproductive tract. Therefore, although mature are produced by males, transferred females, fail enter storage organs. genotype-dependent regional differences motility appear break correlation between tail beating propulsion. Furthermore, we identify a significant change hydrophobicity at residue putative calcium-binding site orthologs split melanogaster obscura species groups, when first became Y-linked. This suggests major functional coincided with its appearance chromosome. Finally, show another PRY also defect may explain their subfertility. Overall, provide direct evidence long-held presumption protein-coding genes regulate motility.

Language: Английский

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