Regulatory logic and transposable element dynamics in nematode worm genomes DOI Creative Commons
Janna L. Fierst,

Victoria Kristian Eggers

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 16, 2024

Abstract Genome sequencing has revealed a tremendous diversity of transposable elements (TEs) in eukaryotes but there is little understanding the evolutionary processes responsible for TE diversity. Non-autonomous TEs have lost machinery necessary transposition and rely on closely related autonomous critical proteins. We studied two mathematical models regulation, one assuming that both tranposons their non-autonomous relatives operate under same regulatory logic, competing resources, self-attenuate while transposons continually increase, parasitizing relatives. implemented these stochastic simulations how relationships influence populations. found only outcrossing populations evolving with Parasitic regulation resulted stable maintenance TEs. tested our model predictions Caenorhabditis genomes by annotating focal families, LINEs SINE DNA transposon Mutator . broad variation - rapid mutational decay sequences allow to transpose. Together, results suggest individual families evolve according disparate rules are relevant early, acute stages invasion.

Язык: Английский

Most azole resistance mutations in the Candida albicans drug target confer cross-resistance without intrinsic fitness cost DOI
Camille Bédard, Isabelle Gagnon‐Arsenault, Jonathan Boisvert

и другие.

Nature Microbiology, Год журнала: 2024, Номер 9(11), С. 3025 - 3040

Опубликована: Окт. 8, 2024

Язык: Английский

Процитировано

10

Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication DOI Creative Commons
Xavier Dallaire, Raphaël Bouchard,

Philippe Hénault

и другие.

Genome Biology and Evolution, Год журнала: 2023, Номер 15(12)

Опубликована: Дек. 1, 2023

Abstract Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, complexity, resulting from structural variants, paralogous sequences, repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading SNPs that deviate Mendelian expected patterns of heterozygosity allelic ratio. In this study, we employed the ngsParalog software identify such deviant whole-genome sequencing (WGS) data with low (1.5×) intermediate (4.8×) coverage for four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), American Eel (Anguilla rostrata). The analyses revealed accounted 22% 62% all salmonid datasets approximately 11% dataset. These were particularly concentrated within elements regions had recently undergone rediploidization salmonids. Additionally, narrow peaks elevated ubiquitous along genomes, encompassed most SNPs, could be partially associated transposons tandem repeats. Including these led highly distorted site frequency spectra, underestimated pairwise FST values, overestimated diversity. Considering widespread occurrence arising a variety sources, important impact estimating parameters, availability effective them, propose excluding WGS is required improve inferences wide range taxa depths.

Язык: Английский

Процитировано

9

The good, the bad and the ugly of transposable elements annotation tools DOI Creative Commons
Élgion L. S. Loreto, Elverson Soares de Melo, Gabriel Luz Wallau

и другие.

Genetics and Molecular Biology, Год журнала: 2023, Номер 46(3 suppl 1)

Опубликована: Янв. 1, 2023

Transposable elements are repetitive and mobile DNA segments that can be found in virtually all organisms investigated to date. Their complex structure variable nature particularly challenging from the genomic annotation point of view. Many softwares have been developed automate facilitate TEs at level, but they highly heterogeneous regarding documentation, usability methods. In this review, we revisited existing software for TE annotation, concentrating on most often used ones, methodologies apply, usability. Building state art propose best practices highlight strengths weaknesses available solutions.

Язык: Английский

Процитировано

6

Most azole antifungal resistance mutations in the drug target provide cross-resistance and carry no intrinsic fitness cost DOI Creative Commons
Camille Bédard, Isabelle Gagnon‐Arsenault, Jonathan Boisvert

и другие.

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

Опубликована: Дек. 14, 2023

Abstract Azole antifungals are among the most frequently used drugs to treat fungal infections. Amino acid substitutions in and around binding site of azole target Erg11 (Cyp51) a common resistance mechanism pathogenic yeasts such as Candida albicans . How many which mutations confer resistance, at what cost, is however largely unknown. Here, we measure impact nearly 4,000 amino variants ligand pocket on susceptibility six medical azoles. We find that large fraction lead (33%), cross-resistance two or more azoles (88%) importantly, only handful show significant fitness cost absence drug (9%). Our results reveal can arise through set this will likely pan-resistance, with very little evolutionary compromise. Such resource help inform treatment choices clinical settings guide development new drugs.

Язык: Английский

Процитировано

2

Regulatory logic and transposable element dynamics in nematode worm genomes DOI Creative Commons
Janna L. Fierst,

Victoria Kristian Eggers

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 16, 2024

Abstract Genome sequencing has revealed a tremendous diversity of transposable elements (TEs) in eukaryotes but there is little understanding the evolutionary processes responsible for TE diversity. Non-autonomous TEs have lost machinery necessary transposition and rely on closely related autonomous critical proteins. We studied two mathematical models regulation, one assuming that both tranposons their non-autonomous relatives operate under same regulatory logic, competing resources, self-attenuate while transposons continually increase, parasitizing relatives. implemented these stochastic simulations how relationships influence populations. found only outcrossing populations evolving with Parasitic regulation resulted stable maintenance TEs. tested our model predictions Caenorhabditis genomes by annotating focal families, LINEs SINE DNA transposon Mutator . broad variation - rapid mutational decay sequences allow to transpose. Together, results suggest individual families evolve according disparate rules are relevant early, acute stages invasion.

Язык: Английский

Процитировано

0