The genome awakens: transposon-mediated gene regulation

Trends in Plant Science, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

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Ancient diversity in host-parasite interaction genes in a model parasitic nematode

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

Published: Nov. 27, 2023

Host-parasite interactions exert strong selection pressures on the genomes of both host and parasite. These can lead to negative frequency-dependent selection, a form balancing that is hypothesised explain high levels polymorphism seen in many immune parasite antigen loci. Here, we sequence several individuals Heligmosomoides bakeri, model house mice, polygyrus, closely related wood mice. Although H. bakeri commonly referred as polygyrus literature, their show divergence are consistent with at least million years independent evolution. The species contain hyper-divergent haplotypes enriched for proteins interact response. Many these originated prior between suggesting they have been maintained by long-term selection. Together, our results suggest exerted response played key role shaping patterns genetic diversity parasitic nematodes.

Language: Английский

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The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Feb. 19, 2024

Control and elimination of schistosomiasis is an arduous task, with current strategies proving inadequate to break transmission. Exploration genetic approaches interrupt Schistosoma mansoni transmission, the causative agent for human intestinal in sub-Saharan Africa South America, has led genomic research snail vector hosts genus Biomphalaria. Few complete resources exist, African Biomphalaria species being particularly underrepresented despite this where majority S. infections occur. Here we generate annotate first genome assembly sudanica sensu lato, a responsible transmission lake marsh habitats Rift Valley. Supported by whole-genome diversity data among five inbred lines, describe orthologs immune-relevant gene regions American B. glabrata present bioinformatic pipeline identify candidate novel pathogen recognition receptors (PRRs).

Language: Английский

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HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: July 2, 2024

Abstract Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods TE using assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, currently available gold-standard databases are not comprehensive, even extensively studied species, highlighting critical need an automated detection method to supplement repositories. this study, we introduce HiTE, a fast accurate dynamic boundary adjustment approach designed detect full-length TEs. The experimental results demonstrate that HiTE outperforms RepeatModeler2, state-of-the-art tool, across various species. Furthermore, has identified numerous novel transposons with well-defined structures containing protein-coding domains, some which directly inserted within crucial genes, leading direct alterations gene expression. A Nextflow version is also available, enhanced parallelism, reproducibility, portability.

Language: Английский

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Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(24)

Published: Oct. 9, 2023

Large-scale chromosome rearrangements, such as fissions and fusions, are a common feature of eukaryote evolution. They can have considerable influence on the evolution populations, yet it remains unclear exactly how rearrangements become established eventually fix. Rearrangements could fix by genetic drift if they weakly deleterious or neutral, may instead be favoured positive natural selection. Here, we compare genome assemblies three closely related Brenthis butterfly species characterize complex history fission fusion rearrangements. An inferred demographic these suggests that became fixed in populations with large long-term effective size (N

Language: Английский

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Holocentric repeat landscapes: From micro‐evolutionary patterns to macro‐evolutionary associations with karyotype evolution

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(24)

Published: Aug. 14, 2023

Repetitive elements can cause large-scale chromosomal rearrangements, for example through ectopic recombination, potentially promoting reproductive isolation and speciation. Species with holocentric chromosomes, that lack a localized centromere, might be more likely to retain rearrangements lead karyotype changes such as fusions fissions. This is because chromosome segregation during cell division should less affected than in organisms centromere. The relationships between repetitive how they may translate patterns of speciation are though poorly understood. Here, we use reference-free approach based on low-coverage short-read sequencing data characterize the repeat landscape two independently evolved groups: Erebia butterflies Carex sedges. We consider both micro- macro-evolutionary scales investigate differentiation populations association repeats phylogenetic framework Carex. At micro-evolutionary scale, found population increases overall intraspecific genetic among four species. indications an along phylogenies. Altogether, our results suggest associated level clades therefore play role adaptation species diversification.

Language: Английский

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Chromosome-level genome assembly of the common chiton, Liolophura japonica (Lischke, 1873)

Gigabyte, Journal Year: 2024, Volume and Issue: 2024, P. 1 - 14

Published: April 25, 2024

Chitons (Polyplacophora) are marine molluscs that can be found worldwide from cold waters to the tropics, and play important ecological roles in environment. However, only two chiton genomes have been sequenced date. The Liolophura japonica (Lischke, 1873) is one of most abundant polyplacophorans throughout East Asia. Our PacBio HiFi reads Omni-C sequencing data resulted a high-quality near chromosome-level genome assembly ∼609 Mb with scaffold N50 length 37.34 (96.1% BUSCO). A total 28,233 genes were predicted, including 28,010 protein-coding ones. repeat content (27.89%) was similar other Chitonidae species approximately three times lower than Hanleyidae genome. genomic resources provided by this work will help expand our understanding evolution adaptation chitons.

Language: Английский

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Teaching transposon classification as a means to crowd source the curation of repeat annotation – a tardigrade perspective

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

Published: May 6, 2024

Abstract Background The advancement of sequencing technologies results in the rapid release hundreds new genome assemblies a year providing unprecedented resources for study evolution. Within this context, significance in-depth analyses repetitive elements, transposable elements (TEs) particular, is increasingly recognized understanding Despite plethora available bioinformatic tools identifying and annotating TEs, phylogenetic distance target species from curated classified database element sequences constrains any automated annotation effort. Moreover, manual curation raw repeat libraries deemed essential due to frequent incompleteness automatically generated consensus sequences. Results Here, we present an example crowd-sourcing effort aimed at curating TE two non-model built around collaborative, peer-reviewed teaching process. Manual classification are time-consuming processes that offer limited short-term academic rewards typically confined few research groups where methods taught through hands-on experience. Crowd-sourcing efforts could therefore significant opportunity bridge gap between learning effectively empowering scientific community with high-quality, reusable libraries. Conclusions collaborative TEs tardigrade species, which there were no available, resulted successful characterization diverse reasonable time frame. Our setting can be used as reference guide similar projects: A hidden treasure awaits discovery within organisms.

Language: Английский

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Identification of transposable element families from pangenome polymorphisms

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

Published: June 26, 2024

Abstract Background Transposable Elements (TEs) are segments of DNA, typically a few hundred base pairs up to several tens thousands bases long, that have the ability generate new copies themselves in genome. Most existing methods used identify TEs newly sequenced genome based on their repetitive character, together with detection homology and structural features. As high quality assemblies become more common, including availability multiple independent from same species, an alternative strategy for identification TE families becomes possible which we focus polymorphism at insertion sites caused by mobility. Results We develop idea using polymorphisms found pangenomes create library recently active or closely related group species. present tool, pantera, achieves this task, illustrate its use both species well-curated libraries, assemblies. Conclusions Our results show pantera is sensitive accurate, tending correctly complete elements precise boundaries, particularly well suited detect larger, low copy number often undetected de novo methods.

Language: Английский

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The genome of a globally invasive passerine, the common myna, Acridotheres tristis

DNA Research, Journal Year: 2024, Volume and Issue: 31(2)

Published: Jan. 1, 2024

Abstract In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns diversity how they impact species health their ability persist under future regimes. Invasive offer vital model systems in investigate questions regarding adaptive potential, with a particular focus on changes effective population size interact novel selection The common myna (Acridotheres tristis) globally invasive passerine excellent for research both into the persistence low-diversity populations mechanisms biological invasion. To underpin invasion genetics this species, we present genome assembly myna. We describe genomic landscape including wide allelic diversity, methylation, repeats, recombination rate, as well examination gene family evolution. Finally, use demographic analysis identify that some native regions underwent dramatic increase between two most recent periods glaciation, reveal artefactual impacts bottlenecks analysis.

Language: Английский

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