Coexistence versus collapse in transposon populations

Physical review. E, Journal Year: 2025, Volume and Issue: 111(5)

Published: May 27, 2025

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Factors determining chromosomal localization of transposable elements in plants

Plant Biology, Journal Year: 2025, Volume and Issue: unknown

Published: May 29, 2025

Abstract Transposable elements (TEs) constitute a significant part of plant genomes and shape their genomic landscape. While some TEs are ubiquitously dispersed, other specifically occupy discrete loci. The evolutionary forces behind the chromosomal localization poorly understood. Therefore, we first review specific niches where often localized including (i) centromeres, (ii) (sub)telomeres, (iii) genes, (iv) sex chromosomes. In second this review, focus on processes standing non‐equal distribution various in purifying selection, insertion site preference or targeting TEs, post‐insertion ectopic recombination between spatiotemporal regulation TE jumping. Using combination above processes, explain We also describe phenomena mutual nesting epigenetic mark silencing interactions 3D interphase nucleus concerning localization. summarize functional consequences relate them to cell functioning genome evolution.

Language: Английский

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Comparative repeatome analysis of Pyrgomorphidae and Acrididae (Orthoptera: Caelifera) revealed the contribution of repetitive DNA in genome gigantism

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(6), P. e0325165 - e0325165

Published: June 2, 2025

Eukaryotic genomes are often rich in DNA repetitive elements, involving both transposable elements (TE) and tandemly repeated satellite DNA. Grasshopper species, known for their large genome sizes, comprising relatively a high proportion of genomic repeats. This study aimed to identify perform comparative analysis content eight grasshopper species from the Pyrgomorphidae Acrididae families. We utilized unassembled low-coverage Illumina paired-end short reads RepeatExplorer2 pipeline repeats, RepeatMasker estimate abundance divergence activity. Flow cytometry estimated ranging 1C = 7.670 pg 18.612 pg, with Aularches miliaris (18.612 pg) being second largest insect reported date. The repeat ranged 51% 74%, mean value 64.26% total genome. major identified included LINE, Ty3_Gypsy, Penelope, Ty1-copia, Helitron, Maverick, LINE most abundant, constituting 24% 54% Apalacris varicornis A. , respectively. positive correlation TEs size suggests that expansion has contributed sizes observed. Satellite 65 satDNA families across species. Additionally, phylogenetic TE protein domains revealed consensus sequences same domain cluster together, suggesting domain-specific evolutionary pathways reveals new dynamics into role gigantism as well other mechanisms Orthoptera.

Language: Английский

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Comparative genomics and transcriptomics reveal differences in effector complement and expression between races of Fusarium oxysporum f.sp. lactucae

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Oct. 10, 2024

This study presents the first genome and transcriptome analyses for

Language: Английский

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Comparative genomics and transcriptomics reveal differences in effector complement and expression between races ofFusarium oxysporumf.sp.lactucae

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 13, 2024

Abstract This study presents the first genome and transcriptome analyses for Fusarium oxysporum f.sp. lactucae (Fola) which causes wilt disease of lettuce. Long-read sequencing three race 1 (Fola1) 4 (Fola4) isolates revealed key differences in putative effector complement between races with other F. f.spp. following mimp -based bioinformatic analyses. Notably, homologues Secreted Xylem ( SIX ) genes, also present many f.spp, were identified Fola, both SIX9 SIX14 (multiple copies sequence variants) Fola1 Fola4. All Fola4 contained an additional single copy SIX8 . RNAseq lettuce infection highly expressed effectors, some those reported including several apii Although , all Fola4, two genes Fola1, only was as further analysis that gene disrupted by insertion a transposable element. Two variants based on different effector-based included divergently transcribed from shared promoter either PSE1 or PSL1 respectively. In addition there evidence independent instances HCT variants. The involvement helitrons Fola rearrangement expression is discussed.

Language: Английский

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Transcriptomic insights into the epigenetic modulation of turnip mosaic virus evolution in Arabidopsis thaliana

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

Published: Sept. 30, 2024

Abstract Background Plant-virus interaction models propose that a virus’s ability to infect host genotype depends on the compatibility between virulence and resistance genes. Recently, we conducted an evolution experiment in which lineages of turnip mosaic virus (TuMV) were passaged Arabidopsis thaliana genotypes carrying mutations components DNA methylation histone demethylation epigenetic pathways. All evolved increased infectivity, viral load genotype-dependent manner. Results To better understand underlying reasons for these relationships, delved into transcriptomic responses mutant WT plant mock conditions infected with either ancestral or viruses. Such comparison allowed us classify every gene nine basic expression profiles. Regarding targets adaptation, our analyses identification common as well genotype-specific genes categories biological processes. As expected, immune response-related found be altered upon infection. However, also noticed pervasive over-representation other functional groups, suggesting adaptation was not solely driven by level In addition, significant association presence transposable elements within upstream differentially expressed observed. Finally, integration data virus-host protein-protein network highlighted most impactful interactions. Conclusions These findings shed extra light complex dynamics plants viruses, indicating infectivity various factors beyond just plant’s

Language: Английский

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Graphical pangenomics-enabled characterisation of structural variant impact on gene expression in Brassica napus

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 16, 2024

Abstract Structural variants (SVs, eg. insertions and deletions) are genomic variations > 50 bp that known to be associated with a range of crop traits, from yield flowering behaviour stress responses. Recently, pangenome graphs have emerged as powerful framework for analysing data by encoding population- or species-level diversity in one structure. Pangenome the potential serve unbiased references downstream applications, including SV genotyping pan-transcriptomic analyses. In this work, we hypothesized extensive variation affects transcript quantification expression quantitative trait locus (eQTL) analysis when relying on single reference, using can mitigate reference sequence bias. We combined long short read whole genome sequencing profiling Brassica napus (oilseed rape) assess impact SVs gene regulation explored utility eQTL analysis. demonstrate provides superior eliminating bias quantification. Combined graph-based SVs, identified 240 eQTL-SVs found close proximity target loci. These affect genes related important often not linkage SNPs represent unaccounted classical SNP-based This study highlights multiple advantages approaches population-scale studies novel insight into an crop.

Language: Английский

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A first look at the genome structure of hexaploid 'Black Mitcham' peppermint (Mentha piperita L.)

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 16, 2024

Peppermint, Mentha xpiperita L., is a hexaploid (2n = 6x 72) and the predominant cultivar of commercial mint oil production in US. This threatened because high susceptibility to fungal disease Verticillium wilt, caused by dahliae . report details first draft polyploid chromosome-level genome assembly for this species. The Black Mitcham resource will broaden comparative studies resistance, essential biosynthesis, hybridization events within genus It also be valuable contribution body phylogenetic involving other genera that contain species with varying ploidy levels.

Language: Английский

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Transcriptomic Insights into the Epigenetic Modulation of Turnip Mosaic Virus Evolution inArabidopsis thaliana

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 22, 2024

Abstract Plant-virus interaction models propose that a virus’s ability to infect host genotype depends on the compatibility between virulence and resistance genes. Recently, we conducted an evolution experiment in which lineages of turnip mosaic virus (TuMV) were passaged Arabidopsis thaliana genotypes carrying mutations components DNA methylation histone demethylation epigenetic pathways. All evolved increased infectivity, viral load genotype-dependent manner. To better understand underlying reasons for these relationships, delved into transcriptomic responses mutant WT plant mock conditions infected with either ancestral or viruses. Such comparison allowed us classify every gene nine basic expression profiles. Regarding targets adaptation, our analyses identification common as well genotype-specific genes categories biological processes. As expected, immune response-related found be altered upon infection. However, also noticed pervasive over-representation other functional groups, suggesting adaptation was not solely driven by level In addition, significant association presence transposable elements within upstream differentially expressed observed. Finally, integration data virus-host protein-protein network highlighted most impactful interactions. These findings shed extra light complex dynamics plants viruses, indicating infectivity various factors beyond just plant’s

Language: Английский

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Dysregulation of locus-specific repetitive elements in TCGA pan-cancers

Published: Oct. 23, 2024

Abstract Understanding the role of repetitive elements (REs) in cancer development is crucial for identifying novel biomarkers and therapeutic targets. This study investigated locus-specific dysregulation REs, including differential expression methylation across 12 TCGA types stratified by their genomic context ( i.e. , genic intergenic REs). We found uniquely dysregulated REs co-regulated with corresponding transcripts associated distinct biological functions different types. Uniquely were identified each type used to cluster sample Recurrently several types, genes up-regulated involved cell cycle processes those down-regulated extracellular matrix. Interestingly, 4 out 5 consistently all located intronic region TMEM252, a recently discovered tumor suppressor gene. TMEM252 was also 10 suggesting its potential importance wide range With DNA array data, we higher prevalence hypo-methylated most (10 12). Despite slight overlaps between differentially expressed methylated showed that negatively correlates some

Language: Английский

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