The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role DOI Creative Commons
Róbert Horváth, Nikolaos Minadakis, Yann Bourgeois

et al.

eLife, Journal Year: 2023, Volume and Issue: 12

Published: Dec. 5, 2023

Understanding how plants adapt to changing environments and the potential contribution of transposable elements (TEs) this process is a key question in evolutionary genomics. While TEs have recently been put forward as active players context adaptation, few studies thoroughly investigated their precise role plant evolution. Here, we used wild Mediterranean grass Brachypodium distachyon model species identify quantify forces acting on during adaptation various conditions, across its entire geographic range. Using sequencing data from more than 320 natural B. accessions suite population genomics approaches, reveal that putatively adaptive TE polymorphisms are rare populations. After accounting for changes past activity, show only small proportion evolved neutrally (<10%), while vast majority them under moderate purifying selection regardless distance genes. should not be ignored when conducting studies, they can linked adaptation. However, our study clearly shows large cause phenotypic variation distachyon, favored evolution over other types mutations (such point mutations) species.

Language: Английский

A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice DOI Creative Commons
Xiaoxia Li,

Xiaofan Dai,

Huiying He

et al.

National Science Review, Journal Year: 2024, Volume and Issue: 11(6)

Published: May 3, 2024

Transposable elements (TEs) are ubiquitous genomic components and hard to study due being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing data. Coupling the with 15 existing assemblies, developed a pan-TE map comprising both cultivated wild Asian rice. We detected 177 084 high-quality TE variations inferred their derived state using outgroups. found TEs were one source of phenotypic variation during rice domestication differentiation. identified 1246 genes whose expression was associated but not single-nucleotide polymorphisms (SNPs), such as

Language: Английский

Citations

9
The role of mobile DNA elements in the dynamic of plants genome plasticity DOI Creative Commons
Robyn Emmerson, Marco Catoni

Journal of Experimental Botany, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

Abstract Plants host a range of DNA elements capable self-replication. These molecules, usually associated to the activity transposable or viruses, are found integrated in genome form extrachromosomal DNA. The these can impact plasticity by variety mechanisms, including generation structural variants, shuffling regulatory coding sequences across genome, and endoduplication. This dynamically alter gene expression stability, ultimately affecting plant development response environmental changes. While activation is often considered deleterious their role creating variation important adaptation evolution. Moreover, mechanisms which mobile proliferate have been exploited for engineering, contributed understand how desirable traits be generated crops. In this review, we discuss origins roles element on biology, as well potential function current application biotechnology.

Language: Английский

Citations

1
Transposons are important contributors to gene expression variability under selection in rice populations DOI Creative Commons
Raúl Castanera, Noemia Morales-Díaz, Sonal Gupta

et al.

eLife, Journal Year: 2023, Volume and Issue: 12

Published: May 5, 2023

Transposable elements (TEs) are an important source of genome variability. Here, we analyze their contribution to gene expression variability in rice by performing a TE insertion polymorphism quantitative trait locus mapping using data from 208 varieties the Oryza sativa ssp. indica and O. japonica subspecies. Our show that insertions associated with changes many genes known be targets domestication breeding. An fraction these were already present wild ancestors, have been differentially selected populations. Taken together, our results small signal transduction induced accompany adaptation

Language: Английский

Citations

15
A phased genome of the highly heterozygous ‘Texas’ almond uncovers patterns of allele-specific expression linked to heterozygous structural variants DOI Creative Commons
Raúl Castanera,

Carlos de Tomás,

Valentino Ruggieri

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(6)

Published: April 9, 2024

Abstract The vast majority of traditional almond varieties are self-incompatible, and the level variability species is very high, resulting in a high-heterozygosity genome. Therefore, information on different haplotypes particularly relevant to understand genetic basis trait this species. However, although reference genomes for several exist, none them phased has genome at haplotype level. Here, we present assembly cv. Texas. This new 13% more assembled sequence than previous version Texas an increased contiguity, particular repetitive regions such as centromeres. Our analysis shows that ‘Texas’ high degree heterozygosity, both SNPs, short indels, structural variants Many SVs result heterozygous transposable element insertions, many cases, they also contain genic sequences. In addition direct consequences presence/absence genes, our results show located close genes often associated with allele-specific gene expression, which highlights importance almond.

Language: Английский

Citations

5
Harbinger transposon insertion in ethylene signaling gene leads to emergence of new sexual forms in cucurbits DOI Creative Commons
Hsin-Ya Huang, Siqi Zhang, Fadi Abou-Choucha

et al.

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

Published: June 7, 2024

Abstract In flowering plants, the predominant sexual morph is hermaphroditism, and emergence of unisexuality poorly understood. Using Cucumis melo (melon) as a model system, we explore mechanisms driving forms. We identify spontaneous mutant exhibiting transition from bisexual to unisexual male flower, causal mutation Harbinger transposon impairing expression Ethylene Insensitive 2 ( CmEIN2 ) gene. Genetics transcriptomic analysis reveal dual role in both sex determination fruit shape formation. Upon CmACS11 , EIN2 recruited repress carpel inhibitor, CmWIP1 . Subsequently, mediate stamina inhibition. Following phase, promotes elongation. Genome-wide reveals that mobilization triggered by environmental cues, integrates preferentially active chromatin, particularly within promoter regions. Characterization large collection melon germplasm points transpositions wild, compared cultivated accessions. Our study underscores association between chromatin dynamics temporal aspects mobile genetic element insertions, providing valuable insights into plant adaptation crop genome evolution.

Language: Английский

Citations

4
Miniature-inverted-repeat transposable elements contribute to phenotypic variation regulation of rice induced by space environment DOI Creative Commons

Lishan Chen,

Qing Yang, Yan Zhang

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 8, 2025

Rice samples exposed to the space environment have generated diverse phenotypic variations. Miniature-inverted-repeat transposable elements (MITEs), often found adjacent genes, play a significant role in regulating plant genome. Herein, contribution of MITEs space-mutagenic phenotypes was explored. The phenotype changes F3 F5 generations three lines from rice varieties Dongnong423 (DN423) and Dongnong (DN416) were meticulously traced. leaves at heading stage subjected high coverage whole-genome bisulfite sequencing sequencing. These analyses conducted investigate effects related epigenetic genetic variations on phenotypes. Studies indicated that within gene regulatory regions might contribute formation differentiation has been shown induce insertion polymorphisms (MITEs-TIPs), with notable preference for near genes involved stress response regulation. space-induced MITEs-TIPs contributed by modulating expression site. This study underscored pivotal variation induced environment, as well transgenerational stability these variants.

Language: Английский

Citations

0
Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus DOI Creative Commons
Gözde Yildiz, Silvia Zanini, Sven E. Weber

et al.

Theoretical and Applied Genetics, Journal Year: 2025, Volume and Issue: 138(4)

Published: April 1, 2025

Language: Английский

Citations

0
Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon DOI Creative Commons
Michael Thieme, Nikolaos Minadakis,

Christophe Himber

et al.

PLoS Genetics, Journal Year: 2024, Volume and Issue: 20(3), P. e1011200 - e1011200

Published: March 12, 2024

Long terminal repeat retrotransposons (LTR-RTs) are powerful mutagens regarded as a major source of genetic novelty and important drivers evolution. Yet, the uncontrolled potentially selfish proliferation LTR-RTs can lead to deleterious mutations genome instability, with large fitness costs for their host. While population genomics data suggest that an ongoing LTR-RT mobility is common in many species, understanding dual role evolution limited. Here, we harness diversity 320 sequenced natural accessions Mediterranean grass Brachypodium distachyon characterize how environmental factors influence plant dynamics wild. When combining coverage-based approach estimate global copy number variations mobilome-sequencing nine exposed eight different stresses, find little evidence accumulations B . accessions. Instead, show loss RNA polymerase IV (Pol IV), which mediates RNA-directed DNA methylation plants, results high transcriptional transpositional activities RLC_BdisC024 ( HOPPLA ) family elements, these effects not stress-specific. This work supports findings indicating reveals host rather than controls this wild model.

Language: Английский

Citations

3
Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum DOI Creative Commons
Juanita Gutiérrez‐Valencia, Panagiotis‐Ioannis Zervakis, Zoé Postel

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(5)

Published: May 1, 2024

Abstract Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs flowers, often coupled with heteromorphic self-incompatibility. has evolved convergently multiple flowering plant lineages, but also broken down repeatedly, resulting homostylous, self-compatible populations elevated rates self-fertilization. Here, we aimed to study genetic causes genomic consequences shift homostyly Linum trigynum, closely related distylous tenue. Building on high-quality genome assembly, show that L. trigynum harbors region homologous dominant haplotype distyly supergene conferring long stamens short styles tenue, suggesting loss first occurred short-styled individual. In contrast homostylous Primula Fagopyrum, no fixed loss-of-function mutations coding sequences S-linked candidate genes. Instead, gene expression analyses controlled crosses suggest downregulating LtWDR-44 for male self-incompatibility and/or anther height could underlie self-compatibility trigynum. Population 224 whole-genome further demonstrate highly self-fertilizing, exhibits significantly lower diversity genome-wide, experiencing relaxed purifying selection less frequent positive nonsynonymous relative Our shed light advance our understanding common evolutionary transition plants.

Language: Английский

Citations

2
Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels DOI Open Access

Keliang Lyu,

Jiajing Xiao,

Shiheng Lyu

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(23), P. 16935 - 16935

Published: Nov. 29, 2023

Transposable elements (TEs) make up a large portion of plant genomes and play vital role in genome structure, function, evolution. Cultivated strawberry (Fragaria x ananassa) is one the most important fruit crops, its octoploid was formed through several rounds duplications from diploid ancestors. Here, we built pan-genome TE library for Fragaria genus using ten published at different ploidy levels, including seven diploids, tetraploid, two octoploids, performed comparative analysis content these genomes. The TEs comprise 51.83% (F. viridis) to 60.07% nilgerrensis) Long terminal repeat retrotransposons (LTR-RTs) are predominant type (20.16% 34.94%), particularly F. iinumae (34.94%). Estimating LTR-RT insertion times revealed that species-specific have shaped each genome. Additionally, copy number families inserted last million years reflects genetic distance between species. Comparing cultivated subgenomes extant ancestors showed vesca likely strawberry, but not viridis. These findings provide new insights into variations their roles

Language: Английский

Citations

4