Biology subjects

Baduel, P.

Publications and source records attributed to Baduel, P..

7 recordsLinked to original sources

bioRxiv2026

Fragmented landscapes of mobile transposable element families bolster the diversity of large-effect alleles in Arabidopsis

Transposable elements (TEs) are powerful endogenous mutagens, but our understanding of the 'mobilome' - the set of mobile TEs at the species level - has largely been shaped by the study of a single reference genome. To overcome this reference-centric view, we produced long-read genome assemblies for 91 Arabidopsis thaliana strains and performed a reference-free pangenomic graph analysis of structural variants. Our analysis revealed the presence of twice as many TE families with recent mobilization activity as previously described. These >200 newly identified TE families are ancestral, with a third experimentally shown to be mobile and although they are often characterized by the presence of full-length copies in only a few rather than in most strains, they nonetheless contribute significantly to the generation of large-effect alleles. These findings uncover a much more fragmented and impactful mobilome than previously documented and highlight how pangenome approaches dramatically improve the study of genetic diversity.

genomics↗

bioRxiv2024

The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research

Arabidopsis thaliana was the first plant for which a high-quality genome sequence became available. The publication of the first reference genome sequence almost 25 years ago was already accompanied by genome-wide data on sequence polymorphisms in another accession, or naturally occurring strain. Since then, inventories of genome-wide diversity have been generated at increasingly precise levels. High-density genotype data for A. thaliana, including those from the 1001 Genomes Project, were key to demonstrating the enormous power of GWAS in inbred populations of wild plants, and the comparison of intraspecific polymorphism with interspecific divergence has illuminated many aspects of plant genome evolution. Over the past decade, an increasing number of nearly complete genome sequences have been published for many more accessions. Here, we highlight the diversity of a curated collection of previously published and so far unpublished genome sequences assembled using different types of long reads, including PacBio Continuous Long Reads (CLR), PacBio High Fidelity (HiFi) reads, and Oxford Nanopore Technologies (ONT) reads. This 1001 Genomes Plus (1001G+) resource is being made available at http://1001genomes.org. We invite colleagues with yet unpublished genome assemblies from A. thaliana accessions to contribute to this effort.

genomics↗

bioRxiv2024

Transposable elements are prevalent vectors of transgenerational epigenetic inheritance in nature

Loss of DNA methylation over transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritance are unknown. Here, we demonstrate at thousands of TE loci across the Arabidopsis thaliana genome, that experimentally-induced hypomethylation can be transmitted transgenerationally and reveal the role of small RNAs derived from related copies in counteracting this transmission. Using data from >700 strains collected worldwide, we uncover natural hypomethylation at hundreds of the same TE loci, often situated near stress-responsive genes. Like their experimental counterparts, most natural epivariants we tested can be inherited without DNA sequence changes and are therefore bona fide epialleles, although genetic factors modulate their recurrence or persistence. Crucially, we demonstrate that TE-mediated epiallelic variation associated with differential gene expression is generally causal and may be target of selection in specific environments, thus establishing its importance in nature.

genomics↗

bioRxiv2023

Retrotransposon-driven environmental regulation of FLC leads to adaptive response to herbicide

The mobilization of retrotransposons yields major-effect mutations. Here, we report an adaptive retrotransposon insertion within the first intron of the Arabidopsis floral-repressor locus FLOWERING LOCUS C (FLC). The insertion-mutation augments the environmental sensitivity of FLC by affecting the balance between coding and non-coding transcript isoforms in response to environmental threads. We show that this balance is modulated epigenetically by DNA methylation and orchestrated by IBM2, a factor involved in the processing of intronic heterochromatin. The stress-sensitive allele of FLC has recently spread across populations subjected to recurrent chemical weeding, and we demonstrate that retrotransposon-driven acceleration of life cycle represents a rapid response to herbicide. Our findings illustrate how retrotransposition can create environmentally-sensitive alleles that facilitate adaptation to anthropogenic disturbances of the environment.

plant biology↗

bioRxiv2020

Efficient detection of transposable element insertion polymorphisms between genomes using short-read sequencing data

Transposable elements (TEs) are powerful generators of major-effect mutations, most of which are deleterious at the species level and maintained at very low frequencies within populations. As reference genomes can only capture a minor fraction of such variants, methods were developed to detect TE insertion polymorphisms (TIPs) in non-reference genomes from short-read sequencing data, which are becoming increasingly available. We present here a bioinformatic framework combining an improved version of the SPLITREADER and TEPID pipelines to detect non-reference TE presence and reference TE absence variants, respectively. We benchmark our method on ten non-reference Arabidopsis thaliana genomes and demonstrate its high specificity and sensitivity in the detection of TIPs between genomes.

bioinformatics↗

bioRxiv2018

Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa

Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced [~]300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species. We find the impacts of polyploidy on population genomic processes are subtle yet pervasive, including reduced efficiency on linked and purifying selection as well as rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution, and interploidy introgression all conspire to shape the evolutionary potential of polyploids.

evolutionary biology↗

bioRxiv2017

A ticket to ride - Allele delivery by rail in secondary ruderal colonization by Arabidopsis arenosa

Human-generated ruderal habitats are abundant, but challenging for plants. Some ruderal habitats, however, provide networked corridors (e.g. roadsides and railways) that can facilitate rapid long-distance spread of successfully adapted variants. Here we use transcriptomic and genomic analyses, coupled with genetic mapping and transgenics to understand adaptation to railways in Arabidopsis arenosa. We show normally perennial A. arenosa switched to rapid cycling, a common adaptation for ruderal plants, at least twice upon railway colonization. We further show substantial gene flow from a widely distributed railway colonist likely contributed to secondary colonization by a non-ruderal type, highlighting how connectivity can affect adaptability. We find loss of expression of the reproductive repressor FLOWERING LOCUS C (FLC) is likely primarily responsible for rapid cycling in the widely distributed railway variant. However, a second railway colonist in the Alps also cycles rapidly, but retains high FLC. Some alleles in this population encode non-functional proteins, suggesting FLC has started to decay, but most are functional. Instead, this population likely circumvents FLC via a derived allele of CONSTANS (CO), which shows strong evidence of selection in this population. Importantly, we find this CO allele arrived via gene flow from the widespread ruderal, where it was also previously under selection. This suggests ruderal adaptation may have been progressive, perhaps in both cases, with FLC-circumvention arising first, and FLC loss arising later but ultimately obscuring its earlier circumvention. These snapshots of railway adaptation highlight that gene flow from widespread ruderals can provide opportunities for subsequent adaptation by local genotypes.

evolutionary biology↗