Biology subjects

Mari-Ordonez, A.

Publications and source records attributed to Mari-Ordonez, A..

5 recordsLinked to original sources

bioRxiv2026

Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis

Genome expansion in angiosperms is largely driven by transposable element (TE) proliferation, counteracted by epigenetic silencing. To investigate how TE amplification reshapes silencing landscapes, we compared two closely related, clonally propagating duckweeds, the TE-rich Wolffia brasiliensis, for which we report a draft genome assembly, and the TE-poor Spirodela polyrhiza, that share a broadly conserved silencing and methylation machinery. W. brasiliensis displays extensive and recent TE amplification with pervasive TE-gene interspersion, elevated genome-wide CG methylation, and high levels of both 22- and 24-nt siRNAs. Systematic cross-species comparison reveals that per-element silencing rules are conserved between the two duckweeds: TE length predicting siRNA-producing capacity, inverted-repeat-forming TEs as productive PTGS-associated loci, 24-nt siRNA production predicting non-CG methylation, and intragenic constraint on RdDM-associated methylation. What differs is the genome-wide deployment of these rules across dramatically different TE loads and genome architectures: some divergent outcomes, including elevated 24-nt siRNA abundance and pervasive TE-wide CG methylation, scale directly with TE content, whereas others: near-exclusive 22-nt processing of PTGS substrates, gene-proximity-dependent RdDM at intergenic TEs, and a strong correlation between gene body CG methylation and intragenic TE content that is not detectable in S. polyrhiza; require additional W. brasiliensis-specific contributions. These findings position TEs as central determinants of the epigenetic architecture that emerges from plant genome expansion, and reveal previously underappreciated plasticity in conserved silencing pathways. Significance statementComparing closely related duckweeds with contrasting TE loads but conserved silencing machinery, we show that per-element silencing rules are shared between the two species while the genome-wide outcomes those rules produce diverge profoundly with TE amplification and genome architecture. This reframes TE proliferation as a determinant not only of genome size but of the epigenetic architecture that emerges from it, uncovers a Wolffia-specific coupling between intragenic TE content and gene body CG methylation, and reveals unexpected plasticity in small RNA biogenesis pathways.

plant biology↗

bioRxiv2025

Strain, procedures, and tools for reproducible genetic transformation and genome editing of Spirodela polyrhiza (L.) Schleid.

Duckweeds (Lemnaceae) have excellent potential for fundamental and applied research due to ease of cultivation, small size, and continuous fast clonal growth. However, their usage as model organisms and platforms for biotechnological applications is often limited by the lack of universal genetic manipulation methods necessary for transgene expression, gene editing, and other methods to modify gene expression. To identify suitable strains for genetic manipulation of the giant duckweed, Spirodela polyrhiza, we screened several genotypes for callus induction and regeneration and established genetic transformation. We have identified SP162 to be amenable to Agrobacterium-mediated transformation via tissue culture. The procedure is robust and reproducible across laboratories, allowing stable expression of different reporter genes and selectable markers, enabling CRISPR/Cas9-mediated genome editing. In addition, due to a weak small RNA-based silencing response, S. polyrhiza sustains prolonged periods of transgene activity in transient expression assays. To promote duckweed research and encourage the adoption of S. polyrhiza, we have made SP162 (ID#: 5676) and its genome publicly available and provide here detailed procedures for its cultivation and transformation. Furthermore, we created a web server to explore its genome, retrieve gene sequences, and implemented orthologous gene search and a gRNA design function for diverse CRISPR/Cas-based applications (https://agxu.uni-mainz.de/SP162/).

plant biology↗

bioRxiv2024

PTGS is dispensable for the initiation of epigenetic silencing of an active transposon in Arabidopsis

Transposable elements (TEs) are largely repressed in plants through transcriptional gene silencing (TGS), which is maintained by heritable epigenetic silencing marks such as DNA methylation. However, the mechanisms by which silencing is installed in the first place remains poorly understood in plants. Small interfering (si)RNAs and post-transcriptional gene silencing (PTGS) play a role in the initial response by reducing mRNA and protein levels of active TEs and are believed to mediate the initiation of TGS by guiding the first deposition of DNA methylation. To determine how this silencing installation works, we took advantage of EVADE (EVD), an endogenous retroelement in Arabidopsis, which can be used to recapitulate true de novo silencing with a well-established sequence of PTGS followed by a TGS phase. To test whether PTGS is a prerequisite for TGS, active EVD copies were introduced into RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) mutants lacking an essential PTGS component. EVD activity and silencing were monitored across several generations. Unexpectedly, even in the absence of PTGS, TGS and silencing of EVD were still achieved through installation of RNA-directed DNA methylation (RdDM) at EVD regulatory sequences without any prior DNA methylation at its coding sequence. Hence, our study shows that PTGS is dispensable for de novo EVD silencing. Although we cannot rule out that PTGS might facilitate the initiation of TGS, or control TE activity until then, initiation of epigenetic silencing can take place in its absence.

plant biology↗

bioRxiv2024

Atypical epigenetic and small RNA control of transposons in clonally reproducing Spirodela polyrhiza.

A handful of model plants have provided insight into silencing of transposable elements (TEs) through RNA-directed DNA methylation (RdDM). Guided by 24-nt long small-interfering RNAs (siRNAs), this epigenetic regulation installs DNA methylation and histone modifications like H3K9me2, which can be subsequently maintained independently of siRNAs. However, the genome of the clonally propagating duckweed Spirodela polyrhiza (Lemnaceae) has low levels of DNA methylation, very low expression of RdDM components, and near absence of 24-nt siRNAs. Moreover, some genes encoding RdDM factors, DNA methylation maintenance, and RNA silencing mechanisms are missing from the genome. Here, we investigated the distribution of TEs and their epigenetic marks in the Spirodela genome. While abundant degenerated TEs have largely lost DNA methylation and H3K9me2 is low, they remain marked by the heterochromatin associated H3K9me1 and H3K27me1 modifications. By contrast, we found high levels of DNA methylation and H3K9me2 in the relatively few intact TEs which are source of 24-nt siRNAs like RdDM-controlled TEs in other angiosperms. The data suggest that, potentially as adaptation to vegetative propagation, RdDM extent, silencing components, and targets are different from other angiosperms, preferentially focused on potentially intact TEs. It also provides evidence for heterochromatin maintenance independently of DNA methylation in flowering plants. These discoveries highlight the diversity of silencing mechanisms that exist in plants and the importance of using disparate model species to discover these mechanisms.

plant biology↗

bioRxiv2021

Innate, translation-dependent silencing of an invasive transposon in Arabidopsis

Co-evolution between hosts and parasites genomes shapes diverse pathways of acquired immunity based on silencing small (s)RNAs. In plants, sRNAs cause heterochromatinization, sequence-degeneration and, ultimately, loss-of-autonomy of most transposable elements (TEs). Recognition of newly-invasive plant TEs, by contrast, involves an innate antiviral-like silencing response. To investigate this responses activation, we studied the single-copy element EVADE (EVD), one of few representatives of the large Ty1/Copia family able to proliferate in Arabidopsis when epigenetically-reactivated. In Ty1/Copia-elements, a short subgenomic mRNA (shGAG) provides the necessary excess of structural GAG protein over the catalytic components encoded by the full-length genomic flGAG-POL. We show here that the predominant cytosolic distribution of shGAG strongly favors its translation over mostly-nuclear flGAG-POL, during which an unusually intense ribosomal stalling event coincides precisely with the starting-point of sRNA production exclusively on shGAG. mRNA breakage occurring at this starting-point yields unconventional 5OH RNA fragments that evade RNA-quality-control and concomitantly likely stimulate RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) to initiate sRNA production. This hitherto-unrecognized "translation-dependent silencing" (TdS) is independent of codon-usage or GC-content and is not observed on TE remnants populating the Arabidopsis genome, consistent with their poor association, if any, with polysomes. We propose that TdS forms a primal defense against de novo invasive TEs that underlies their associated sRNA patterns.

plant biology↗