Biology subjects

Movilli, A.

Publications and source records attributed to Movilli, A..

7 recordsLinked to original sources

bioRxiv2026

Multiple redundant mechanisms account for the majority of gene silencing downstream of DNA methylation

DNA methylation is a conserved epigenetic modification crucial for silencing genes and transposable elements (TEs). However, the mechanisms that cause silencing remain unclear, partly because methyl reader protein mutants in both plants and animals show minimal transcriptional changes. To explore the possibility of redundancy among these silencing mechanisms, we generated combinatorial mutants of H1.1, H1.2, ADCP1, MOM1, MBD2, MBD5, and MBD6 lacking key methyl readers and related silencing pathways. We observed massive derepression of genes and TEs at DNA-methylated loci, showing that these pathways account for 73% of silencing compared to DNA methylation-free mutants. We also observed that immune response genes were upregulated, causing an imbalance between growth and defense. Loss of downstream silencing pathways further disrupted 3D genome organization, leading to increased euchromatin-heterochromatin interactions. These findings highlight the cooperative action of multiple downstream mechanisms in DNA methylation-mediated silencing and genome organization.

molecular biology↗

bioRxiv2025

SPOROCYTELESS/NOZZLE acts together with MADS-domain transcription factors to regulate an auxin-dependent network controlling the Megaspore Mother Cell development

The formation of the female gamete is a complex developmental process that begins with the differentiation of the Megaspore Mother Cell (MMC) within the ovule. SPOROCYTELESS/NOZZLE (SPL/NZZ) is the principal regulator of the MMC formation, as mutations in the SPL/NZZ gene lead to the failure of the MMC differentiation. Nonetheless, the SPL/NZZ-dependent regulatory pathway governing the MMC development remains largely unknown. Using a multi-omics approach, we identify direct SPL/NZZ targets and their downstream network. We discovered that SPL/NZZ interacts with ovule-identity MADS-domain transcription factor complexes, to regulate the expression of common target genes. By integrating the omics data with the analysis of either complementation or mutant lines, we describe a comprehensive regulatory mechanism, in which SPL/NZZ determines the differentiation of the MMC by acting on an auxin-dependent downstream network.

plant biology↗

bioRxiv2025

Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals

BackgroundBecause transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypomethylated plants. It is, however, well-known that TEs can also be active in the soma, although the high-confidence detection of somatic events has been challenging. Here, we leveraged the high accuracy of PacBio HiFi long reads to evaluate the somatic mobility of TEs in individuals of an A. thaliana non-reference strain lacking activity of METHYLTRANSFERASE1 (MET1), a major component of the DNA methylation maintenance machinery. Most somatically mobile families coincided with those found in germline studies of hypomethylated genotypes, although the exact TE copies differed. We also discovered mobile elements that had been missed by standard TE annotation methods. Somatic TE activity was variable among individual plants, but also within TE families. Finally, our approach pointed to the possible involvement of alternative transposition as a cause for somatic hypermutability in a region that contains two closely spaced VANDAL21 elements. We conclude that long-read sequencing can reveal widespread TE transposition in the soma of A. thaliana hypomethylated mutants. Assessing somatic instead of germline mobilization is a fast and reliable method to investigate different aspects of TE mobility at the single plant level.

genomics↗

bioRxiv2025

The structure of mitochondrial genomes is associated with geography in Arabidopsis thaliana

Chloroplasts and mitochondria are the primary sites for photosynthesis and respiration, each harboring its own unique genome. Although the organellar genomes are considerably smaller compared to the nuclear genome, they are nonetheless essential for survival of the organism. A common feature of many chloroplast and mitochondrial genomes is the presence of large repeated sequences longer than 1 kb. These can be either in inverted or direct orientation, and recombination between them leads to structural heteroplasmy. To understand the intraspecific evolution of organellar genomes, we assembled chloroplast and mitochondrial genomes of 143 A. thaliana accessions from PacBio HiFi sequencing data. We find large repeats to be associated with heteroplasmy and structural variation. Our extensive genome annotation identifies novel open reading frames (ORFs) in those accessions that lost large repeats, potentially introduced via horizontal gene transfer, illuminating additional paths for diversification of plant organelles. The loss of large repeats correlates with geography and phenotypes, pointing to their adaptive importance. The assembled and annotated organellar genomes constitute a rich source for future functional studies of the interaction between the three genomes of a plant.

evolutionary biology↗

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↗

bioRxiv2023

Atlas of telomeric repeat diversity in Arabidopsis thaliana

Telomeric repeat arrays at the ends of chromosomes are highly dynamic but their repetitive nature and technological limitations have made it difficult to assess the variation in genome diversity surveys. Here we present a comprehensive characterization of the sequence variation immediately adjacent to the canonical telomeric repeat arrays at the very ends of chromosomes in 49 genetically diverse Arabidopsis thaliana accessions. We reveal several types of distinct telomeric repeat units and identify evolutionary processes such as local homogenization and higher-order repeat formation that shape diversity of chromosome ends. The identification of segmental duplications and at least one recombination event suggests a plausible history of telomerase-independent maintenance generation. By comparing largely isogenic samples, we are able to determine variant telomeric repeat number variation at both the germline and somatic levels. Analysis of haplotype structure uncovers chromosome end-specific as well as genetic group-specific patterns in telomeric repeat diversity and provides evidence for linkage disequilibrium between repeat arrays and their adjacent non-coding regions. Together, our findings illustrate the fine-scale telomeric repeat spectrum in A. thaliana, expanding our knowledge of the evolution of chromosome ends.

genomics↗

bioRxiv2023

Transposon dynamics in the emerging oilseed crop Thlaspi arvense

Genome evolution is partly driven by the mobility of transposable elements (TEs) which often leads to deleterious effects, but their activity can also facilitate genetic novelty and catalyze local adaptation. We explored how the intraspecific diversity of TE polymorphisms is shaping the broad geographic success and adaptation capacity of the emerging oil crop Thlaspi arvense. We achieved this by classifying the TE inventory of this species based on a high-quality genome assembly, age estimation of retrotransposon TE families and a comprehensive assessment of their mobilization potential. Our survey of TE insertion polymorphisms (TIPs) captured 280 accessions from 12 regions across the Northern hemisphere. We quantified over 90,000 TIPs, with their distribution mirroring genetic differentiation as measured by single nucleotide polymorphisms (SNPs). The number and types of mobile TE families vary substantially across populations, but there are also shared patterns common to all accessions. We found that Ty3/Athila elements are the main drivers of TE diversity in T. arvense populations, while a single Ty1/Alesia lineage might be particularly important for molding transcriptome divergence. We further observed that the number of retrotransposon TIPs is associated with variation at genes related to epigenetic regulation while DNA transposons are associated with variation at a Heat Shock Protein (HSP19). We propose that the high rate of mobilization activity can be harnessed for targeted gene expression diversification, which may ultimately present a toolbox for the potential use of transposition in breeding and domestication of T. arvense.

genomics↗