Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

International audienceBackground: Transposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri. Results: Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either 'recent' or 'old' insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. Orthologous TE fragments (i.e. those that have been maintained in both species), tend to be located closer to genes than those that are retained in one species only. Compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing nearly neutral TE insertions when they are close to genes. Conclusion: Our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion

Natural occurring epialleles determine vitamin E accumulation in tomato fruits

Vitamin E (VTE) content is a low heritability nutritional trait for which the genetic determinants are poorly understood. Here, we focus on a previously detected major tomato VTE quantitative trait loci (QTL; mQTL9-2-6) and identify the causal gene as one encoding a 2-methyl-6-phytylquinol methyltransferase (namely VTE3(1)) that catalyses one of the final steps in the biosynthesis of γ- and α-tocopherols, which are the main forms of VTE. By reverse genetic approaches, expression analyses, siRNA profiling and DNA methylation assays, we demonstrate that mQTL9-2-6 is an expression QTL associated with differential methylation of a SINE retrotransposon located in the promoter region of VTE3(1). Promoter DNA methylation can be spontaneously reverted leading to different epialleles affecting VTE3(1) expression and VTE content in fruits. These findings indicate therefore that naturally occurring epialleles are responsible for regulation of a nutritionally important metabolic QTL and provide direct evidence of a role for epigenetics in the determination of agronomic traits.L.Q. was recipient of a fellowship of Agencia Nacional de Promoción Científica y Tecnológica and Consejo Nacional de Investigaciones Científicas y Técnicas in Argentina and supported by a postdoctral fellowship from Investissements d’Avenir ANR-10-LABX-54 MEMO LIFE in France. J.A. and L.B. were recipients of a fellowship of Fundação à Amparo da Pesquisa do Estado de São Paulo (Brazil). J.V.C.d.S. was recipient of a fellowship of Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brazil). R.A., L.B. and F.C. are members of Consejo Nacional de Investigaciones Científicas y Técnicas (Argentina). This work was carried out in compliance with current laws governing genetic experimentation in Brazil and in Argentina. This work was supported with grants from Instituto Nacional de Tecnologia Agropecuária, Consejo Nacional de Investigaciones Científicas y Técnicas and Agencia Nacional de Promoción Científica y Tecnológica (Argentina), Fundação à Amparo da Pesquisa do Estado de São Paulo, Conselho Nacional de Desenvolvimento Científico e Tecnológico and Universidade de São Paulo (Brazil); Max Planck Society (Germany); the Agence Nationale de la Recherche (Investissements d’Avenir ANR-10-LABX-54 MEMO LIFE and ANR-11-IDEX-0001-02 PSL* Research University to V.C.); and the European Union (EpiGeneSys FP7 Network of Excellence number 257082 to V.C. and the European Solanaceae Integrated Project FOOD-CT-2006-016214 to F.C., M.R. and A.R.F.)

The contribution of transposable elements to transcriptional novelty in plants: the FLC affair

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Jumpstarting evolution: How transposition can facilitate adaptation to rapid environmental changes

International audienceThe ability of Transposable elements (TEs) to replicate across genomes makes them major generators of large effect mutations. Chromatin-based mechanisms control the mutational potential of TEs in multiple ways, notably by the epigenetic silencing of TE sequences, alleviating the impact of new insertions, and modulating the integration space. Most TE insertions are highly deleterious at the species level, yet some can provide key adaptive variation. Together with their remarkable sensitivity to the environment and precise integration preferences, these unique characteristics place TEs as potent genomic engines of adaptive innovation. Herein, we review recent works exploring the regulation and impact of transposition in nature and discuss their implications for the rapid adaptation of species to drastic environmental changes

Functional analysis of the genetic determinants involved in the vitamine E metabolism in tomato

El conocimiento acerca de los mecanismos fisiológicos y moleculares que determinan la calidad nutricional de los vegetales es de fundamental importancia tanto para el diseño de estrategias de mejoramiento vegetal como para ganar conocimiento en los mecanismos regulatorios del metabolismo secundario. La presente Tesis se focaliza en el estudio de los mecanismos que determinan los contenidos de Vitamina E de los frutos de tomate. Para ello caracterizamos estructuralmente y localizamos en el mapa genético todos los genes involucrados en la biosíntesis de vitamina E e identificamos QTLs para los contenidos de esta vitamina en los frutos de tomate. Así mismo identificamos los principales componentes de la red de regulación a nivel de la expresión génica que opera en la síntesis de vitamina E en tomate a partir del desarrollo de una plataforma de RT-qPCR capaz de evaluar la acumulación de RNA mensajeros para todos los genes de esta ruta biosintética. Adicionalmente y con el objetivo de estudiar funcionalmente genes involucrados en el metabolismo de vitamina E, desarrollamos un sistema de silenciamiento transiente mediado por virus basado en la expresión constitutiva de la proteína verde fluorescente para su silenciamiento como reportero. Por último, nos centramos en la identificación los determinantes genéticos del mayor QTL de vitamina E de tomate localizado durante la primera parte de esta Tesis.Understanding the molecular and physiological mechanisms that determine the quality of vegetables-derived foods is of fundamental importance to design programs centered in plant breeding as well as to gain further insight on regulatory mechanisms of secondary metabolism.In this work we studied the regulatory mechanisms of Vitamin E content of the tomato fruits. We first structurally characterized and mapped all the genes involved in the vitamin E biosynthesis. Furthermore, we developed and take advantage of a RT-qPCR array which allow us to study the major players gene network determining the vitamin E synthesis. Additionally we developed a VIGS (Viral Induced Gene Silencing) system capable of silencing a target gene, coupled to a fluorescent reporter gene. Moreover we used this approach to study the function of several genes presumably involved or related to the vitamin E metabolism. Finally, we identified the molecular factors determining a major QTL of vitamin E in tomato fruit, identified during the first part of this thesis, and localized in the chromosome 9.Fil:Quadrana, Leandro Daniel. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina

Plant Transgenerational Epigenetics

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Shaping inheritance: How distinct reproductive strategies influence DNA methylation memory in plants

International audienceDNA methylation is a major epigenetic mark involved in the silencing of genes and transposable elements (TEs). DNA methylation varies significantly across the plant life cycle, but is efficiently reinforced during reproduction, ensuring stable silencing of TEs. Plants are remarkably flexible in their mode of reproduction and numerous species including crops can propagate asexually, skipping one or more of these critical reinforcement steps. In this review we summarize recent advances in the characterization of DNA methylation inheritance in sexual and asexual plants. We argue that because most epigenetic reinforcement appears to occur during seed formation, methylomes of asexual seeds should resemble that of their sexual counterparts. Conversely, clonally propagated plants are expected to be hypomethylated and undergo frequent stochastic epigenetic changes. Last, we provide insights on how the use of nonmodel organisms will advance our understanding of epigenetic inheritance in plants

Efficient Detection of Transposable Element Insertion Polymorphisms Between Genomes Using Short-Read Sequencing Data

International audienceTransposable 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 the short-read sequencing data that 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

Simultaneous Profiling of Chromatin Accessibility and DNA Methylation in Complete Plant Genomes Using Long-Read Sequencing

ABSTRACT Epigenetic regulations, including chromatin accessibility, nucleosome positioning, and DNA methylation intricately shape genome function. However, current chromatin profiling techniques relying on short-read sequencing technologies face limitations in adequately characterising repetitive genomic regions and detecting multiple chromatin features simultaneously. Here, we present Simultaneous Accessibility and DNA Methylation Sequencing (SAM-seq), a robust method leveraging bacterial adenine methyltransferases (m6A-MTases) to label accessible regions in purified plant nuclei. Coupled with Oxford Nanopore Technology sequencing, SAM-seq enables high-resolution profiling of m6A-tagged chromatin accessibility together with cytosine methylation along chromatin fibres in plants. Analysis of naked genomic DNA revealed significant sequence preference biases of m6A-MTases, controllable through a normalisation step. By applying SAM-seq to Arabidopsis and maize nuclei we obtained fine-grained accessibility and DNA methylation landscapes at genome-wide and local scales. We characterised crosstalk between chromatin accessibility and DNA methylation, notably within nucleosomes of genes, TEs, and centromeric repeats. SAM-seq also facilitated the identification of DNA footprints over cis-regulatory regions. Furthermore, using the single-molecule information provided by SAM-seq we unveiled extensive cellular heterogeneity at chromatin domains harbouring antagonistic chromatin marks, suggesting that bivalency reflects cell-specific regulations of gene activity. In summary, we introduce a robust method for acquiring high-resolution accessibility and DNA methylation landscapes across entire plant genomes. Our results underscore the importance of considering the intrinsic substrate preferences of m6A-MTases for reliable chromatin profiling. SAM-seq opens new opportunities to simultaneously study multiple epigenetic features at unprecedented scale, enabling the investigation of non-model species with limited genomic and epigenomic information