Arbuscular Mycorrhizal Symbiosis Limits Foliar Transcriptional Responses to Viral Infection and Favors Long-Term Virus Accumulation

Tomato (Solanum lycopersicum) can establish symbiotic interactions with arbuscular mycorrhizal (AM) fungi, and can be infected by several pathogenic viruses. Here, we investigated the impact of mycorrhization by the fungus Glomus mosseae on the Tomato spotted wilt virus (TSWV) infection of tomato plants by transcriptomic and hormones level analyses. In TSWV-infected mycorrhizal plants, the AM fungus root colonization limited virus-induced changes in gene expression in the aerial parts. The virus-responsive upregulated genes, no longer induced in infected mycorrhizal plants, were mainly involved in defense responses and hormone signaling, while the virus-responsive downregulated genes, no longer repressed in mycorrhizal plants, were involved in primary metabolism. The presence of the AM fungus limits, in a salicylic acid-independent manner, the accumulation of abscissic acid observed in response to viral infection. At the time of the molecular analysis, no differences in virus concentration or symptom severity were detected between mycorrhizal and nonmycorrhizal plants. However, in a longer period, increase in virus titer and delay in the appearance of recovery were observed in mycorrhizal plants, thus indicating that the plant's reaction to TSWV infection is attenuated by mycorrhization. </jats:p

The role of mobile DNA elements in the dynamic of plants genome plasticity

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

EpiRILs

International audienceIn recent times, epigenetic marks have emerged as important players involved in the regulation of gene expression and transposable element silencing in many organisms. In plants, many epigenetic changes, mainly at the level of DNA methylation, are transgenerational stable and contribute to formation of epialleles, affecting developmental and agronomical traits. In this scenario, it becomes critical to differentiate the genetic from the epigenetic contribution to plant phenotypes. In Arabidopsis, epigenetic Recombinant Inbred Lines (epiRILs), obtained by an initial cross of isogenic parents with different DNA methylation profiles, provide a powerful tool to investigate the role and significance of epigenetic alteration in identical or almost identical genetic backgrounds. Such populations have greatly increased our knowledge in mechanisms involved in epialleles formation and stability, as well as in the consequences of DNA methylation changes in genomic stability, transposable elements activation and phenotypic traits

Long distance signalling and epigenetic changes in crop grafting

Humans have used grafting for more than 4000 years to improve plant production, through physically joining two different plants, which can continue to grow as a single organism. Today, grafting is becoming increasingly more popular as a technique to increase the production of herbaceous horticultural crops, where rootstocks can introduce traits such as resistance to several pathogens and/or improving the plant vigour. Research in model plants have documented how long-distance signalling mechanisms across the graft junction, together with epigenetic regulation, can produce molecular and phenotypic changes in grafted plants. Yet, most of the studied examples rely on proof-of-concept experiments or on limited specific cases. This review explores the link between research findings in model plants and crop species. We analyse studies investigating the movement of signalling molecules across the graft junction and their implications on epigenetic regulation. The improvement of genomics analyses and the increased availability of genetic resources has allowed to collect more information on potential benefits of grafting in horticultural crop models. Ultimately, further research into this topic will enhance our ability to use the grafting technique to exploit genetic and epigenetic variation in crops, as an alternative to traditional breeding

DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts

DNA methylation has been associated with transcriptional repression and detection of differential methylation is important in understanding the underlying causes of differential gene expression. Bisulfite-converted genomic DNA sequencing is the current gold standard in the field for building genome-wide maps at a base pair resolution of DNA methylation. Here we systematically investigate the underlying features of detecting differential DNA methylation in CpG and non-CpG contexts, considering both the case of mammalian systems and plants. In particular, we introduce DMRcaller, a highly efficient R/Bioconductor package, which implements several methods to detect Differentially Methylated Regions (DMRs) between two samples. Most importantly, we show that different algorithms are required to compute DMRs and the most appropriate algorithm in each case depends on the sequence context and levels of methylation. Furthermore, we show that DMRcaller outperforms other available packages and we propose a new method to select the parameters for this tool and for other available tools. DMRcaller is a comprehensive tool for differential methylation analysis which displays high sensitivity and specificity for the detection of DMRs and performs entire genome wide analysis within a few hours

Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies

Methylation of cytosine is an epigenetic mark involved in the regulation of transcription, usually associated with transcriptional repression. In mammals, methylated cytosines are found predominantly in CpGs but in plants non-CpG methylation (in the CpHpG or CpHpH contexts, where H is A, C or T) is also present and is associated with the transcriptional silencing of transposable elements. In addition, CpG methylation is found in coding regions of active genes. In the absence of the demethylase of lysine 9 of histone 3 (IBM1), a subset of body-methylated genes acquires non-CpG methylation. This was shown to alter their expression and affect plant development. It is not clear why only certain body-methylated genes gain non-CpG methylation in the absence of IBM1 and others do not. Here we describe a link between CpG methylation and the establishment of methylation in the CpHpG context that explains the two classes of body-methylated genes. We provide evidence that external cytosines of CpCpG sites can only be methylated when internal cytosines are methylated. CpCpG sites methylated in both cytosines promote spreading of methylation in the CpHpG context in genes protected by IBM1. In contrast, CpCpG sites remain unmethylated in IBM1-independent genes and do not promote spread of CpHpG methylation.</p

Specific suppression of long terminal repeat retrotransposon mobilization in plants

The tissue culture passage necessary for the generation of transgenic plants induces genome instability. This instability predominantly involves the uncontrolled mobilization of LTR retrotransposons (LTR-TEs), which are the most abundant class of mobile genetic elements in plant genomes. Here, we demonstrate that in conditions inductive for high LTR-TE mobilization, like abiotic stress in Arabidopsis (Arabidopsis thaliana) and callus culture in rice (Oryza sativa), application of the reverse transcriptase (RT) inhibitor known as Tenofovir substantially affects LTR-TE RT activity without interfering with plant development. We observed that Tenofovir reduces extrachromosomal DNA accumulation and prevents new genomic integrations of the active LTR-TE ONSEN in heat-stressed Arabidopsis seedlings, and transposons of O. sativa 17 and 19 (Tos17 and Tos19) in rice calli. In addition, Tenofovir allows the recovery of plants free from new LTR-TE insertions. We propose the use of Tenofovir as a tool for studies of LTR-TE transposition and for limiting genetic instabilities of plants derived from tissue culture.</p

Plant epigenetics: controlling genome expression to integrate developmental and environmental cues

Gene expression changes induced in response to developmental and environmental cues, as well as the maintenance and inheritance of these altered expression states, require epigenetic regulation. Epigenetic mechanisms comprise modifications at the chromatin level, including DNA methylation and alterations in nucleosome organization through the incorporation of specific histone variants and their post-translational modifications, as well as the involvement of various non-coding RNAs. Many of these processes and factors are evolutionarily conserved, while others are specific to photosynthetic organisms. This Special Issue is published in association with the EPIPLANT/SEB conference 2024 and the sessions dedicated to epigenetic plasticity and plant epigenetics at the SEB Prague 2024 conference, which brought together researchers working in model and crop species. It comprises reviews and original articles discussing insights into the epigenetic mechanisms in plants and other photosynthetic organisms, as well as avenues to improve their adaptability to the changing environment