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The generation of mitotically stable alterations in gene expression due to epigenetic marks is a fast and relatively long-lasting manner for stablishing a genomic memory of past stress events. Environment-triggered deregulation of genetic factors associated with epigenetic machineries can also lead to phenotypic plasticity and stress mitigation. Therefore, host’s epigenetic machinery can pose an important but largely unmeasured selective pressure on pathogens. Plant viruses offer a convenient model for studying this kind of interactions. Firstly, a large-scale evolution experiment for checking how virus populations evolve and interact in plants with compromised or enhanced epigenetic pathways is proposed. Arabidopsis thaliana plants with mutations in key genes associated with active or repressive chromatin marks, including DNA methylation and histone modification, will be challenged against independent lineages of turnip mosaic potyvirus (TuMV).
Massively parallel or next-generation sequencing (NGS) has been a revolution in genetic studies, having important applications in research and in clinics. Some are the study of the genome, transcriptome, microbiome, methylome, genetic diagnosis and personalised medicine, such as pharmacogenetics and the detection of somatic tumour markers, studies of tumour mutations in circulating DNA, determination of the mutation rate for oncology immunotherapy studies. An important application is the study of specific regions of the genome for many clinical or research studies, mainly of one or several genes (NGS panel) due to the high costs of genome-wide studies.