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Abbreviations 3C Chromosome conformation capture 4C Circularized chromosome conformation capture cenH3 Centromere-specific histone H3 DSB Double-strand break Hi-C Genome conformation capture technique HR Homologous recombination LINC Linker of nucleoskeleton and cytoskeleton NGS Next-generation sequencing NHEJ Non-homologous end joining RdDM RNA-directed DNA methylation SAC Spindle assembly checkpoint smRNA Small RNA TE Transposable element WGD Whole-genome duplication

From transposon to chromosome and polyploidy. An update on cytogenetics and genomics of Arabidopsis