The Plant Nucleus at War and Peace: Genome Organization in the Interphase Nucleus

The interphase nucleus is highly dynamic, anything but the 'resting stage' of the cell cycle. In terms of genome organisation the diploid nucleus is the most 'peaceful' but even here there are differences in structure relative to size, with a blurred border between large (> 5,000 Mbp) small (<1,000 Mbp) genomes. The extent of chromosome territories varies, and virtually every individual of a species has plasticity in its dynamic properties, including non-repetitive copy number, heterochromatic repeats, mobile elements, R-genes and interchromosomal associations. Tensions in the nucleus arise in newly created interspecific hybrids and allopolyploids, where two genomes share a common cytoplasm and experience numerous and rapid interactions, including: loss or gain of sequences, transposon activation, epigenetic changes, interaction of regulatory elements, genome drift and modifications to cell cycling. The story of order and chaos in the plant nucleus is thus incomplete and open-ended, since our current knowledge is based on only a small number of model species. We also have to bear in mind recent findings (e.g. maize and Arabidopsis ) that many diploids, if not all, have a history of having passed through earlier cycles of ploidy events, and still bear the duplications as evidence. New discoveries on genome readjustment in hybrids and allopolyploids have implications for our understanding of genome change in evolution, as well as presenting opportunities for the release of new forms of genetic and epigenetic variation in crop plants.