Zea mays subsp. mays Genome sequencing. Zea mays subsp. mays

Because transposable elements (TEs) constitute most angiosperm nuclear DNA, the interaction between TEs and their host genome is a key component for understanding the function and evolution of plant genomes. The diversity of the host response has been studied a great deal, including the biogenesis of small interfering RNAs (siRNAs) that target TEs for epigenetic modifications. However, little is known about variation in TE content among closely related genomes and whether siRNA expression tracks this variation. To that end, we surveyed both the copy number and the siRNA targeting of more than 1500 distinct TE subfamilies in the B73 maize reference genome. These surveys indicated that TE subfamilies fall naturally into three distinctive groups based on their class and copy number, but these groups also differ with respect to their location in the genome, their age, their expression and their siRNA regulation. The presence and consistency of these TE groups was also assessed in two genetically distant maize landraces with contrasting genome sizes. The variation in siRNA targeting across different TE groups and families, as well as the lack of correlation between TE and siRNA abundances, argues for the existence of multiple mechanisms and strategies for TE silencing.