Repetitive Sequences: Impacts and Uses in the Spirodela Genome

Repetitive DNA, consisting of small and large satellite repeats and transposable elements, comprises over 50% of most plant genomes. The Lemnaceae family demonstrates a ~12-fold difference in genome size and relatively similar number of genes, indicating a wide variability in repeat content. The best studied genome of the family Spirodela polyrhiza had a normal total satellite DNA content, yet a surprisingly high 50% of those were dinucleotide microsatellite repeats. The telomeres and 119 bp centromere repeats were typical, although ribosomal repeats appear scarce. Genomic studies showed a small number of 24nt heterochromatic siRNAs accompanied by the lowest rate of DNA methylation seen in any plant sequenced at 9% and low rates of heterochromatin formation. Despite this low level of regulation, the transposable elements are unexpectedly rare and old. In fact, they even show high rates of DNA methylation and high rates of inactivation through illegitimate recombination. This suggests that the scarce 24nt siRNAs are surprisingly effective and an intriguing topic of further research.