Phase Change and Phenology in Trees

Abstract

The lack of correlation between genome size and organismal complexity was early on dubbed the “C-value Paradox;” it holds even when gene number is considered instead of overall organismal complexity. The sequencing of large eukaryotic genomes has now conclusively solved this conundrum with the demonstration that most nuclear DNA comprises various classes of repeats, primarily transposable elements (TEs). The inherent and variable capacity of the TEs for mobility and replication explains how genome size can vary so greatly on their account. The Class I TEs or retrotransposons have a replication cycle involving the copying of a transcribed, genomic RNA into dsDNA by reverse transcriptase. As a result of their replicative life cycle, the retrotransposons comprise most of large genomes among plants; differences in their prevalence explain most of the variation in genome size on the monoploid level. However, retrotransposons are not only gained through the propagative life cycle described above, but they also can be lost through a combination of progressive small deletions and truncations. The genome of Brachypodium distachyon, at ~372 Mb, is at the lower end of the distribution for flowering plants. The compactness of the B. distachyon genome is correlated with a relatively low number of retrotransposons, although it contains many recently inserted transposable elements. The B. distachyon genome appears to stay trim through recombinational shedding of retrotransposons, despite their continuing propagation. Nevertheless, the chromosomes show remarkable differences among them regarding the gain and loss of retrotransposons over time and the relative accumulation of the two superfamilies, Copia and Gypsy.