Maize genome structure and evolution

Abstract

The nuclear genome of maize contains the most complex structure of any yet studied in depth, with small gene islands immersed in seas of nested transposable elements. The DNA between genes is exceptionally unstable in maize, such that the ancestral existence of most or all intergenic TE insertions is erased within a few million years. The genes appear to show a very high mobility that is partly an outcome of the mis-annotation of TEs as genes and the presence of ∼10,000 pseudogenes, compared to ∼35,000 true protein-encoding genes and ∼210,000 TE genes. The primary mechanisms of genomic structural change, namely DNA breakage/repair, recombination and transposition, have been identified. All of these processes have been found to be exceptionally active for genome rearrangement in maize, compared to other angiosperms. Further research is needed on the specificities exhibited by these mechanisms, on the reasons for their very high rates of activity in maize, and on the biological outcomes of this continuous genomic fluidity.