Characterization of the Entire Ac/Ds Transposon Family in the Maize Genome

Transposons, recognized today as ubiquitous components of eukaryotic genomes, were first identified six decades ago by their disruption of chromosomal integrity and their mutagenic effects on genes.  The elegant genetic analysis of gene mutations that served as reporters for their movement served to elucidate many transposon properties, but the complexity of transposon families has only been revealed by whole genome sequencing projects.  Here we report on an in-depth analysis of all the sequences in the maize genome that are related to Dissociation (Ds), the first transposon ever described.  Our bioinformatic approach has uncovered over 900 Ds-related sequences, including two novel classes that account for the majority of elements in the family.  These novel elements have diverged significantly from Ds and, though clearly related to Ds, do not appear to transpose in today’s maize genome.  Unlike actively transposing elements, many of the Ds-related elements are inserted in repetitive DNA, where they probably become immobile and begin to decay.  A second maize inbred line shared only half of its Ds insertion sites with B73, suggesting that present-day maize inbred lines differ greatly in their DNA transposon make-up.  The development of gene knock-out tools in maize based on transposons of the Ac/Ds family will also be discussed as well.  A sequence-indexed reverse genetics resource is considered essential to fully exploit the maize genome sequence released in 2009. Our approach to creating such a resource entails generating, sequencing, and indexing new Ac and Ds insertions in maize.