Maize genome structure and rearrangement

The maize genome contains a complex mix- ture of genes, transposons, tandem repeats and other se- quences of unknown origin or function. The maize genome is unsurpassed among well-studied species in its level of cytogenetic, genetic and molecular diversity. Much of this diversity arises from variation in the distribu- tion of transposable elements, including elements that ac- cumulate between gene islands (most LTR-retrotrans- posons) and elements that are primarily found near or in- side genes (most DNA elements). Maize genes number about 36,000-63,000, or less than 8% of the ~2400 Mb haploid genome. A very large number, perhaps as high as 40%, of the gene homologues detected in maize are pre- dicted to have the truncated or otherwise mutated struc- tures of apparent pseudogenes. The intact genes are usu- ally found in islands that contain only one gene, sur- rounded by the seas of LTR-retrotransposons that account for >65% of the maize genome. DNA transposons, LTR- retrotransposons and Helitrons have acquired portions of many maize genes and moved them about the genome. Although most of these mobile DNAs are usually silenced by epigenetic and progressive mutational processes, it is clear that they have provided (and continue to provide) the raw material from which the maize genome and its genic constitution have been assembled.