Evolution of interspersed repetitive elements in Gossypium (Malvaceae).

Very little is known regarding how repetitive elements evolve in polyploid organisms. Here we address this subject by fluorescent in situ hybridization (FISH) of 20 interspersed repetitive elements to metaphase chromosomes of the cotton AD-genome tetraploid Gossypium hirsutum and its putative A- and D-genome diploid ancestors. These elements collectively represent an estimated 18\\% of the G. hirsutum genome, and constitute the majority of high-copy interspersed repetitive elements in G. hirsutum. Seventeen of the elements yielded FISH signals on chromosomes of both G. hirsutum subgenomes, while three were A-subgenome specific. Hybridization of eight selected elements, two of which were A-subgenome specific, to the A2 genome of G. arboreum yielded a signal distribution that was similar to that of the G. hirsutum A-subgenome. However, when hybridized to the D5 genome of G. raimondii, the putative diploid ancestor of the G. hirsutum D-subgenome, none of the probes, including elements that strongly hybridized to both G. hirsutum subgenomes, yielded detectable signal. The results suggest that the majority, although not all, G. hirsutum interspersed repetitive elements have undergone intergenomic concerted evolution following polyploidization and that this has involved colonization of the D-subgenome by A-subgenome elements and/or replacement of D-subgenome elements by elements of the A-subgenome type.