Identification of a genome-specific repetitive element in the Gossypium D genome

The activity of genome-specific repetitive sequence is the main cause of the genome variation between Gossypium A and D genomes. Through the comparative analysis of the two genomes, we got a repetitive element ( ICRd motif), which repeats massively in the diploid Gossypium raimondii (D 5 ) genome while almost absent in the diploid Gossypium arboreum (A 2 ) genome. We further explored the existence of ICRd motif in G. raimondii , G. arboreum , and two tetraploids (AADD) cotton G. hirsutum and G. barbadense by fluorescence in situ hybridization (FISH), and observed the ICRd motif exists in D 5 and D-subgenomes but not in A 2 and A-subgenome. The ICRd motif was investigated through its two constituents , a length variable tandem repeat region (TR) and a conservative sequence (CS), which highly repeat and evenly distribute in chromosomes of D 5 genome. The ICRd motif was revealed as the common conservative region of ancient LTR-TEs. The identifications and investigation of the ICRd motif promote the study on the A and D genome differences, facilitate the research on the Gossypium genome evolution, and provide assistance to subgenome identification and genome assembling.