Identification of a genome-specific repetitive element in theGossypiumD genome

Abstract

The activity of genome-specific repetitive sequences is the main cause of genome variation betweenGossypiumA and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termedICRdmotif, which appears frequently in the diploidGossypium raimondii(D5) genome but rarely in the diploidGossypium arboreum(A2) genome. We further explored the existence of theICRdmotif in chromosomes ofG. raimondii,G. arboreum, and two tetraploid (AADD) cotton species,Gossypium hirsutumandGossypium barbadense, by fluorescencein situhybridization (FISH), and observed that theICRdmotif exists in the D5and D-subgenomes but not in the A2and A-subgenomes. TheICRdmotif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. TheICRdmotif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of theICRdmotif promotes the study of A and D genome differences, facilitates research onGossypiumgenome evolution, and provides assistance to subgenome identification and genome assembling.