Description:
<jats:title>Summary</jats:title><jats:p>Centromeric chromatin in most eukaryotes is composed of highly repetitive centromeric retrotransposons and satellite repeats that are highly variable even among closely related species. The evolutionary mechanisms that underlie the rapid evolution of centromeric repeats remain unknown. To obtain insight into the evolution of centromeric repeats following polyploidy, we studied a model diploid progenitor (<jats:italic>Gossypium raimondii</jats:italic>, D‐genome) of the allopolyploid (<jats:styled-content style="fixed-case">AD</jats:styled-content>‐genome) cottons, <jats:italic>G. hirsutum</jats:italic> and <jats:italic>G. barbadense</jats:italic>. Sequence analysis of chromatin‐immunoprecipitated <jats:styled-content style="fixed-case">DNA</jats:styled-content> showed that the <jats:italic>G. raimondii</jats:italic> centromeric repeats originated from retrotransposon‐related sequences. Comparative analysis showed that nine of the 10 analyzed centromeric repeats were absent from the centromeres in the A‐genome and related diploid species (B‐, F‐ and G‐genomes), indicating that they colonized the centromeres of D‐genome lineage after the divergence of the A‐ and D‐ ancestral species or that they were ancestrally retained prior to the origin of <jats:italic>Gossypium</jats:italic>. Notably, six of the nine repeats were present in both the A‐ and D‐subgenomes in tetraploid <jats:italic>G. hirsutum</jats:italic>, and increased in abundance in both subgenomes. This finding suggests that centromeric repeats may spread and proliferate between genomes subsequent to polyploidization. Two repeats, Gr334 and Gr359 occurred in both the centromeres and nucleolar organizer regions (<jats:styled-content style="fixed-case">NOR</jats:styled-content>s) in D‐ and <jats:styled-content style="fixed-case">AD</jats:styled-content>‐genome species, yet localized to just the <jats:styled-content style="fixed-case">NOR</jats:styled-content>s in A‐, B‐, F‐, and G‐genome species. Contained within is a story of an established centromeric repeat that is eliminated and allopolyploidization provides an opportunity for reinvasion and reestablishment, which broadens our evolutionary understanding behind the cycles of centromeric repeat establishment and targeting.</jats:p>