Structure and evolution of the centromere of chromosome 8 in three Oryza species

Centromeres are often composed of rapidly evolving tandem repeated sequences and retrotransposons, and are critical for proper chromosome segregation. The functional domain of centromeres is defined by the presence of a centromere-specific histone H3 variant, CENH3. The single copy CenH3 gene was found to evolve under positive selection in several species, which was hypothesized to be in response to the rapidly changing DNA sequences associated with centromeres.;The expression and evolution of CenH3 genes in two allotetraploid rice species, along with their diploid progenitor species was investigated. Two distinct copies of CenH3 were actively transcribed in the allotetraploid species, in a nonpreferential pattern. Lineage-specific evolution of contrasting adaptive and stabilizing selection of the CenH3 genes was associated with different diploid species and maintained in the allotetraploid species. This demonstrates that allopolyploidization events did not alter the expression or evolutionary pattern of CenH3 genes in the Oryza species.;The functional domain of the centromere of chromosome 8 (Cen8) in Oryza glaberrima and O. brachyatha was mapped using chromatin immunoprecipitation with CENH3 antibodies combined with 454 sequencing. The sequence reads were mapped to Cen8 and the short arm of chromosome 3 of the two species. Combined with previously published CENH3 mapping in O. sativa Cen8, the CENH3-binding domain in Cen8 across the Oryza species was static in size, even though the size of the satellite array at the centromeres varied by a factor of five or ten between the species. In addition, some sequences not binding CENH3 in O. sativa Cen8 bind with CENH3 in O. glaberrima.;To study the diversity of centromere tandem repeats across Oryza species a k-mer frequency reconstruction method for CENH3 ChIP-seq datasets was used. Conserved regions in tandem repeats were found between species, which could be important for centromere function. The consensus sequence of the tandem repeat, the diversity within and between species, regions of conservation, and evolution was reported.;The data presented expands upon previous centromere research to multiple Oryza species. This novel and unique orthologous centromere research strategy allowed CENH3 domains and tandem repeat diversity within centromeres to be better understood.