Comparative genomics of a rice centromere across 3 species of Oryza.

摘要

Centromeres are found on all chromosomes of eukaryotes studied to date and are absolutely necessary for sister chromatid cohesion, kinetochore assembly and faithful chromatid segregation. Given their ubiquitous presence, we know surprisingly very little regarding the formation, constituents and evolutionary dynamics of functional centromeres. This is largely due to the fact that centromeres are difficult subjects to study, particularly at the DNA level. They are buried in heterochromatin, contain characteristically long tracts of homogenized repetitive DNA and are riddled with retroelements. For these reasons, the vast majority of "complete" genome sequences produced to date, including human and Arabidopsis thaliana, do not include the sequences underlying the functional centromeres. Currently the only distinguishing molecular feature of a centromere is a centromere-specific histone (CENH3), which is loaded onto nucleosomes underlying the kinetochore.;The centromere of chromosome 8 (Cen8) in rice ( Oryza sativa) was the first centromere in higher eukaryotes to have been completely sequenced. Cen8 in rice resembles neocentromeres in that it contains limited satellite DNA and genic regions that support transcription. For these reasons, Cen8 in rice is not considered a fully mature centromere, but rather has been proposed to reside developmentally, somewhere between a newly formed neocentromere and a satellite dominated mature centromere.;In this dissertation I used Cen8 in O. sativa as a model to study the structure of the orthologous Cen8 in three related species of Oryza: O. glaberrima, O. punctata , and O. brachyantha that together shared a common ancestor over 15 million years ago. The results from this study suggest that during centromere evolution: 1) the satellite DNA can change substantially in size and sequence; 2) the size of the region bound with CENH3 nucleosomes has remained static between two species; and 3) that gene transcription of all conserved orthologs within the centromere region is maintained across these species. Together these data paint a picture of an evolving centromere that fits the model of neocentromere development via the accumulation of centromere satellite repeats.