RT Journal Article
SR Electronic
T1 Diversity and evolution of centromere repeats in the maize genome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 005058
DO 10.1101/005058
A1 Paul Bilinski
A1 Kevin Distor
A1 Jose Gutierrez-Lopez
A1 Gabriela Mendoza Mendoza
A1 Jinghua Shi
A1 R. Kelly Dawe
A1 Jeffrey Ross-Ibarra
YR 2014
UL http://biorxiv.org/content/early/2014/05/12/005058.abstract
AB Centromere repeats are found in most eukaryotes and play a critical role in kinetochore formation. Though CentC repeats exhibit considerable diversity both within and among species, little is understood about the mechanisms that drive centromere repeat evolution. Here, we use maize as a model to investigate how a complex history involving polyploidy, fractionation, and recent domestication has impacted the diversity of the maize CentC repeat. We first validate the existence of long tandem arrays of repeats in maize and other taxa in the genus Zea. Although we find considerable sequence diversity among CentC copies genome-wide, genetic similarity among repeats is highest within these arrays, suggesting that tandem duplications are the primary mechanism for the generation of new copies. Genetic clustering analyses identify similar sequences among distant repeats, and simulations suggest that this pattern may be due to homoplasious mutation. Although the two ancestral subgenomes of maize have contributed nearly equal numbers of centromeres, our analysis shows that the vast majority of all CentC repeats derive from one of the parental genomes. Finally, by comparing maize with its wild progenitor teosinte, we find that the abundance of CentC has decreased through domestication while the pericentromeric repeat Cent4 has drastically increased.