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Diversity and evolution of centromere repeats in the maize genome

Paul Bilinski, Kevin Distor, Jose Gutierrez-Lopez, Gabriela Mendoza Mendoza, Jinghua Shi, R. Kelly Dawe, Jeffrey Ross-Ibarra
doi: https://doi.org/10.1101/005058
Paul Bilinski
1Department of Plant Sciences, UC Davis, Davis, California, 95616
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Kevin Distor
1Department of Plant Sciences, UC Davis, Davis, California, 95616
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Jose Gutierrez-Lopez
1Department of Plant Sciences, UC Davis, Davis, California, 95616
3Department of Natural Resources and the Environment University of New Hampshire Durham, New Hampshire, 03820
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Gabriela Mendoza Mendoza
1Department of Plant Sciences, UC Davis, Davis, California, 95616
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Jinghua Shi
4Department of Plant Biology, University of Georgia Athens, Georgia, 30602
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R. Kelly Dawe
4Department of Plant Biology, University of Georgia Athens, Georgia, 30602
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Jeffrey Ross-Ibarra
1Department of Plant Sciences, UC Davis, Davis, California, 95616
2The Genome Center and Center for Population Biology, University of California Davis, California, 95616
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Abstract

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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 12, 2014.
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Diversity and evolution of centromere repeats in the maize genome
Paul Bilinski, Kevin Distor, Jose Gutierrez-Lopez, Gabriela Mendoza Mendoza, Jinghua Shi, R. Kelly Dawe, Jeffrey Ross-Ibarra
bioRxiv 005058; doi: https://doi.org/10.1101/005058
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Diversity and evolution of centromere repeats in the maize genome
Paul Bilinski, Kevin Distor, Jose Gutierrez-Lopez, Gabriela Mendoza Mendoza, Jinghua Shi, R. Kelly Dawe, Jeffrey Ross-Ibarra
bioRxiv 005058; doi: https://doi.org/10.1101/005058

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