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Genome-Wide Characterization of Centromeric Satellites from Multiple Mammalian Genomes
Genome Research
  • Can Alkan, University of Washington - Seattle
  • Maria Francesca Cardone, University of Bari - Italy
  • Claudia Rita Catacchio, University of Bari - Italy
  • Francesca Antonacci, University of Washington - Seattle
  • Stephen J. O'Brien, National Cancer Institute at Frederick
  • Oliver A. Ryder, Zoological Society of San Diego
  • Stefania Purgato, University of Bologna - Italy
  • Monica Zoli, University of Bologna - Italy
  • Evan E. Eichler, University of Washington - Seattle
  • Mario Ventura, University of Washington - Seattle; University of Bari - Italy
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Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.


©2011 by Cold Spring Harbor Laboratory Press

Citation Information
Can Alkan, Maria Francesca Cardone, Claudia Rita Catacchio, Francesca Antonacci, et al.. "Genome-Wide Characterization of Centromeric Satellites from Multiple Mammalian Genomes" Genome Research Vol. 21 Iss. 1 (2011) p. 137 - 145 ISSN: 1088-9051
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