title: Genome-wide characterization of centromeric satellites from multiple mammalian genomes.
abstract: 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.
authors.affiliation: Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington 98195, USA.
authors.forename: Can
authors.initials: C
authors.lastname: Alkan
authors.forename: Maria Francesca
authors.initials: MF
authors.lastname: Cardone
authors.forename: Claudia Rita
authors.initials: CR
authors.lastname: Catacchio
authors.forename: Francesca
authors.initials: F
authors.lastname: Antonacci
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: O'Brien
authors.forename: Oliver A
authors.initials: OA
authors.lastname: Ryder
authors.forename: Stefania
authors.initials: S
authors.lastname: Purgato
authors.forename: Monica
authors.initials: M
authors.lastname: Zoli
authors.forename: Giuliano
authors.initials: G
authors.lastname: Della Valle
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
authors.forename: Mario
authors.initials: M
authors.lastname: Ventura
mesh_terms: D000818:Animals; D001135:Armadillos / Q000235:genetics; D001483:Base Sequence; D002503:Centromere / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D016384:Consensus Sequence; D004276:DNA, Satellite / Q000235:genetics*; D004285:Dogs / Q000235:genetics; D004606:Elephants / Q000235:genetics; D016678:Genome / Q000235:genetics*; D006736:Horses / Q000235:genetics; D008322:Mammals / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D009893:Opossums / Q000235:genetics; D010987:Platypus / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D004276:DNA, Satellite