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.[Supplemental material is available online at http://www.genome.org. The RepeatNet algorithm is freely available at

Sequences Associated with Centromere Competency in the Human Genome

“…All identified CENP-B boxes were characterized relative to their distance from the alpha satellite consensus CENP-B motif (CTTCGTTG GAAACGGGA) (24,25) and estimated density per 10-kb sliding window. A total of 2,018 CENP-B boxes were initially defined; however, 35% appeared to be highly divergent (defined as more than five differences from the CENP-B box consensus, with all nine critical bases correctly identified) and largely associated with non-alpha satellite regions of the genome (802 divergent CENP-B boxes were detected outside alpha satellite regions in low density, defined as a single motif identified in a 20-kb window).…”

Reconstructing complex regions of genomes using long-read sequencing technology

“…Although we can generate much more sequence, the short sequence read data and inability to scaffold across repetitive structures translates into more gaps, missing data, and more incomplete reference assemblies (Alkan et al 2011a;Salzberg et al 2012). Due to budgetary constraints, traditional capillary-based sequencing capacity as well as genome finishing efforts have dwindled in sequencing centers leaving most of the complex regions of working draft genomes unresolved.…”

Centromere Evolution: Digging into Mammalian Primary Constriction

“…Recently dog fosmid clones containing satellite DNA were mapped to the centromere of a different subgroup of dog chromosomes. These heterogeneous patterns support the existence of a complex patchwork organization of satellites at dog centromeres, similar to horse centromeric sequence organization (Alkan et al, 2010). …”

“…Alkan and colleagues extracted six distinct satellite consensus sequences in the E. caballus genome of 221, 221, 419, 450, 451, and 475 bp, respectively. Their FISH hybridization patterns included the centromeres of all or a part of horse chromosomes except chromosome 11 (Alkan et al, 2010). All horse centromeres have either one or more than one satellite whereas horse chromosome 11 is the only one lacking any satellite (Alkan et al, 2010;Piras et al, 2010;Wade et al, 2009).…”

“…In 2010, Alkan and colleagues included in their list of sequenced mammalian genomes to analyze in regard to centromeric satellite sequences, the armadillo (Dasypus novemcinctus), a species of the superorder Xenarthra, order Cingulata, and the African elephant (Loxodonta africana), a species of the superorder Afrotheria, order Proboscidea. Using the RepeatNet algorithm, they extracted a 173 bp satellite consensus from the armadillo genome and a 1220 bp satellite consensus from the African elephant genome, and localized both satellites at the centromere of all chromosomes of the corresponding species (Alkan et al, 2010).…”