title: Repeatless and repeat-based centromeres in potato: implications for centromere evolution.
abstract: Centromeres in most higher eukaryotes are composed of long arrays of satellite repeats. By contrast, most newly formed centromeres (neocentromeres) do not contain satellite repeats and instead include DNA sequences representative of the genome. An unknown question in centromere evolution is how satellite repeat-based centromeres evolve from neocentromeres. We conducted a genome-wide characterization of sequences associated with CENH3 nucleosomes in potato (Solanum tuberosum). Five potato centromeres (Cen4, Cen6, Cen10, Cen11, and Cen12) consisted primarily of single- or low-copy DNA sequences. No satellite repeats were identified in these five centromeres. At least one transcribed gene was associated with CENH3 nucleosomes. Thus, these five centromeres structurally resemble neocentromeres. By contrast, six potato centromeres (Cen1, Cen2, Cen3, Cen5, Cen7, and Cen8) contained megabase-sized satellite repeat arrays that are unique to individual centromeres. The satellite repeat arrays likely span the entire functional cores of these six centromeres. At least four of the centromeric repeats were amplified from retrotransposon-related sequences and were not detected in Solanum species closely related to potato. The presence of two distinct types of centromeres, coupled with the boom-and-bust cycles of centromeric satellite repeats in Solanum species, suggests that repeat-based centromeres can rapidly evolve from neocentromeres by de novo amplification and insertion of satellite repeats in the CENH3 domains.
authors.affiliation: Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Zhiyun
authors.initials: Z
authors.lastname: Gong
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Wu
authors.forename: Andrea
authors.initials: A
authors.lastname: Koblízková
authors.forename: Giovana A
authors.initials: GA
authors.lastname: Torres
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.forename: Marina
authors.initials: M
authors.lastname: Iovene
authors.forename: Pavel
authors.initials: P
authors.lastname: Neumann
authors.forename: Wenli
authors.initials: W
authors.lastname: Zhang
authors.forename: Petr
authors.initials: P
authors.lastname: Novák
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
authors.forename: Jirí
authors.initials: J
authors.lastname: Macas
authors.forename: Jiming
authors.initials: J
authors.lastname: Jiang
mesh_terms: D001483:Base Sequence; D002503:Centromere / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D004276:DNA, Satellite / Q000235:genetics*; D019143:Evolution, Molecular; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D009707:Nucleosomes / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA; D011198:Solanum tuberosum / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D004276:DNA, Satellite; D006657:Histones; D009707:Nucleosomes; D010940:Plant Proteins