title: Comparative analysis of complete orthologous centromeres from two subspecies of rice reveals rapid variation of centromere organization and structure.
abstract: Centromeres are sites for assembly of the chromosomal structures that mediate faithful segregation at mitosis and meiosis. This function is conserved across species, but the DNA components that are involved in kinetochore formation differ greatly, even between closely related species. To shed light on the nature, evolutionary timing and evolutionary dynamics of rice centromeres, we decoded a 2.25-Mb DNA sequence covering the centromeric region of chromosome 8 of an indica rice variety, 'Kasalath' (Kas-Cen8). Analysis of repetitive sequences in Kas-Cen8 led to the identification of 222 long terminal repeat (LTR)-retrotransposon elements and 584 CentO satellite monomers, which account for 59.2% of the region. A comparison of the Kas-Cen8 sequence with that of japonica rice 'Nipponbare' (Nip-Cen8) revealed that about 66.8% of the Kas-Cen8 sequence was collinear with that of Nip-Cen8. Although the 27 putative genes are conserved between the two subspecies, only 55.4% of the total LTR-retrotransposon elements in 'Kasalath' had orthologs in 'Nipponbare', thus reflecting recent proliferation of a considerable number of LTR-retrotransposons since the divergence of two rice subspecies of indica and japonica within Oryza sativa. Comparative analysis of the subfamilies, time of insertion, and organization patterns of inserted LTR-retrotransposons between the two Cen8 regions revealed variations between 'Kasalath' and 'Nipponbare' in the preferential accumulation of CRR elements, and the expansion of CentO satellite repeats within the core domain of Cen8. Together, the results provide insights into the recent proliferation of LTR-retrotransposons, and the rapid expansion of CentO satellite repeats, underlying the dynamic variation and plasticity of plant centromeres.
authors.affiliation: Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
authors.forename: Jianzhong
authors.initials: J
authors.lastname: Wu
authors.forename: Masaki
authors.initials: M
authors.lastname: Fujisawa
authors.forename: Zhixi
authors.initials: Z
authors.lastname: Tian
authors.forename: Harumi
authors.initials: H
authors.lastname: Yamagata
authors.forename: Kozue
authors.initials: K
authors.lastname: Kamiya
authors.forename: Michie
authors.initials: M
authors.lastname: Shibata
authors.forename: Satomi
authors.initials: S
authors.lastname: Hosokawa
authors.forename: Yukiyo
authors.initials: Y
authors.lastname: Ito
authors.forename: Masao
authors.initials: M
authors.lastname: Hamada
authors.forename: Satoshi
authors.initials: S
authors.lastname: Katagiri
authors.forename: Kanako
authors.initials: K
authors.lastname: Kurita
authors.forename: Mayu
authors.initials: M
authors.lastname: Yamamoto
authors.forename: Ari
authors.initials: A
authors.lastname: Kikuta
authors.forename: Kayo
authors.initials: K
authors.lastname: Machita
authors.forename: Wataru
authors.initials: W
authors.lastname: Karasawa
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kanamori
authors.forename: Nobukazu
authors.initials: N
authors.lastname: Namiki
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Mizuno
authors.forename: Jianxin
authors.initials: J
authors.lastname: Ma
authors.forename: Takuji
authors.initials: T
authors.lastname: Sasaki
authors.forename: Takashi
authors.initials: T
authors.lastname: Matsumoto
mesh_terms: D001483:Base Sequence; D002503:Centromere / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D032461:Chromosomes, Plant; D017124:Conserved Sequence; D014644:Genetic Variation; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics* / Q000378:metabolism / Q000648:ultrastructure; D017422:Sequence Analysis, DNA