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Comparative analysis of complete orthologous centromeres from two subspecies of rice reveals rapid variation of centromere organization and structure
Author(s) -
Wu Jianzhong,
Fujisawa Masaki,
Tian Zhixi,
Yamagata Harumi,
Kamiya Kozue,
Shibata Michie,
Hosokawa Satomi,
Ito Yukiyo,
Hamada Masao,
Katagiri Satoshi,
Kurita Kanako,
Yamamoto Mayu,
Kikuta Ari,
Machita Kayo,
Karasawa Wataru,
Kanamori Hiroyuki,
Namiki Nobukazu,
Mizuno Hiroshi,
Ma Jianxin,
Sasaki Takuji,
Matsumoto Takashi
Publication year - 2009
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/j.1365-313x.2009.04002.x
Subject(s) - retrotransposon , biology , centromere , genetics , subspecies , long terminal repeat , chromosome , oryza sativa , japonica , genome , transposable element , gene , botany , paleontology
Summary 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.