Composition and structure of the centromeric region of rice chromosome 8.
Understanding the organization of eukaryotic centromeres has both fundamental and applied importance because of their roles in chromosome segregation, karyotypic stability, and artificial chromosome-based cloning and expression vectors. Using clone-by-clone sequencing methodology, we obtained the complete genomic sequence of the centromeric region of rice (Oryza sativa) chromosome 8. Analysis of 1.97 Mb of contiguous nucleotide sequence revealed three large clusters of CentO satellite repeats (68.5 kb of 155-bp repeats) and >220 transposable element (TE)-related sequences; together, these account for approximately 60% of this centromeric region. The 155-bp repeats were tandemly arrayed head to tail within the clusters, which had different orientations and were interrupted by TE-related sequences. The individual 155-bp CentO satellite repeats showed frequent transitions and transversions at eight nucleotide positions. The 40 TE elements with highly conserved sequences were mostly gypsy-type retrotransposons. Furthermore, 48 genes, showing high BLAST homology to known proteins or to rice full-length cDNAs, were predicted within the region; some were close to the CentO clusters. We then performed a genome-wide survey of the sequences and organization of CentO and RIRE7 families. Our study provides the complete sequence of a centromeric region from either plants or animals and likely will provide insight into the evolutionary and functional analysis of plant centromeres.
Wu
Jianzhong
J
Rice Genome Research Program, National Institute of Agrobiological Sciences/Institute of the Society for Techno-Inovation of Agriculture, Forestry, and Fisheries, Tsukuba, Ibaraki 305-8602, Japan.
Yamagata
Harumi
H
Hayashi-Tsugane
Mika
M
Hijishita
Saori
S
Fujisawa
Masaki
M
Shibata
Michie
M
Ito
Yukiyo
Y
Nakamura
Mari
M
Sakaguchi
Miyuki
M
Yoshihara
Rie
R
Kobayashi
Harumi
H
Ito
Kazue
K
Karasawa
Wataru
W
Yamamoto
Mayu
M
Saji
Shoko
S
Katagiri
Satoshi
S
Kanamori
Hiroyuki
H
Namiki
Nobukazu
N
Katayose
Yuichi
Y
Matsumoto
Takashi
T
Sasaki
Takuji
T
D001482:Base Composition; D001483:Base Sequence; D002503:Centromere / Q000235:genetics; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D027042:Chromosomes, Artificial, P1 Bacteriophage / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics*; D017124:Conserved Sequence; D004251:DNA Transposable Elements / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D004276:DNA, Satellite / Q000235:genetics; D018745:Genome, Plant; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D020161:Physical Chromosome Mapping; D012091:Repetitive Sequences, Nucleic Acid
D004251:DNA Transposable Elements; D018744:DNA, Plant; D004276:DNA, Satellite