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PMID: 15037733 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Composition and structure of the centromeric region of rice chromosome 8.

The Plant cell ·Vol. 16 ·No. 4 ·2004-04-00 ·Pages 967-76

Wu J, Yamagata H, Hayashi-Tsugane M, Hijishita S, Fujisawa M, Shibata M, Ito Y, Nakamura M, Sakaguchi M, Yoshihara R, Kobayashi H, Ito K, Karasawa W, Yamamoto M, Saji S, Katagiri S, Kanamori H, Namiki N, Katayose Y, Matsumoto T, Sasaki T

Abstract

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.

MeSH Terms
Base Composition Base Sequence Centromere/genetics Chromosomes, Artificial, Bacterial/genetics Chromosomes, Artificial, P1 Bacteriophage/genetics Chromosomes, Plant/genetics Conserved Sequence DNA Transposable Elements/genetics DNA, Plant/chemistry,genetics DNA, Satellite/genetics Genome, Plant Molecular Sequence Data Oryza/genetics Physical Chromosome Mapping Repetitive Sequences, Nucleic Acid
Chemicals
DNA Transposable Elements DNA, Plant DNA, Satellite
Authors & Affiliations
21 authors, click to expand affiliations / ORCID
Wu Jianzhong
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
Hayashi-Tsugane Mika
Hijishita Saori
Fujisawa Masaki
Shibata Michie
Ito Yukiyo
Nakamura Mari
Sakaguchi Miyuki
Yoshihara Rie
Kobayashi Harumi
Ito Kazue
Karasawa Wataru
Yamamoto Mayu
Saji Shoko
Katagiri Satoshi
Kanamori Hiroyuki
Namiki Nobukazu
Katayose Yuichi
Matsumoto Takashi
Sasaki Takuji
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Article Info
Journal
The Plant cell
Abbr.
Plant Cell
ISSN
1040-4651
DOI
10.1105/tpc.019273
Published
2004-04-00
Epub
2004-00-22
Pages
967-76
Language
English
Region
England
NLM ID
9208688
PMCID
PMC412870
Subset
IM
Databases
GENBANK
AB013613, AB033234, AB033235, AF058903, AF058904, AF058905, AF078903, AP004041, AP004228, AP004458, AP004561, AP005162, AP005166, AP005305, AP005407, AP005498, AP005500, AP005540, AP005693, AP005819, AP005832, AP005843, AP006480, AP006481, AP006482, AY129008
External Links
PubMed source DOI: 10.1105/tpc.019273 PMC Full Text View journal details
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