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GrainGenes Reference Report: PLC-16-967

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Reference	PLC-16-967
Title	Composition and structure of the centromeric region of rice chromosome 8
Journal	Plant Cell
Year	2004
Volume	16
Pages	967-976
Author	Wu JZ [ Show all 21 ]
Abstract	Summary: 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 ~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
External Databases	Pubmed: 15037733
Keyword	[ Hide all but 1 of 47 ] alpha-satellite dna apr blast cdna centromeric region chromosome cloning cluster composition conserved sequences evolutionary evolutionary dynamics family full-length cdna functional-analysis gene genetic definition genome evolution homology linkage map maize methodology nucleotide organization orientation oryza oryza sativa oryza sativum plant centromeres position repetitive dna retrotransposon retrotransposons rice roles saccharomyces cerevisiae satellite satellite repeat segregation sequence sequence organization stability structure transition transposable element vector vectors

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