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DNA Research Advance Access published online on February 12, 2007
DNA Research, doi:10.1093/dnares/dsm001
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© The Author 2007. Kazusa DNA Research Institute.
Received November 2, 2006
Revised January 14, 2007

Full Papers

Identification and Mapping of Expressed Genes, Simple Sequence Repeats and Transposable Elements in Centromeric Regions of Rice Chromosomes

Hiroshi Mizuno 1, Kazue Ito 2, Jianzhong Wu 1, Tsuyoshi Tanaka 1, Hiroyuki Kanamori 2, Yuichi Katayose 1, Takuji Sasaki 1, and Takashi Matsumoto 1 *

1 National Institute of Agrobiological Sciences, 1-2, Kannondai 2-chome, Tsukuba, Ibaraki 305-8602, Japan
2 Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan

* To whom correspondence should be addressed.
Takashi Matsumoto, E-mail: mat{at}nias.affrc.go.jp


  Abstract

The genomic sequences derived from rice centromeric regions were analyzed to facilitate the comprehensive understanding of the rice genome. A rice centromere-specific satellite sequence, RCS2/TrsD/CentO, was used to screen P1-derived artificial chromosome (PAC) and bacterial artificial chromosome (BAC) genomic libraries derived from Oryza sativa L. ssp. japonica cultivar Nipponbare. Physical maps of the centromeric regions were constructed by DNA fingerprinting methods and the aligned clones were analyzed by end sequencing. BLAST analysis revealed the composition of genes, centromeric satellites and other repetitive elements, such as RIRE7/CRR, RIRE8, Squiq, Anaconda, CACTA and miniature inverted-repeat transposable elements. Fiber-fluorescent in situ hybridization analysis also indicated the presence of distinct clusters of RCS2/TrsD/CentO satellite interspersed with other elements, instead of a long homogeneous region. Several expressed genes, sequences representative of ancestral organellar insertions, relatively long simple sequence repeats (SSRs), and sequences corresponding to 5S and 45S ribosomal RNA genes were also identified. Thirty-one gene sequences showed high-similarity to rice full-length cDNA sequences that had not been matched to the published rice genome sequence in silico. These results suggest the presence of expressed genes within and around the clusters of RCS2/TrsD/CentO satellites in unsequenced centromeric regions of the rice chromosomes.

Keywords: genome; FL-cDNA; centromere; transposon.
Communicated by Satoshi Tabata
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This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
H. Mizuno, J. Wu, Y. Katayose, H. Kanamori, T. Sasaki, and T. Matsumoto
Chromosome-Specific Distribution of Nucleotide Substitutions in Telomeric Repeats of Rice (Oryza sativa L.)
Mol. Biol. Evol., January 1, 2008; 25(1): 62 - 68.
[Abstract] [Full Text] [PDF]


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