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DNA Research Advance Access originally published online on February 12, 2007
DNA Research 2006 13(6):267-274; doi:10.1093/dnares/dsm001
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© The Author 2007. Kazusa DNA Research Institute.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

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

Hiroshi Mizuno1, Kazue Ito2, Jianzhong Wu1, Tsuyoshi Tanaka1, Hiroyuki Kanamori2, Yuichi Katayose1, Takuji Sasaki1 and Takashi Matsumoto1,*

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

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.

Key words: genome; FL-cDNA; centromere; transposon

*To whom correspondence should be addressed. Tel: +81 29 838 7441, Fax: +81 29 838 7468, E-mail: mat{at}nias.affrc.go.jp

Communicated by Satoshi Tabata


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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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