Composition and Structure of the Centromeric Region of Rice Chromosome 8[W]

Wu, Jianzhong; Yamagata, Harumi; Hayashi-Tsugane, Mika; Hijishita, Saori; Fujisawa, Masaki; Michie, S; Ito, Yukiyo; Nakamura, Mari; Sakaguchi, Miyuki; Yoshihara, Rie; Kobayashi, Harumi; Ito, Kazue; Karasawa, Wataru; Yamamoto, Masanori; Saji, Shoko; Katagiri, Satoshi; Kanamori, Hajime; Namiki, Nobukazu; Katayose, Yūichi; Matsumoto, Takashi; Sasaki, Takuji

doi:10.1105/tpc.019273

Cited by 124 publications

(122 citation statements)

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“…The CentO satellites are located within the functional domain of the rice centromere 10,26 . Complete sequencing of the centromeres of rice chromosomes 4 and 8 revealed that they consist of 59 kb and 69 kb of clustered CentO repeats (respectively) [8][9][10] , tandemly arrayed head-to-tail within the clusters. Numerous retrotransposons, including the centromere-specific RIRE7, are found between and around the CentO repeats.…”

Section: Centromere Locationmentioning

confidence: 99%

“…The IRGSP released a high-quality map-based draft sequence in December 2002. Three completely sequenced chromosomes have been published [5][6][7] , as well as two completely sequenced centromeres [8][9][10] . As the IRGSP subscribed to an immediate-release policy, high-quality map-based sequence has been public for some time.…”

Section: The International Rice Genome Sequencing Projectmentioning

confidence: 99%

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The map-based sequence of the rice genome

Matsumoto¹,

Wu²,

Kanamori³

et al. 2005

Nature

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3,253

990

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Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 nontransposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

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Section: Centromere Locationmentioning

confidence: 99%

Section: The International Rice Genome Sequencing Projectmentioning

confidence: 99%

The map-based sequence of the rice genome

Matsumoto¹,

Wu²,

Kanamori³

et al. 2005

Nature

Self Cite

3,253

990

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show abstract

“…A combination of structural analyses and sequence homology comparisons were used to identify LTR-RTs in the 12 rice chromosomes (IRGSP Build 4.0 pseudomolecules), including two with completely sequenced and comprehensively analyzed centromeres (Wu et al 2004;Zhang et al 2004;Ma and Bennetzen 2006;Ma and Jackson 2006). The intact elements were identified by using LTR_STRUC, an LTR-RT mining program (McCarthy and McDonald 2003), and by methods previously described Bennetzen 2004, 2006;.…”

Section: Identification and Classification Of Ltr-rtsmentioning

confidence: 99%

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

Tian

Rizzon²,

Du³

et al. 2009

Genome Res.

142

175

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In flowering plants, the accumulation of small deletions through unequal homologous recombination (UR) and illegitimate recombination (IR) is proposed to be the major process counteracting genome expansion, which is caused primarily by the periodic amplification of long terminal repeat retrotransposons (LTR-RTs). However, the full suite of evolutionary forces that govern the gain or loss of transposable elements (TEs) and their distribution within a genome remains unclear. Here, we investigated the distribution and structural variation of LTR-RTs in relation to the rates of local genetic recombination (GR) and gene densities in the rice (Oryza sativa) genome. Our data revealed a positive correlation between GR rates and gene densities and negative correlations between LTR-RT densities and both GR and gene densities. The data also indicate a tendency for LTR-RT elements and fragments to be shorter in regions with higher GR rates; the size reduction of LTR-RTs appears to be achieved primarily through solo LTR formation by UR. Comparison of indica and japonica rice revealed patterns and frequencies of LTR-RT gain and loss within different evolutionary timeframes. Different LTR-RT families exhibited variable distribution patterns and structural changes, but overall LTR-RT compositions and genes were organized according to the GR gradients of the genome. Further investigation of non-LTR-RTs and DNA transposons revealed a negative correlation between gene densities and the abundance of DNA transposons and a weak correlation between GR rates and the abundance of long interspersed nuclear elements (LINEs)/short interspersed nuclear elements (SINEs). Together, these observations suggest that GR and gene density play important roles in shaping the dynamic structure of the rice genome.

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“…By contrast, rice (Oryza sativa) provides an excellent model for studying epigenetic modifications of CEN chromatin. Four rice centromeres (Cen4, Cen5, Cen7, and Cen8) have been fully or nearly fully sequenced (Nagaki et al, 2004;Wu et al, 2004;Zhang et al, 2004;Matsumoto et al, 2005), representing the best sequenced and characterized endogenous centromeres from any multicellular eukaryote. We used this sequence resource to develop a genomic tiling array that contains these four centromeres and the entire rice chromosome 8.…”

Section: Introductionmentioning

confidence: 99%

Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription

Kikuchi

Yan

et al. 2011

The Plant Cell

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The presence of the centromere-specific histone H3 variant, CENH3, defines centromeric (CEN) chromatin, but poorly understood epigenetic mechanisms determine its establishment and maintenance. CEN chromatin is embedded within pericentromeric heterochromatin in most higher eukaryotes, but, interestingly, it can show euchromatic characteristics; for example, the euchromatic histone modification mark dimethylated H3 Lys 4 (H3K4me2) is uniquely associated with animal centromeres. To examine the histone marks and chromatin properties of plant centromeres, we developed a genomic tiling array for four fully sequenced rice (Oryza sativa) centromeres and used chromatin immunoprecipitation-chip to study the patterns of four euchromatic histone modification marks: H3K4me2, trimethylated H3 Lys 4, trimethylated H3 Lys 36, and acetylated H3 Lys 4, 9. The vast majority of the four histone marks were associated with genes located in the H3 subdomains within the centromere cores. We demonstrate that H3K4me2 is not a ubiquitous component of rice CEN chromatin, and the euchromatic characteristics of rice CEN chromatin are hallmarks of the transcribed sequences embedded in the centromeric H3 subdomains. We propose that the transcribed sequences located in rice centromeres may provide a barrier preventing loading of CENH3 into the H3 subdomains. The separation of CENH3 and H3 subdomains in the centromere core may be favorable for the formation of three-dimensional centromere structure and for rice centromere function.

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Composition and Structure of the Centromeric Region of Rice Chromosome 8[W]

Cited by 124 publications

References 50 publications

The map-based sequence of the rice genome

The map-based sequence of the rice genome

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription

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