Physical Map-Based Sizes of the Centromeric Regions of Arabidopsis thaliana Chromosomes 1, 2, and 3

Hosouchi, Tsutomu; Kumekawa, Norikazu; Tsuruoka, Hisano; Kotani, Hirokazu

doi:10.1093/dnares/9.4.117

Cited by 108 publications

(97 citation statements)

References 11 publications

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“…This result agrees very well with those previously obtained by FISH analysis Kurata et al, 2002). In Arabidopsis, the sizes of genetically de®ned centromeres for the ®ve chromosomes ranged from 4.0 to 9.0 Mbp, corresponding to 18.5% of the entire genome size (Hosouchi et al, 2002;Kumekawa et al, 2000Kumekawa et al, , 2001. Within each centromeric region, the central domain, mainly containing a 180-bp satellite repeat, is about 3 Mbp long.…”

Section: Discussionsupporting

confidence: 90%

Physical maps and recombination frequency of six rice chromosomes

Wu¹,

Mizuno²,

et al. 2003

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These authors contributed equally to this work. SummaryWe constructed physical maps of rice chromosomes 1, 2, and 6±9 with P1-derived arti®cial chromosome (PAC) and bacterial arti®cial chromosome (BAC) clones. These maps, with only 20 gaps, cover more than 97% of the predicted length of the six chromosomes. We submitted a total of 193 Mbp of non-overlapping sequences to public databases. We analyzed the DNA sequences of 1316 genetic markers and six centromere-speci®c repeats to facilitate characterization of chromosomal recombination frequency and of the genomic composition and structure of the centromeric regions. We found marked changes in the relative recombination rate along the length of each chromosome. Chromosomal recombination at the centromere core and surrounding regions on the six chromosomes was completely suppressed. These regions have a total physical length of about 23 Mbp, corresponding to 11.4% of the entire size of the six chromosomes. Chromosome 6 has the longest quiescent region, with about 5.6 Mbp, followed by chromosome 8, with quiescent region about half this size. Repetitive sequences accounted for at least 40% of the total genomic sequence on the partly sequenced centromeric region of chromosome 1. Rice CentO satellite DNA is arrayed in clusters and is closely associated with the presence of Centromeric Retrotransposon of Rice (CRR )-and RIce RetroElement 7 (RIRE7 )-like retroelement sequences. We also detected relatively small coldspot regions outside the centromeric region; their repetitive content and gene density were similar to those of regions with normal recombination rates. Sequence analysis of these regions suggests that either the amount or the organization patterns of repetitive sequences may play a role in the inactivation of recombination.

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Section: Discussionsupporting

confidence: 90%

Physical maps and recombination frequency of six rice chromosomes

Wu¹,

Mizuno²,

et al. 2003

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“…Centromeric satellites serve as the core of the centromere, which is flanked by pericentric heterochromatin rich in middle repetitive elements, including retroelements and transposons. Because of the abundance of various repeats, centromeres of most eukaryotic chromosomes are upward of 1 Mb in size, mostly devoid of genes, and their sequencing and assembly pose a big challenge (Su et al 1997;Hosouchi et al 2002). Among the sequenced genomes of many multicellular eukaryotes, including Drosophila melanogaster, human, mouse, Arabidopsis thaliana, and rice, only the centromeres of rice chromosomes 3, 4, 5, and 8 have been fully assembled Wu et al 2004;Y.…”

Section: Entromeres and Their Associated Kinetochoresmentioning

confidence: 99%

A Molecular-Cytogenetic Method for Locating Genes to Pericentromeric Regions Facilitates a Genomewide Comparison of Synteny Between the Centromeric Regions of Wheat and Rice

Friebe

Zhang³

et al. 2009

Genetics

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Centromeres, because of their repeat structure and lack of sequence conservation, are difficult to assemble and compare across organisms. It was recently discovered that rice centromeres often contain genes. This suggested a method for studying centromere homologies between wheat and rice chromosomes by mapping rice centromeric genes onto wheat aneuploid stocks. Three of the seven cDNA clones of centromeric genes from rice centromere 8 (Cen8), 6729.t09, 6729.t10, and 6730.t11 which lie in the Cen8 kinetochore region, and three wheat ESTs, BJ301191, BJ305475, and BJ280500, with similarity to sequences of rice centromeric genes, were mapped to the centromeric regions of the wheat group-7 (W7) chromosomes. A possible pericentric inversion in chromosome 7D was detected. Genomewide comparison of wheat ESTs that mapped to centromeric regions against rice genome sequences revealed high conservation and a one-to-one correspondence of centromeric regions between wheat and rice chromosome pairs W1-R5, W2-R7, W3-R1, W5-R12, W6-R2, and W7-R8. The W4 centromere may share homology with R3 only or with R3 1 R11. Wheat ESTs that mapped to the pericentromeric region of the group-5 long arm anchored to the rice BACs located in the recently duplicated region at the distal ends of the short arms of rice chromosomes 11 and 12. A pericentric inversion specific to the rice lineage was detected. The depicted framework provides a working model for further studies on the structure and evolution of cereal chromosome centromeres.

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“…For example, the best-studied human centromere comprises a 2-Mb to 4-Mb core of homogeneous 171-bp alpha satellite DNA repeats flanked by ∼0.5 Mb of diverged alpha satellite that is densely populated with L1 transposable elements 3 . The enormous tracts of highly repetitive sequences at centromeres have precluded complete sequencing, not only for human centromeres, but also for those from model organisms 4,5 . Indeed, not a single centromere that has been mapped in a multicellular eukaryote has been completely sequenced.…”

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Sequencing of a rice centromere uncovers active genes

Nagaki

Cheng

Ouyang³

et al. 2004

Nat Genet

487

525

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Centromeres are the last frontiers of complex eukaryotic genomes, consisting of highly repetitive sequences that resist mapping, cloning and sequencing. The centromere of rice Chromosome 8 (Cen8) has an unusually low abundance of highly repetitive satellite DNA, which allowed us to determine its sequence. A region of ∼750 kb in Cen8 binds rice CENH3, the centromere-specific H3 histone. CENH3 binding is contained within a larger region that has abundant dimethylation of histone H3 at Lys9 (H3-Lys9), consistent with Cen8 being embedded in heterochromatin. Fourteen predicted and at least four active genes are interspersed in Cen8, along with CENH3 binding sites. The retrotransposons located in and outside of the CENH3 binding domain have similar ages and structural dynamics. These results suggest that Cen8 may represent an intermediate stage in the evolution of centromeres from genic regions, as in human neocentromeres, to fully mature centromeres that accumulate megabases of homogeneous satellite arrays.

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Physical Map-Based Sizes of the Centromeric Regions of Arabidopsis thaliana Chromosomes 1, 2, and 3

Cited by 108 publications

References 11 publications

Physical maps and recombination frequency of six rice chromosomes

Physical maps and recombination frequency of six rice chromosomes

A Molecular-Cytogenetic Method for Locating Genes to Pericentromeric Regions Facilitates a Genomewide Comparison of Synteny Between the Centromeric Regions of Wheat and Rice

Sequencing of a rice centromere uncovers active genes

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