Functional centromeres in soybean include two distinct tandem repeats and a retrotransposon

Tek, Ahmet L.; Kashihara, Kazunari; Murata, Minoru; Nagaki, Kiyotaka

doi:10.1007/s10577-010-9119-x

Cited by 63 publications

(76 citation statements)

References 51 publications

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“…Currently, even a pixelated view of centromere organization is visible only in a handful of resource-intense genomes with a focus on centromeres enriched for unique sequences (Schueler et al 2001;Nagaki et al 2004;Wolfgruber et al 2009;Miga et al 2014). On the other hand, given the ease of ChIPseq, we have catalogs of consensus sequences bound by CENH3 from a wide range of species (Tek et al 2010;Lee et al 2011;Gong et al 2012;Cerutti et al 2016). However, in these cases, the evolutionary variation and genomic context that characterize the functional centromere sequences remain unknown.…”

Section: Discussionmentioning

confidence: 99%

Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence

et al. 2017

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During cell division, spindle fibers attach to chromosomes at centromeres. The DNA sequence at regional centromeres is fast evolving with no conserved genetic signature for centromere identity. Instead CENH3, a centromere-specific histone H3 variant, is the epigenetic signature that specifies centromere location across both plant and animal kingdoms. Paradoxically, CENH3 is also adaptively evolving. An ongoing question is whether CENH3 evolution is driven by a functional relationship with the underlying DNA sequence. Here, we demonstrate that despite extensive protein sequence divergence, CENH3 histones from distant species assemble centromeres on the same underlying DNA sequence. We first characterized the organization and diversity of centromere repeats in wild-type Arabidopsis thaliana. We show that A. thaliana CENH3-containing nucleosomes exhibit a strong preference for a unique subset of centromeric repeats. These sequences are largely missing from the genome assemblies and represent the youngest and most homogeneous class of repeats. Next, we tested the evolutionary specificity of this interaction in a background in which the native A. thaliana CENH3 is replaced with CENH3s from distant species. Strikingly, we find that CENH3 from Lepidium oleraceum and Zea mays, although specifying epigenetically weaker centromeres that result in genome elimination upon outcrossing, show a binding pattern on A. thaliana centromere repeats that is indistinguishable from the native CENH3. Our results demonstrate positional stability of a highly diverged CENH3 on independently evolved repeats, suggesting that the sequence specificity of centromeres is determined by a mechanism independent of CENH3.

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Section: Discussionmentioning

confidence: 99%

Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence

et al. 2017

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“…Based on these findings, the selection and homogenization of centromeric DNA sequences by a mutated CENH3 has been hypothesized (Henikoff et al 2001). However, an exceptional case was reported recently in soybean, which possesses two different satellite-DNA sequences in its centromeres (Gill et al 2009;Tek et al 2010). In this study, five different centromeric satellite sequences coexisted with NtCENH3 (Fig.…”

Section: Discussionmentioning

confidence: 55%

Isolation of centromeric-tandem repetitive DNA sequences by chromatin affinity purification using a HaloTag7-fused centromere-specific histone H3 in tobacco

et al. 2011

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The centromere is a multi-functional complex comprising centromeric DNA and a number of proteins. To isolate unidentified centromeric DNA sequences, centromere-specific histone H3 variants (CENH3) and chromatin immunoprecipitation (ChIP) have been utilized in some plant species. However, anti-CENH3 antibody for ChIP must be raised in each species because of its species specificity. Production of the antibodies is time-consuming and costly, and it is not easy to produce ChIP-grade antibodies. In this study, we applied a HaloTag7-based chromatin affinity purification system to isolate centromeric DNA sequences in tobacco. This system required no specific antibody, and made it possible to apply a highly stringent wash to remove contaminated DNA. As a result, we succeeded in isolating five tandem repetitive DNA sequences in addition to the centromeric retrotransposons that were previously identified by ChIP. Three of the tandem repeats were centromere-specific sequences located on different chromosomes. These results confirm the validity of the HaloTag7-based chromatin affinity purification system as an alternative method to ChIP for isolating unknown centromeric DNA sequences. The discovery of more than two chromosome-specific centromeric DNA sequences indicates the mosaic structure of tobacco centromeres.

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“…The 2 repetitive elements have been found in various plants. For example, the rice centromere satellite CentO and centromere retrotransposon CRR have been shown in centromeres of all 12 chromosomes [Cheng et al, 2002], and functional centromeres of soybean are marked by 2 satellite DNAs (GmCent-1 and GmCent-4) and a retrotransposon (GmCR) [Tek et al, 2010]. The 2 different satellite DNAs marking 2 subsets of chromosomes in soybean suggest the paleopolyploid origin of the soybean genome.…”

Section: Retrotransposons In Cot-1 Library: Fidel and A Centromere Rementioning

confidence: 99%

“…At centromeres, CenH3 replaces the canonical H3, binds to centromere satellite and retrotransposon DNAs, and is essential for the proper formation of kinetochores for chromosome segregation during cell division [Cheng et al, 2002;Zhong et al, 2002;Nagaki et al, 2003;Tek et al, 2010]. The cloned centromere-localized satellite and retrotransposon are abundant repetitive elements at centromeres based on their hybridizations pattern.…”

Section: Retrotransposons In Cot-1 Library: Fidel and A Centromere Rementioning

confidence: 99%

“…For example, most plant species have the Arabidopsis -type microsatellite (TTTAGGG) array at the ends of each chromosome [Richards and Ausubel, 1988]. Centromere satellites from many plant species such as CentO in rice, CentC in maize, the 180-bp tandem repeat sequence in Arabidopsis, and the CentGm in soybean have been cloned and used to mark the centromeres [Cheng et al, 2002;Zhong et al, 2002;Nagaki et al, 2003;Tek et al, 2010]. rDNAs were among the earliest markers used for ISH and FISH.…”

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confidence: 99%

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Cloning and Characterization of Chromosomal Markers from a Cot-1 Library of Peanut (<b><i>Arachis hypogaea</i></b> L.)

Zhang

2012

Cytogenet Genome Res

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The cultivated peanut, Arachis hypogaea (AABB, 2n = 40), is an allotetraploid which was probably originated from a hybridization event between 2 ancestors, A. duranensis (A genome) and A. ipaensis (B genome) followed by chromosome doubling. The wild species in the Arachis section are useful genetic resources for genes that confer biotic and abiotic stress resistance for peanut breeding. However, the resource is not well exploited because little information on the genetic, cytogenetic, and phylogenetic relationships between cultivated peanut and its wild relatives is known. Characterization of its chromosome components will benefit the understanding of these issues. But the paucity of information on the DNA sequence and the presence of morphologically similar chromosomes impede the construction of a detailed karyotype for peanut chromosome identification. In our study, a peanut Cot-1 library was constructed to isolate highly and moderately repetitive sequences from the cultivated peanut, and the chromosomal distributions of these repeats were investigated. Both genome and chromosome specific markers were identified that allowed the distinguishing of A and B genomes in tetraploid peanut and a possible karyotyping of peanut chromosomes by FISH. In particular, a 115-bp tandem repetitive sequence was identified to be a possible centromere repetitive DNA, mainly localized in the centromeres of B chromosomes, and a partial retrotransposable element was also identified in the centromeres of B chromosomes. The cloning and characterization of various chromosomal markers is a major step for FISH-based karyotyping of peanut. The FISH markers are expected to provide a reference tool for sequence assembly, phylogenetic studies of peanut and its wild species, and breeding.

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Functional centromeres in soybean include two distinct tandem repeats and a retrotransposon

Cited by 63 publications

References 51 publications

Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence

Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence

Isolation of centromeric-tandem repetitive DNA sequences by chromatin affinity purification using a HaloTag7-fused centromere-specific histone H3 in tobacco

Cloning and Characterization of Chromosomal Markers from a Cot-1 Library of Peanut (<b><i>Arachis hypogaea</i></b> L.)

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