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

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Abstract

The centromere as a kinetochore assembly site is fundamental to the partitioning of genetic material during cell division. In order to determine the functional centromeres of soybean, we characterized the soybean centromere-specific histone H3 (GmCENH3) protein and developed an antibody against the N-terminal end. Using this antibody, we cloned centromere-associated DNA sequences by chromatin immunoprecipitation. Our analyses indicate that soybean centromeres are composed of two distinct satellite repeats (GmCent-1 and GmCent-4) and retrotransposon-related sequences (GmCR). The possible allopolyploid origin of the soybean genome is discussed in view of the centromeric satellite sequences present.

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Abbreviations

CENH3:

Centromere-specific histone H3

EST:

Expressed sequence tag

RACE:

Rapid amplification of cDNA ends

PHEMES:

PIPES (piperazine-1,4-bis (2-ethanesulfonic acid)), HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), EGTA (ethylene glycol tetraacetic acid), MgCl2, sorbitol

PBS:

Phosphate-buffered saline

ChIP:

Chromatin immunoprecipitation

DAPI:

4,6-Diamino-2-phenylindole

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Acknowledgements

We thank Dr. Jiri Macas for the help in sequence analysis. This work was supported by the Fellowship Program of the Japan Society for the Promotion of Science (JSPS) to ALT and KN.

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Authors and Affiliations

  1. Research Institute for Bioresources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046, Japan

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

  2. Department of Agronomy, Faculty of Agriculture, Harran University, Sanliurfa, Turkey

    Ahmet L. Tek

Authors
  1. Ahmet L. Tek
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  2. Kazunari Kashihara
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  3. Minoru Murata
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  4. Kiyotaka Nagaki
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Correspondence to Ahmet L. Tek or Kiyotaka Nagaki.

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Responsible Editor: Herbert Macgregor.

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Fig. S1

Alignment of CentGm-1 family with sequences derived from the ChIP analysis. Five complete 92-bp monomers and six partial sequences extracted from clones G48, G56, G61, G71, and G87 are aligned with the two representative CentGm-1 (accession no.) and -2 (accession no.) sequences. The nucleotide position is marked at the beginning and end of the sequence for each monomer. Conserved and diverged regions with thick and thin lines, respectively, are shown below (GIF 101 kb)

High resolution image (TIFF 1375 kb)

Fig. S2

Sequence alignment of CentGm-4 sequences. For illustration purposes, the G30 sequence is divided into two fragments: 5′ (G30-b) and 3′ (G30-a) ends and are boxed with thick and thin lines, respectively. A 153-bp fragment (G92-b, 700–852 bp) of the G92 clone is marked with dotted lines. Sequence positions are shown for each clone at the first and last nucleotides (GIF 136 kb)

High resolution image (TIFF 3373 kb)

Fig. S3

Multiple sequence alignment of gag-pol regions derived from G92-a and four retrotransposons (accession nos. FJ197991, FJ197992, FJ197994, and FJ197995). A single frameshift is corrected at position 13846 in FJ197992. Similarities are shaded in black for 100%, dark gray for 80–99%, light gray for 60–79%, and white for less than 60% (GIF 118 kb)

High resolution image (TIFF 1594 kb)

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Tek, A.L., Kashihara, K., Murata, M. et al. Functional centromeres in soybean include two distinct tandem repeats and a retrotransposon. Chromosome Res 18, 337–347 (2010). https://doi.org/10.1007/s10577-010-9119-x

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  • DOI: https://doi.org/10.1007/s10577-010-9119-x

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