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Divergence in centromere structure distinguishes related genomes in Coix lacryma-jobi and its wild relative

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Abstract

Knowledge about the composition and structure of centromeres is critical for understanding how centromeres perform their functional roles. Here, we report the sequences of one centromere-associated bacterial artificial chromosome clone from a Coix lacryma-jobi library. Two Ty3/gypsy-class retrotransposons, centromeric retrotransposon of C. lacryma-jobi (CRC) and peri-centromeric retrotransposon of C. lacryma-jobi, and a (peri)centromere-specific tandem repeat with a unit length of 153 bp were identified. The CRC is highly homologous to centromere-specific retrotransposons reported in grass species. An 80-bp DNA region in the 153-bp satellite repeat was found to be conserved to centromeric satellite repeats from maize, rice, and pearl millet. Fluorescence in situ hybridization showed that the three repetitive sequences were located in (peri-)centromeric regions of both C. lacryma-jobi and Coix aquatica. However, the 153-bp satellite repeat was only detected on 20 out of the 30 chromosomes in C. aquatica. Immunostaining with an antibody against rice CENH3 indicates that the 153-bp satellite repeat and CRC might be both the major components for functional centromeres, but not all the 153-bp satellite repeats or CRC sequences are associated with CENH3. The evolution of centromeric repeats of C. lacryma-jobi during the polyploidization was discussed.

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Acknowledgments

The authors are grateful to Dr. J.S. Li (China Agricultural University) for supplying the seeds of Coix. This research was supported by grant (30771208) from the National Science Foundation, State Key Basic Research and Development Plan of China (973; 2009CB118400), and National Transgenic Research Program of China (2008ZX08009-001).

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Authors and Affiliations

  1. National Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, People’s Republic of China

    Yonghua Han, Guixiang Wang, Jinhua Liu & Weiwei Jin

  2. Key Laboratory of Crop Germplasm and Utilization, MOA, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, The National Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, People’s Republic of China

    Zhao Liu, Wei Yue & Xueyong Zhang

  3. State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China

    Yonghua Han

  4. Shanghai Key Laboratory of Bio-Energy Crop, School of Life Sciences, Shanghai University, Shanghai, 200444, People’s Republic of China

    Rentao Song

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  1. Yonghua Han
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  2. Guixiang Wang
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  3. Zhao Liu
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  4. Jinhua Liu
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Correspondence to Xueyong Zhang or Weiwei Jin.

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Communicated by: I. Schubert

Yonghua Han and Guixiang Wang made an equal contribution to this work.

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Supplementary Fig. 1

Analysis of chromosome distribution and insert sizes of representative BAC clones 9-6-12 and 9-18-39. (a) FISH analysis of BAC 9-6-12. The signals dispersed along all chromosomes with an increased concentration around centromeric regions. (b) FISH analysis of BAC 9-18-39. The signals were exclusively detected in centromeres. (c) Insert sizes and fingerprint of BAC 9-6-12(12) and 9-18-39(39). After restriction of NotI and removing the 7.5 kb-length vector, the insert sizes were ∼130 and 110 kb, respectively. BAC 12 and 39 were not in the same contig as revealed in fingerprint by restriction with HindIII (GIF 72 kb)

High resolution image (TIFF 4353 kb)

Supplementary Fig. 2

Sequence comparison between 20 variant monomers of the 153-bp satellite repeat. Sequence conservation is indicated by background shading, where black represents 100% identity, dark gray represents at least 80%, and light gray represents at least 60%. Asterisks represent nucleotide position 10, 30, 50, and 70, respectively (GIF 1261 kb)

High resolution image (TIFF 576 kb)

Supplementary Fig. 3

Highly conserved sequence motifs identified in the LTRs of the centromere-specific retrotransposons in the grass species were found in the LTRs of CRC (GIF 5275 kb)

High resolution image (TIFF 6680 kb)

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Han, Y., Wang, G., Liu, Z. et al. Divergence in centromere structure distinguishes related genomes in Coix lacryma-jobi and its wild relative. Chromosoma 119, 89–98 (2010). https://doi.org/10.1007/s00412-009-0239-z

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