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Centromeric and non-centromeric satellite DNA organisation differs in holocentric Rhynchospora species

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Abstract

Satellite DNA repeats (or satDNA) are fast-evolving sequences usually associated with condensed heterochromatin. To test whether the chromosomal organisation of centromeric and non-centromeric satDNA differs in species with holocentric chromosomes, we identified and characterised the major satDNA families in the holocentric Cyperaceae species Rhynchospora ciliata (2n = 10), R. globosa (2n = 50) and R. tenuis (2n = 2x = 4 and 2n = 4x = 8). While conserved centromeric repeats (present in R. ciliata and R. tenuis) revealed linear signals at both chromatids, non-centromeric, species-specific satDNAs formed distinct clusters along the chromosomes. Colocalisation of both repeat types resulted in a ladder-like hybridisation pattern at mitotic chromosomes. In interphase, the centromeric satDNA was dispersed while non-centromeric satDNA clustered and partly colocalised to chromocentres. Despite the banding-like hybridisation patterns of the clustered satDNA, the identification of chromosome pairs was impaired due to the irregular hybridisation patterns of the homologues in R. tenuis and R. ciliata. These differences are probably caused by restricted or impaired meiotic recombination as reported for R. tenuis, or alternatively by complex chromosome rearrangements or unequal condensation of homologous metaphase chromosomes. Thus, holocentricity influences the chromosomal organisation leading to differences in the distribution patterns and condensation dynamics of centromeric and non-centromeric satDNA.

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Acknowledgements

We thank the Brazilian agency Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for scholarships to T. Ribeiro and A. Marques and for the Special Visiting Research grant to A. Houben, the Brazilian agency Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for the financial support to A. Pedrosa-Harand and the Czech Science Foundation (BP501/12/G090) for the financial support to J. Macas. In addition, we would like to thank A. Himmelbach (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)) for the generation of NGS data.

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  1. André Marques

    Present address: Laboratory of Genetic Resources, Campus Arapiraca, Federal University of Alagoas, Arapiraca, AL, Brazil

Authors and Affiliations

  1. Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco (UFPE), Recife, PE, Brazil

    Tiago Ribeiro, André Marques & Andrea Pedrosa-Harand

  2. Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic

    Petr Novák & Jiri Macas

  3. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany

    Veit Schubert & Andreas Houben

  4. State University of Londrina, Paraná, 86057970, Brazil

    André L. L. Vanzela

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  1. Tiago Ribeiro
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Correspondence to Andrea Pedrosa-Harand.

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Electronic supplementary material

Online resource 1

Online resource 1

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(DOC 30 kb)

Online resource 3

Dot-plot analysis showing the complex organisation of satellite repeats RcSAT2, RcSAT20 and RtSAT239 identified in R. ciliata and R. tenuis. (JPEG 468 kb)

Online resource 4

Individual chromosomes of three selected metaphases from different individuals of R. tenuis (2n = 4x = 8), showing the contrasting labelling pattern of the RtSAT239 repeat between homologous chromosomes. Arrowheads indicate partial decondensation of RtSAT239 in metaphase chromosomes forming chromatin loops. Bar = 5 μm. (JPEG 590 kb)

Online resource 5

Comparative banding pattern for repeats RcSAT2 and RcSAT20 (a, b) or 45S rDNA (c) in R. ciliata. In (b), chromosomes were organised in two groups based on the number of RcSAT2 signals: left (up to four major clusters) and right (more than four clusters). (JPEG 1545 kb)

Movie 1

Arrangement of RgSAT1/1 (red) and RgSAT1/2 (green) superimposed to total DNA (blue) in a root interphase nucleus of R. globosa. Both subfamilies colocolise complementarily to the chromocentres and form globular or ring-like structures. (AVI 14195 kb)

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Ribeiro, T., Marques, A., Novák, P. et al. Centromeric and non-centromeric satellite DNA organisation differs in holocentric Rhynchospora species. Chromosoma 126, 325–335 (2017). https://doi.org/10.1007/s00412-016-0616-3

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