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Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe’s oldest Camellia japonica

Chromosome Research volume 23, pages 791–806 (2015)Cite this article

Abstract

Northern Europe’s oldest and largest Camellia japonica growing at the Pillnitz Castle (Germany) for over 200 years is of botanical and cultural importance and is a reference for C. japonica molecular scale analysis. In order to provide a fundament for genome analysis of the genus Camellia, we characterize the C. japonica tandem repeat fraction, constituting 12.5 % of the Pillnitz camellia’s genome. A genomic library of the Pillnitz C. japonica was produced and Illumina sequenced to generate 36 Gb of paired-end reads. We performed graph-based read clustering implemented in the RepeatExplorer pipeline to estimate the C. japonica repeat fraction of 73 %. This enabled us to identify and characterize the most prominent satellite DNAs, Camellia japonica satellite 1–4 (CajaSat1–CajaSat4), and the 5S ribosomal DNA (rDNA) by bioinformatics, fluorescent in situ and Southern hybridization. Within the Camellia genus, satellite spreading, array expansion and formation of higher-order structures highlight different modes of repeat evolution. The CajaSat satellites localize at prominent chromosomal sites, including (peri)centromeres and subtelomeres of all chromosomes, thus serving as chromosomal landmarks for their identification. This work provides an insight into the C. japonica chromosome organization and significantly expands the Camellia genomic knowledge, also with respect to the tea plant Camellia sinensis.

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Abbreviations

BAC:

Bacterial artificial chromosome

bp:

Base pair

BSA:

Bovine serum albumin

CajaSat:

Camellia japonica satellite

cDNA:

Copy DNA

Cy3:

Cyanine 3

DAPI:

4′,6′-Diamidino-2-phenylindole

FISH:

Fluorescent in situ hybridization

FITC:

Fluorescein isothiocyanate

Gb:

Gigabase

LINE:

Long interspersed nuclear element

LTR:

Long terminal repeat

PCR:

Polymerase chain reaction

rDNA:

Ribosomal DNA

rRNA:

Ribosomal RNA

SDS:

Sodium dodecyl sulfate

SSC:

Saline sodium citrate (1× SSC = 0.15 M NaCl + 0.015 M Na3 citrate)

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Acknowledgments

We thank Ines Walter for her excellent technical assistance. Furthermore, we sincerely thank Christoph Neinhuis for supporting our cooperative camellia research initiative. We show gratitude to the TU Dresden Botanical Garden and its camellia collection at the Landschloss Pirna-Zuschendorf for providing the plant material. Moreover, the TU Dresden Center for Information Services and High Performance Computing (ZIH) are acknowledged for computer time allocations.

Author’s contributions

TH and SP wrote the paper. TH designed the research, took part in project coordination and carried out the bioinformatical analysis. SP performed the wet lab experiments and took part in bioinformatical analysis. FZ analyzed satellite higher-order structures. SW provided Illumina sequence data. TS and FZ contributed to writing the manuscript. TS, TW, AK and SW participated in the coordination of the project. All the authors read and approved the manuscript.

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    1. Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany

      Tony Heitkam, Stefan Petrasch, Falk Zakrzewski, Anja Kögler, Torsten Wenke, Stefan Wanke & Thomas Schmidt

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    1. Tony Heitkam
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    Correspondence to Thomas Schmidt.

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    This work was supported by the Staatliche Schlösser, Burgen und Gärten Sachsen gGmbH.

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    Tony Heitkam and Stefan Petrasch contributed equally to this work.

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    Heitkam, T., Petrasch, S., Zakrzewski, F. et al. Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe’s oldest Camellia japonica . Chromosome Res 23, 791–806 (2015). https://doi.org/10.1007/s10577-015-9500-x

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    Keywords

    • Camellia japonica
    • RepeatExplorer
    • Fluorescent in situ hybridization
    • Satellite DNA
    • Tandem repeats