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Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome

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Abstract

One of the most powerful technologies in unraveling the organization of a eukaryotic plant genome is high-resolution Fluorescent in situ hybridization of repeats and single copy DNA sequences on pachytene chromosomes. This technology allows the integration of physical mapping information with chromosomal positions, including centromeres, telomeres, nucleolar-organizing region, and euchromatin and heterochromatin. In this report, we established chromosomal positions of different repeat fractions of the potato genomic DNA (Cot100, Cot500 and Cot1000) on the chromosomes. We also analysed various repeat elements that are unique to potato including the moderately repetitive P5 and REP2 elements, where the REP2 is part of a larger Gypsy-type LTR retrotransposon and cover most chromosome regions, with some brighter fluorescing spots in the heterochromatin. The most abundant tandem repeat is the potato genomic repeat 1 that covers subtelomeric regions of most chromosome arms. Extensive multiple alignments of these repetitive sequences in the assembled RH89-039-16 potato BACs and the draft assembly of the DM1-3 516 R44 genome shed light on the conservation of these repeats within the potato genome. The consensus sequences thus obtained revealed the native complete transposable elements from which they were derived.

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Abbreviations

BAC:

Bacterial artificial chromosome

BESs:

BAC end sequences

CCD:

Charge-coupled device

Cot:

(=Co × t) Co is the initial concentration of single-stranded DNA in mole per liter, and t is the reannealing time in seconds. Cot is a measure of DNA complexity

Cy 3, 3.5, 5:

Cyanide dyes

DAPI:

4′,6-Diamidino-2-phenylindole

DEAC:

Diethylaminocoumarin

DM:

DM1-3 516 R44 genotype

FISH:

Fluorescent in situ hybridization

FITC:

Fluorescein isothiocyanate

ISH:

In situ hybridization

LINEs:

Long interspersed nuclear elements

LTRs:

Long terminal repeats

NOR:

Nucleolar-organizing region

ORFs:

Open reading frames

PFGE:

Pulsed field gel electrophoresis

PGR1:

Potato genomic repeat 1: a subtelomeric tandem repeat family in potato

PGSC:

Potato genome sequencing consortium

RH:

RH89-039-16 genotype

SINEs:

Short interspersed nuclear elements

TEs:

Transposable elements

TGRI:

Tomato genomic repeat I: a subtelomeric tandem repeat family in tomato

TPE:

Telomere position effect

TR:

Telomeric repeat

TRF:

Tandem repeats finder

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Acknowledgments

We thank Irma Straatman very much for technical assistance of propagation of the clones. This work was supported by grants from PGSC-NL funded by the Netherlands Technology Foundation (FES; Grant no. WGC.7795) and the Fund for Economic Structural Support (Netherlands Ministries of Economic Affairs and Agriculture).

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Authors and Affiliations

  1. Wageningen UR Plant Breeding, Wageningen University and Research Centre, 6708 PB, Wageningen, The Netherlands

    Xiaomin Tang, Jan M. de Boer, Herman J. van Eck, Christian W. B. Bachem & Richard G. F. Visser

  2. Keygene N.V., 216, 6700 AE, Wageningen, The Netherlands

    Erwin Datema

  3. Laboratory of Genetics, Wageningen University, 6700 AH, Wageningen, The Netherlands

    Myriam Olortegui Guzman & Hans de Jong

  4. Center for BioSystems Genomics (CBSG), Wageningen, The Netherlands

    Herman J. van Eck & Richard G. F. Visser

  5. Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA

    Xiaomin Tang

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  1. Xiaomin Tang
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  2. Erwin Datema
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Correspondence to Hans de Jong.

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Tang, X., Datema, E., Guzman, M.O. et al. Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome. Mol Genet Genomics 289, 1307–1319 (2014). https://doi.org/10.1007/s00438-014-0891-8

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