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Rye B chromosomes are weakly transcribed and might alter the transcriptional activity of A chromosome sequences

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Abstract

B chromosomes (Bs) are dispensable components of the genomes of numerous species. To test whether the transcriptome of a host is influenced by Bs, we looked for differences in expression in response to additional Bs. Comparative complementary DNA amplified fragment length polymorphism experiments resulted in the identification of 16 putative B-chromosome-associated transcripts. This comprises 0.7% of the total transcript number and indicates a low activity of Bs. We also provide evidence that B chromosome influences in trans the transcription of A chromosome sequences. The B-specific transcribed sequences B1334, B8149, and B2465 belong to high-copy families with similarity to mobile elements. For all analyzed B-chromosome-derived transcripts, similar A chromosome-encoded sequences were found which supports an A-derived origin of rye B chromosomes.

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Acknowledgements

We are grateful to O. Weiss (IPK, Germany) for excellent technical assistance, as well as R. Pickering and I. Schubert for critically reading the manuscript. We would like to thank M. Puertas (Spain), W. Viegas (Portugal), and R. N. Jones (UK) for providing the valuable plant material. MC and AH were supported by grants of the IPK (Gatersleben) and the DFG (HO1779/10-1).

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Authors and Affiliations

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

    Mariana Carchilan, Katrin Kumke & Andreas Houben

  2. Bayerische Landesanstalt für Landwirtschaft, Lange Point 4, 85354, Freising, Germany

    Sabine Mikolajewski

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  1. Mariana Carchilan
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  2. Katrin Kumke
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  3. Sabine Mikolajewski
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  4. Andreas Houben
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Correspondence to Andreas Houben.

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Communicated by L. Comai

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Suppl. Material and Methods

cDNA-amplified fragment length polymorphism (AFLP) analysis and DNA cloning (DOC 29 kb)

Suppl Fig. 1

Southern hybridization of probe B1334 with XbaI-, DraI-, BamHI-, and EcoRI-digested genomic rye DNA from plants with (+B) and without Bs (0B). 1, 2, 3 are the three different rye inbred lines. W—Lindström wheat with (+B) and without Bs (0B). Note identical hybridization patterns of 0B and +B rye and wheat plants with B chromosomes (GIF 238 KB)

High resolution image file (TIFF 7 mb)

Suppl Fig. 2

Southern hybridization of probe rye B2465 with XbaI-, BamHI-, and EcoRI-digested genomic rye DNA from plants with (+B) and without Bs (0B). 1, 2, 3 are the three different rye inbred lines. Note identical hybridization patterns of 0B and +B rye plants (GIF 119 KB)

High resolution image file (TIFF 3.5 mb)

Suppl Fig. 3

Southern hybridization of probe B8149 with XbaI- and DraI-digested genomic rye and wheat DNA from plants with (+B) and without Bs (0B). 1, 2, 3 are three different rye inbred lines. W—Lindström wheat with (+B) and without Bs (0B). Note the highly polymorphic hybridization pattern. Additional B-specific restriction bands are arrowed (GIF 145 KB)

High resolution image file (TIFF 3.4 mb)

Suppl. Fig. 4a

Alignment of B1334-like sequences amplified from cDNA of plants with (+B) and without (0B) B chromosomes. Single-nucleotide polymorphisms are highlighted in red. GenBank sequence AF175285 shows the highest similarity. Sequences B1334-1–9 are sequences obtained via cDNA-AFLP and sequences B1334-10–23 are sequences obtained via RT-PCR (DOC 48.5 kb)

Suppl. Fig. 4b

Alignment of B8149-like sequences amplified from cDNA of plants with (+B) and without (0B) B chromosomes. Single-nucleotide polymorphisms are highlighted in red. Sequences B8149-1–24 are sequences obtained by RT-PCR (DOC 63 kb)

Suppl. Table 1

PCR primers used (DOC 45 kb)

Suppl. Table 2

AFLP adaptor sequences (DOC 26 kb)

Suppl. Table 3

List of AFLP primer sequences (Keygene). Selective nucleotides are highlighted in red. http://wheat.pw.usda.gov/ggpages/keygeneAFLPs.html (DOC 40 kb)

Suppl. Table 4

Primer combinations used for cDNA-AFLP analysis of 0B/+B plants. (DOC 73 kb)

Suppl. Table 5

Total number of cDNA-AFLP bands and of additional bands present in 0B- or +B-positive plants only. *weak, **middle, ***strong intensity of band (DOC 137 kb)

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Carchilan, M., Kumke, K., Mikolajewski, S. et al. Rye B chromosomes are weakly transcribed and might alter the transcriptional activity of A chromosome sequences. Chromosoma 118, 607–616 (2009). https://doi.org/10.1007/s00412-009-0222-8

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