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An assessment of karyotype restructuring in the neoallotetraploid Tragopogon miscellus (Asteraceae)

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Abstract

Tragopogon miscellus and Tragopogon mirus are two rare examples of allopolyploids that have formed recently in nature. Molecular cytogenetic studies have revealed chromosome copy number variation and intergenomic translocations in both allotetraploids. Due to a lack of interstitial chromosome markers, there remained the possibility of additional karyotype restructuring in these neopolyploids, via intrachromosomal and intragenomic rearrangements. To address this issue, we searched for additional high-copy tandem repeats in genomic sequences of the diploid progenitor species—Tragopogon dubius, Tragopogon pratensis and Tragopogon porrifolius—for application to the chromosomes of the allotetraploids. Eight novel repeats were localised by fluorescence in situ hybridisation (FISH) in the diploids; one of these repeats, TTR3, provided interstitial coverage. TTR3 was included in a cocktail with other previously characterised probes, producing better-resolved karyotypes for the three diploids. The cocktail was then used to test a hypothesis of karyotype restructuring in the recent allotetraploid T. miscellus by comparing repeat distributions to its diploid progenitors, T. dubius and T. pratensis. Five individuals of T. miscellus were selected from across the range of karyotypic variation previously observed in natural populations. FISH signal distributions mostly matched those observed in the diploid progenitors, with the exception of several losses or gains of signal at chromosomal subtermini and previously noted intergenomic translocations. Thus, in T. miscellus, we find most changes restricted to the subterminal regions, and although some were recurrent, none of the changes were common to all individuals analysed. We consider these findings in relation to the gene loss reported previously for T. miscellus.

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Abbreviations

Cy3:

Cyanine 3

Cy5:

Cyanine 5

DAPI:

4′,6-Diamidino-2-phenylindole

dsDNA:

Double-stranded deoxyribonucleic acid

FISH:

Fluorescence in situ hybridisation

GISH:

Genomic in situ hybridisation

NGS:

Next-generation sequencing

rDNA:

Ribosomal DNA

TGP7:

Tragopogon porrifolius subtelomeric repeat-7

TPRMBO:

Tragopogon pratensis tandemly repetitive sequence MboI-rich

TR:

Tandem repeat

TTR:

Tragopogon tandem repeat

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Acknowledgments

We thank Matt Gitzendanner for bioinformatics support. This work was supported by National Science Foundation Grants DEB-0922003 and DEB-1146065.

Author information

Authors and Affiliations

  1. Department of Biology, University of Florida, Gainesville, FL, 32611, USA

    Michael Chester, Malorie J. Lipman, Joseph P. Gallagher & Douglas E. Soltis

  2. Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA

    Joseph P. Gallagher

  3. Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA

    Pamela S. Soltis & Douglas E. Soltis

Authors
  1. Michael Chester
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  2. Malorie J. Lipman
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  3. Joseph P. Gallagher
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  4. Pamela S. Soltis
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  5. Douglas E. Soltis
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Corresponding author

Correspondence to Michael Chester.

Additional information

Responsible Editor: Jiming Jiang.

Electronic supplementary material

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Fig. S1

Bar chart showing the percentage abundance of the 40 most common tandem repeats. (JPEG 16 kb)

High resolution image

(TIFF 563 kb)

Fig. S2

FISH applied to mitotic chromosomes of T. dubius, T. porrifolius and T. pratensis with probes to a dub198; b pra001; c TTR4; d TTR6; e 5S rDNA. In c, arrows indicate hybridisation to minor 35S rDNA sites, on the short arm of chromosome D Po. Scale bar 5 μm. (JPEG 43 kb)

High resolution image

(TIFF 634 kb)

Fig. S3

FISH reprobing with 5S rDNA probe (magenta) merged with the same metaphase chromosomes as shown in Fig. 2d of T. porrifolius. Arrows indicate 5S rDNA array positions. Scale bar 5 μm. (JPEG 5 kb)

High resolution image

(TIFF 139 kb)

Table S1

Repeat monomer consensus sequences (DOC 62 kb)

Table S2

PCR primer sequences and cloned probe sequences (DOC 32 kb)

Table S3

Complementary oligonucleotide probe template sequences (DOC 46 kb)

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Chester, M., Lipman, M.J., Gallagher, J.P. et al. An assessment of karyotype restructuring in the neoallotetraploid Tragopogon miscellus (Asteraceae). Chromosome Res 21, 75–85 (2013). https://doi.org/10.1007/s10577-013-9339-y

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  • DOI: https://doi.org/10.1007/s10577-013-9339-y

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