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The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution, and age

Chromosome Research volume 18, pages 247–263 (2010)Cite this article

Abstract

Long terminal repeat (LTR) retrotransposons are major components of plant genomes influencing genome size and evolution. Using two separate approaches, we identified the Ty1-copia retrotransposon families Cotzilla and SALIRE in the Beta vulgaris (sugar beet) genome. While SALIRE elements are similar to typical Ty1-copia retrotransposons, Cotzilla elements belong to a lineage called Sireviruses. Hallmarks of Cotzilla retrotransposons are the existence of an additional putative env-like open reading frame upstream of the 3′LTR, an extended gag region, and a frameshift separating the gag and pol genes. Detected in a c 0 t-1 DNA library, Cotzilla elements belong to the most abundant retrotransposon families in B. vulgaris and are relatively homogenous and evolutionarily young. In contrast, the SALIRE family has relatively few copies, is diverged, and most likely ancient. As revealed by fluorescent in situ hybridization, SALIRE elements target predominantly gene-rich euchromatic regions, while Cotzilla retrotransposons are abundant in the intercalary and pericentromeric heterochromatin. The analysis of two retrotransposons from the same subclass contrasting in abundance, age, sequence diversity, and localization gives insight in the heterogeneity of LTR retrotransposons populating a plant genome.

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Abbreviations

BAC:

Bacterial artificial chromosome

DAPI:

4′,6′-diamidino-2-phenylindole

env :

Envelope

FISH:

Fluorescent in situ hybridization

FITC:

Fluorescein isothiocyanate

LTR:

Long terminal repeat

ORF:

Open reading frame

PBS:

Primer-binding site

PPT:

Polypurine tract

RT:

Reverse transcriptase

SDS:

Sodium dodecyl sulfate

SSC:

Standard saline citrate (1× SSC = 0.15 M NaCl, 0.015 M Na3-citrate)

TE:

Transposable element

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Acknowledgements

We thank Ines Walter for excellent technical assistance. Tony Heitkam acknowledges a fellowship and financial support of the FAZIT foundation. Torsten Wenke is funded by the BMBF grant “KMU-innovativ-2: Entwicklung von Retrotransposon-basierten molekularen Werkzeugen für die Züchtung, Sortenidentifizierung und Genbankerhaltung von Kartoffeln” (0315425B).

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  1. Department of Biology, Dresden University of Technology, 01069, Dresden, Germany

    Beatrice Weber, Torsten Wenke, Ulrike Frömmel, Thomas Schmidt & Tony Heitkam

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  1. Beatrice Weber
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  2. Torsten Wenke
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  3. Ulrike Frömmel
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  4. Thomas Schmidt
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Correspondence to Thomas Schmidt.

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Beatrice Weber and Torsten Wenke contributed equally to the manuscript.

Responsible Editor: JS (Pat) Heslop-Harrison.

Electronic Supplementary Materials

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S1

Schematic representation of an alignment containing the Cotzilla1 LTRs and 20 c 0 t-1 sequences similar to the Cotzilla1 LTR. Black bars represent sequences. The percentage identity relative to the Cotzilla1 5′LTR is indicated. These c 0 t-1 sequences were crucial for the identification of Cotzilla1. A BLAST search in the EMBL database using their consensus as query showed homology to BAC EF101866 containing the full-length retrotransposon Cotzilla1. (PDF 69 kb)

S2

Schematic representation of an alignment containing the complete Cotzilla1 retrotransposon and 347 homologous BAC sequences. Black bars represent sequences. Compared with Cotzilla1, the minimum sequence identity is 59%, the maximum sequence identity 99%. In average, the identity is 94% indicating that Cotzilla1 is a typical member of the Cotzilla family. Available BAC sequences have been generated by end-sequencing of HindIII cloned Beta vulgaris fragments (McGrath et al. 2004). Several regions of Cotzilla1 are underrepresented by BAC sequences since they do not contain HindIII restriction sites. (PDF 251 kb)

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Weber, B., Wenke, T., Frömmel, U. et al. The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution, and age. Chromosome Res 18, 247–263 (2010). https://doi.org/10.1007/s10577-009-9104-4

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Keywords

  • Ty1-copia
  • LTR retrotransposon
  • Sirevirus
  • FISH
  • sugar beet