Chromosome Research

, Volume 18, Issue 2, pp 247–263 | Cite as

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

  • Beatrice Weber
  • Torsten Wenke
  • Ulrike Frömmel
  • Thomas SchmidtEmail author
  • Tony Heitkam


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.


Ty1-copia LTR retrotransposon Sirevirus FISH sugar beet 



Bacterial artificial chromosome






Fluorescent in situ hybridization


Fluorescein isothiocyanate


Long terminal repeat


Open reading frame


Primer-binding site


Polypurine tract


Reverse transcriptase


Sodium dodecyl sulfate


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


Transposable element



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).

Supplementary material

10577_2009_9104_MOESM1_ESM.pdf (70 kb)
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)
10577_2009_9104_MOESM2_ESM.pdf (252 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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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Beatrice Weber
    • 1
  • Torsten Wenke
    • 1
  • Ulrike Frömmel
    • 1
  • Thomas Schmidt
    • 1
    Email author
  • Tony Heitkam
    • 1
  1. 1.Department of BiologyDresden University of TechnologyDresdenGermany

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