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Molecular characterization of novel Ty1-copia-like retrotransposons in pear (Pyrus pyrifolia)

Abstract

Retrotransposons are present in all plant genomes and play important roles in genome size, genome structure remodeling, gene function, and genome evolution. Eight novel long terminal repeat retrotransposons were identified from a bacterial artificial chromosome library of Japanese pear (Pyrus pyrifolia). On the basis of the order of gene arrangement within the gag and pol domains (protease, integrase, reverse transcriptase, and RNase H), these newly identified retrotransposons appear to be closely related to Ty1-copia retrotransposons. They were designated Ppcrt1–8 and classified into two groups based on the presence or absence of a 142-amino-acid deletion within the group-specific antigen DNA-binding domain. Ppcrt1–8 were grouped with the copia-like retrotransposons RIRE1 and BARE-1 by phylogenetic analysis based on the amino acid sequences encoded by the gag and pol domains. Fluorescence in situ hybridization analysis showed that sequences homologous to Ppcrt4 were dispersed throughout more than half of the pear chromosomes. Southern blot analysis suggested that many copies of Ppcrt retrotransposons exist in the pear genome. Sequence information from these eight retrotransposons should be useful for the development of retrotransposon-based molecular marker systems in Japanese pear.

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Acknowledgments

This work has a contribution no. 1596 of the National Institute of Fruit Tree Science. We are grateful to Drs. T. Imai and T. Saito for their valuable suggestions and useful discussion. This work was partially supported by Grants-in-Aid for Research and Development Projects for Application in Promoting New Policy of Agriculture, Forestry and Fisheries (no. 1970) and by a grant of Genomics for Agricultural Innovation (DD-4040) from the Ministry of Agriculture, Forestry and Fisheries of Japan.

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Correspondence to Toshiya Yamamoto.

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Communicated by A. Dandekar

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Kim, H., Yamamoto, M., Hosaka, F. et al. Molecular characterization of novel Ty1-copia-like retrotransposons in pear (Pyrus pyrifolia). Tree Genetics & Genomes 7, 845–856 (2011). https://doi.org/10.1007/s11295-011-0379-1

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Keywords

  • Copia
  • Fluorescence in situ hybridization
  • Japanese pear
  • LTR retrotransposon
  • Pyrus pyrifolia
  • Reverse transcriptase