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Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and class II transposable elements

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Abstract

Poplar has become a model system for functional genomics in woody plants. Here, we report the sequencing and annotation of the first large contiguous stretch of genomic sequence (95 kb) of poplar, corresponding to a bacterial artificial chromosome clone mapped 0.6 centiMorgan from the Melampsora larici-populina resistance locus. The annotation revealed 15 putative genetic objects, of which five were classified as hypothetical genes that were similar only with expressed sequence tags from poplar. Ten putative objects showed similarity with known genes, of which one was similar to a kinase. Three other objects corresponded to the toll/interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant disease resistance genes, of which two were predicted to encode an amino terminal nuclear localization signal. Four objects were homologous to the Ty1/copia family of class I transposable elements, one of which was designated Retropop and interrupted one of the disease resistance genes. Two other objects constituted a novel Spm-like class II transposable element, which we designated Magali.

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Acknowledgements

The authors thank Jan Gielen, Wilson Ardiles-Diaz, and Raimundo Villarroel for sequencing BAC 60I2 and full-length cDNAs, Patrice Déhais for computer assistance, Marc Van Montagu, Nancy Terryn, Jeroen Raes, and Peter De Keukeleire for helpful discussions, and Martine De Cock for help in preparing the manuscript. This research was supported by grants from the IWT-STWW (980396), the Geconcerteerde Onderzoeksacties (Mefisto-666), OSTC IUAP P4-02, the Flemish government (BN0//BB/2000), and the European Union (POPYOMICS QLK-CT-2002-00953).

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  1. M. Lescot

    Present address: CIRAD-Biotrop, TA40/03, 34398, Montpellier Cedex 5, France

  2. S. Aubourg

    Present address: Unité de Recherche en Génomique Végétale, INRA, 91057 Evry Cedex, France

  3. C. Mathé

    Present address: Laboratoire de Biologie Vasculaire, Institut de Pharmacologie et Biologie Structurale, 205 route de Narbonne, 31077 Toulouse Cedex, France

Authors and Affiliations

  1. Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, 9052, Gent, Belgium

    M. Lescot, S. Rombauts, J. Zhang, S. Aubourg, C. Mathé, P. Rouzé & W. Boerjan

  2. Department of Plant Physiology, University of Umeå, 901 87, Umeå, Sweden

    S. Jansson

  3. Laboratoire Associé de l’Institut National de la Recherche Agronomique (France), Ghent University, 9052, Gent, Belgium

    P. Rouzé

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Communicated by D.B. Neale

M.L. and S.R. contributed equally to this article

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Lescot, M., Rombauts, S., Zhang, J. et al. Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and class II transposable elements. Theor Appl Genet 109, 10–22 (2004). https://doi.org/10.1007/s00122-004-1621-0

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