New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach

Authors

  • ALICE VALENTINI,

    1. Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble cedex 9, France
    2. Dipartimento di Ecologia e Sviluppo Economico Sostenibile, Università degli Studi della Tuscia, via S. Giovanni Decollato 1, I-01100 Viterbo, Italy
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  • CHRISTIAN MIQUEL,

    1. Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble cedex 9, France
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  • MUHAMMAD ALI NAWAZ,

    1. Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, Post Box 5003, NO-1432 Ås, Norway,
    2. Himalayan Wildlife Foundation, 01, Park Road, Sector F-8/1 Islamabad 44000, Pakistan
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  • EVA BELLEMAIN,

    1. Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble cedex 9, France
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  • ERIC COISSAC,

    1. Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble cedex 9, France
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  • FRANÇOIS POMPANON,

    1. Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble cedex 9, France
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  • LUDOVIC GIELLY,

    1. Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble cedex 9, France
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  • CORINNE CRUAUD,

    1. Genoscope — CNS, 2 rue Gaston Crémieux, BP 5706, F-91057 Evry cedex, France
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  • GIUSEPPE NASCETTI,

    1. Dipartimento di Ecologia e Sviluppo Economico Sostenibile, Università degli Studi della Tuscia, via S. Giovanni Decollato 1, I-01100 Viterbo, Italy
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  • PATRICK WINCKER,

    1. Genoscope — CNS, 2 rue Gaston Crémieux, BP 5706, F-91057 Evry cedex, France
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  • JON E. SWENSON,

    1. Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, Post Box 5003, NO-1432 Ås, Norway,
    2. Norwegian Institute for Nature Research, NO-7485 Trondheim, Norway
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  • PIERRE TABERLET

    1. Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble cedex 9, France
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P. Taberlet, Fax: +33(0)4 76 51 42 79; E-mail: pierre.taberlet@ujf-grenoble.fr

Abstract

The development of DNA barcoding (species identification using a standardized DNA sequence), and the availability of recent DNA sequencing techniques offer new possibilities in diet analysis. DNA fragments shorter than 100–150 bp remain in a much higher proportion in degraded DNA samples and can be recovered from faeces. As a consequence, by using universal primers that amplify a very short but informative DNA fragment, it is possible to reliably identify the plant taxon that has been eaten. According to our experience and using this identification system, about 50% of the taxa can be identified to species using the trnL approach, that is, using the P6 loop of the chloroplast trnL (UAA) intron. We demonstrated that this new method is fast, simple to implement, and very robust. It can be applied for diet analyses of a wide range of phytophagous species at large scales. We also demonstrated that our approach is efficient for mammals, birds, insects and molluscs. This method opens new perspectives in ecology, not only by allowing large-scale studies on diet, but also by enhancing studies on resource partitioning among competing species, and describing food webs in ecosystems.

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