Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species

Authors

  • Mingai Li,

    Corresponding author
    1. Center for the Study of Biodiversity –Trentino, Institute for Agriculture Research of San Michele all'Adige, Trento, Italy
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    • These authors equally contributed to this work.

  • Jörg Wunder,

    1. Center for the Study of Biodiversity –Trentino, Institute for Agriculture Research of San Michele all'Adige, Trento, Italy
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    • These authors equally contributed to this work.

  • Gaetano Bissoli,

    1. Center for the Study of Biodiversity –Trentino, Institute for Agriculture Research of San Michele all'Adige, Trento, Italy
    2. Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, Valencia, Spain
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  • Eliana Scarponi,

    1. Center for the Study of Biodiversity –Trentino, Institute for Agriculture Research of San Michele all'Adige, Trento, Italy
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  • Silvia Gazzani,

    1. Center for the Study of Biodiversity –Trentino, Institute for Agriculture Research of San Michele all'Adige, Trento, Italy
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  • Enrico Barbaro,

    1. Center for the Study of Biodiversity –Trentino, Institute for Agriculture Research of San Michele all'Adige, Trento, Italy
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  • Heinz Saedler,

    1. Center for the Study of Biodiversity –Trentino, Institute for Agriculture Research of San Michele all'Adige, Trento, Italy
    2. Department of Molecular Plant Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
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  • Claudio Varotto

    1. Center for the Study of Biodiversity –Trentino, Institute for Agriculture Research of San Michele all'Adige, Trento, Italy
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* E-mail address:claudio.varotto@iasma.it

Abstract

With the aim of developing widely applicable gene markers for phylogenetic reconstructions at low taxonomic level, we tested the low copy nuclear Conserved Ortholog Set (COS) genes. Most of the 15 genes tested provided good amplification efficiency (as compared with rbcL) from a set of 67 representative angiosperm families. Nine selected COS markers were further characterized at both intra- and interfamilial level on a test set, including 25 species representative of 15 different families. While four of the COS led to incongruent results, the remaining five improved the phylogenetic reconstructions of closely related species as illustrated in the case of Orobanchaceae species. They were found to be highly informative in phylogenetic reconstruction of congeneric species, where introns provide a higher proportion of parsimony informative sites in comparison with traditional phylogenetic markers such as ITS and matK. At higher phylogenetic distance, where only coding regions could be aligned, the polymorphism levels of the COS ranged between those of ndhF and matK.

On the basis of these results, the success rate in developing universally amplifiable low copy nuclear markers based on COS genes is about 30%. We report the successful development of five pCOS that, together with a few other well characterized genes, such as Rpb2 and GbssI, can be considered the closest approximation to low-copy “universally” amplifiable markers for phylogeny in plants at present. The possible pitfalls of universally amplifiable COS marker development and their range of applicability at different taxonomic levels in comparison with traditional phylogenetic molecular markers are discussed.

© The Willi Hennig Society 2008.

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