Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome

Authors

  • Nazeema Jannoo,

    1. Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, 13083-970, Campinas, SP, Brazil,
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  • Laurent Grivet,

    1. Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, 13083-970, Campinas, SP, Brazil,
    2. Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR 1096, Avenue Agropolis, TA40/03, 34398 Montpellier Cedex 5, France, and
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  • Nathalie Chantret,

    1. Institut National de la Recherche Agronomique (INRA), UMR 1096, Avenue Agropolis, TA40/03, 34398 Montpellier Cedex 5, France
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    • Present address: INRA, UMR 1097, Domaine de Melgueil, 34130 Maugio, France.

  • Olivier Garsmeur,

    1. Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR 1096, Avenue Agropolis, TA40/03, 34398 Montpellier Cedex 5, France, and
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  • Jean Christophe Glaszmann,

    1. Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR 1096, Avenue Agropolis, TA40/03, 34398 Montpellier Cedex 5, France, and
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  • Paulo Arruda,

    1. Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, 13083-970, Campinas, SP, Brazil,
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  • Angélique D’Hont

    Corresponding author
    1. Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR 1096, Avenue Agropolis, TA40/03, 34398 Montpellier Cedex 5, France, and
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*(fax +33 467 615 605; email dhont@cirad.fr).

Summary

Modern sugarcane (Saccharum spp.) is an important grass that contributes 60% of the raw sugar produced worldwide and has a high biofuel production potential. It was created about a century ago through hybridization of two highly polyploid species, namely S. officinarum and S. spontaneum. We investigated genome dynamics in this highly polyploid context by analyzing two homoeologous sequences (97 and 126 kb) in a region that has already been studied in several cereals. Our findings indicate that the two Saccharum species diverged 1.5–2 million years ago from one another and 8–9 million years ago from sorghum. The two sugarcane homoeologous haplotypes show perfect colinearity as well as high gene structure conservation. Apart from the insertion of a few retrotransposable elements, high homology was also observed for the non-transcribed regions. Relative to sorghum, the sugarcane sequences displayed colinearity, with the exception of two genes present only in sorghum, and striking homology in most non-coding parts of the genome. The gene distribution highlighted high synteny and colinearity with rice, and partial colinearity with each homoeologous maize region, which became perfect when the sequences were combined. The haplotypes observed in sugarcane may thus closely represent the ancestral Andropogoneae haplotype. This analysis of sugarcane haplotype organization at the sequence level suggests that the high ploidy in sugarcane did not induce generalized reshaping of its genome, thus challenging the idea that polyploidy quickly induces generalized rearrangement of genomes. These results also confirm the view that sorghum is the model of choice for sugarcane.

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