High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane

Garsmeur Olivier, Charron Carine, Bocs Stéphanie, Jouffe Vincent, Samain Sylvie, Couloux Arnaud, Droc Gaëtan, Zini Cyrille, Glaszmann Jean-Christophe, Van Sluys Marie-Anne, D'Hont Angélique. 2011. High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane. New Phytologist, 189 (2) : pp. 629-642.

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Quartile : Outlier, Sujet : PLANT SCIENCES

Abstract : Modern sugarcane (Saccharum spp.) is the leading sugar crop and a primary energy crop. It has the highest level of 'vertical' redundancy (2n = 12x = 120) of all polyploid plants studied to date. It was produced about a century ago through hybridization between two autopolyploid species, namely S. officinarum and S. spontaneum. In order to investigate the genome dynamics in this highly polyploid context, we sequenced and compared seven hom(oe)ologous haplotypes (bacterial artificial chromosome clones). Our analysis revealed a high level of gene retention and colinearity, as well as high gene structure and sequence conservation, with an average sequence divergence of 4% for exons. Remarkably, all of the hom(oe)ologous genes were predicted as being functional (except for one gene fragment) and showed signs of evolving under purifying selection, with the exception of genes within segmental duplications. By contrast, transposable elements displayed a general absence of colinearity among hom(oe)ologous haplotypes and appeared to have undergone dynamic expansion in Saccharum, compared with sorghum, its close relative in the Andropogonea tribe. These results reinforce the general trend emerging from recent studies indicating the diverse and nuanced effect of polyploidy on genome dynamics. (Résumé d'auteur)

Mots-clés Agrovoc : Saccharum officinarum, Génome, Polyploïdie, Séquence nucléotidique, Transposition de gènes, Évolution, Phylogénie, Génétique des populations, Saccharum spontaneum, Gène

Mots-clés complémentaires : Chromosome artificiel, Séquencage, Bac

Classification Agris : F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

  • Garsmeur Olivier, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0001-8869-3689
  • Charron Carine, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0003-0281-9936
  • Bocs Stéphanie ORCID: 0000-0001-7850-4426
  • Jouffe Vincent
  • Samain Sylvie, Centre national de séquençage (FRA)
  • Couloux Arnaud, Centre national de séquençage (FRA)
  • Droc Gaëtan, CIRAD-BIOS-UMR DAP (FRA)
  • Zini Cyrille, CIRAD-BIOS-UMR DAP (FRA)
  • Glaszmann Jean-Christophe, CIRAD-BIOS-DIR (FRA) ORCID: 0000-0001-9918-875X
  • Van Sluys Marie-Anne, Universidade de São Paulo (BRA)
  • D'Hont Angélique, CIRAD-BIOS-UMR DAP (FRA)

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