High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane

• DOI: 10.1111/j.1469-8137.2010.03497.x
• Publication Date: 2010-10-29T13:18:09Z
• Authors: Olivier Garsmeur; Carine Charron; Stéphanie Bocs; Vincent Jouffe; Sylvie Samain; Arnaud Couloux; Gaëtan Droc; Cyrille Zini; Jean‐Christophe G...; Marie‐Anne Van Sluys; Angélique D’Hont
• Keywords: 0301 basic medicine; Chromosomes, Artificial, Bacterial; transposition de gènes; Genes, Plant; Synteny; F30 - Génétique et amélioration des plantes; Polyploidy; 03 medical and health sciences; Sequence Homology, Nucleic Acid; polyploïdie; phylogénie; évolution; http://aims.fao.org/aos/agrovoc/c_3224; http://aims.fao.org/aos/agrovoc/c_13325; Alleles; Conserved Sequence; Phylogeny; Sorghum; http://aims.fao.org/aos/agrovoc/c_34326; Saccharum spontaneum; 2. Zero hunger; Saccharum officinarum; génome; gène; http://aims.fao.org/aos/agrovoc/c_2745; http://aims.fao.org/aos/agrovoc/c_6094; http://aims.fao.org/aos/agrovoc/c_27583; génétique des populations; http://aims.fao.org/aos/agrovoc/c_6727; Molecular Sequence Annotation; Oryza; http://aims.fao.org/aos/agrovoc/c_6729; Sequence Analysis, DNA; séquence nucléotidique; http://aims.fao.org/aos/agrovoc/c_27529; 15. Life on land; Saccharum; Haplotypes; DNA Transposable Elements; http://aims.fao.org/aos/agrovoc/c_3214

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.