Modern sugarcane (Saccharum spp.) has been recognized as one of the world's most efficient crops in solar energy conversion and as havlng the mast favorable input: output ratios. Beside ils importance for sugar production, ilthus became recently aprimary energy crop. Sugarcane also presents 01)6 the most complex crop genome studied to date, rnainly due to avery high degree of polyploidy (2n=ca 12x=ca 120), together wiltl an inlerspecffic origin. In arder to invesligate genome dynamics in this highly polyploid context and 10 provide guidelines for future whole genome sequencing project, we sequenced and compared seven homoeologous haplotypes (BAC clones). Our analysis revealed ahigh conservation at the gene level (high colinearlty and high gene structure and sequence conservation). Remarkably, ail homoeo-alleles are predicted functional and no apparent general decrease of purilying selection was observed. Thus Ihe high polyploldy of sugarcane does not seem to have induced a major reshaping of ils genome, alleast at the gene levaI. By contras~ transposable elements displayed ageneral absence 01 colinearily among homoeologous haplotypes and appeared fo have uooergone dynamic expansion in Saccharum, compared Vlith sorghum, its clOse relative ln the Andropogonea tribe. Our data sugges! lt1e presence of broad sets of funcllonal homologous alleles in the sugarcane genome, which could explain ,. ils unique efficiency, ils hlgh phenolypic plaslicily and wide adaptation. (Texte intégral)