AIMS:

Inter(sub)specific hybridizations are frequent events in plants and represent key factors in the evolution and domestication of many crops. Banana is one of such crop plants where domesticated cultivars result from hybridization events between Musa acuminata (2n=2x=22, A genome) subspecies and sometimes with Musa balbisiana (2n=2x=22, B genome). These species and subspecies diverged following geographical isolation in Southeast Asian continental regions and islands. Plant movement fostered by human migrations lead to inter(sub)specific hybridization that generated diploid and triploid hybrids with low fertility. Large chromosomal rearrangements between the species and subspecies are suspected to be involved in this low fertility. Seedless parthenocarpic hybrids were then selected by early farmers and since then dispersed by centuries of vegetative propagation. We developed methods to exploit sequencing data and the Musa acuminata reference sequence to characterize the interspecific genome structure of several diploid and triploid banana cultivars. The mosaic structure that we unveiled allowed refining our understanding of cultivars origin revealing a history of hybridization that is sometimes more complex than previously expected with more rounds of hybridisation and additional unknown contributors.  We identified and characterized so far, five large chromosomal structural variations (LSV) that differentiate founding genomes of cultivated bananas. We showed that in structurally heterozygous accessions, these LSV induce biased chromosomal segregations, reduced recombination and aneuploidy in polyploid progenies. For one of these LSV, the rearranged structure was found preferentially transmitted to progenies and frequently present in triploid cultivars.