IntroductionNicotianasectionSuaveolentesis an almost all-Australian clade of allopolyploid tobacco species that emerged through hybridization between diploid relatives of the genus. In this study, we aimed to assess the phylogenetic relationship of theSuaveolentessection with severalNicotianadiploid species based on both plastidial and nuclear genes.MethodsTheNicotianaplastome-based phylogenetic analysis representing 47 newly re-built plastid genomes suggested that an ancestor ofN. sectionNoctifloraeis the most likely maternal donor of theSuaveolentesclade. Nevertheless, we found clear evidence of plastid recombination with an ancestor from theSylvestresclade. We analyzed 411 maximum likelihood-based phylogenetic trees from a set of conserved nuclear diploid single copy gene families following an approach that assessed the genomic origin of each homeolog.ResultsWe found thatNicotianasectionSuaveolentesis monophyletic with contributions from the sectionsAlatae,Sylvestres,PetunioidesandNoctiflorae. The dating of the divergence between these sections indicates that theSuaveolenteshybridization predates the split betweenAlatae/Sylvestres, andNoctiflorae/Petunioides.DiscussionWe propose thatNicotianasectionSuaveolentesarose from the hybridization of two ancestral species from which theNoctiflorae/PetunioidesandAlatae/Sylvestressections are derived, withNoctifloraethe maternal parent. This study is a good example in which the use of genome wide data provided additional evidence about the origin of a complex polyploid clade.