Polyploid section originated by hybridization of two ancestral clades.

Introduction: section is 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 the section with several diploid species based on both plastidial and nuclear genes.

Methods: The plastome-based phylogenetic analysis representing 47 newly re-built plastid genomes suggested that an ancestor of . section is the most likely maternal donor of the clade. Nevertheless, we found clear evidence of plastid recombination with an ancestor from the clade. 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.

Results: We found that section is monophyletic with contributions from the sections , , and . The dating of the divergence between these sections indicates that the hybridization predates the split between , and .

Discussion: We propose that section arose from the hybridization of two ancestral species from which the and sections are derived, with the 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.