Nicotiana section Suaveolentes is an almost all-Australian clade of allopolyploid tobacco species including the important plant model Nicotiana benthamiana. The homology relationships of this clade and its formation are not completely understood. To address this gap, we assessed phylogenies of all individual genes of N. benthamiana and the well studied N. tabacum (section Nicotiana) and their homologues in six diploid Nicotiana species. We generated sets of 44 424 and 65 457 phylogenetic trees of N. benthamiana and N. tabacum genes, respectively, each collectively called a phylome. Members of Nicotiana sections Noctiflorae and Sylvestres were represented as the species closest to N. benthamiana in most of the gene trees. Analyzing the gene trees of the phylome we: (i) dated the hybridization event giving rise to N. benthamiana to 4-5 MyA, and (ii) separated the subgenomes. We assigned 1.42 Gbp of the genome sequence to section Noctiflorae and 0.97 Gbp to section Sylvestres based on phylome analysis. In contrast, read mapping of the donor species did not succeed in separating the subgenomes of N. benthamiana. We show that the maternal progenitor of N. benthamiana was a member of section Noctiflorae, and confirm a member of section Sylvestres as paternal subgenome donor. We also demonstrate that the advanced stage of long-term genome diploidization in N. benthamiana is reflected in its subgenome organization. Taken together, our results underscore the usefulness of phylome analysis for subgenome characterization in hybrid species.

中文翻译：

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异源四倍体烟草本塞姆氏烟草的亲本起源。


烟草属 Suaveolentes 是几乎全澳大利亚异源多倍体烟草物种的分支，包括重要的植物模型本塞姆氏烟草 (Nicotiana Benthamiana)。该进化枝的同源关系及其形成尚不完全清楚。为了解决这一差距，我们评估了本塞姆氏烟草和经过深入研究的烟草（烟草科）的所有个体基因及其在六个二倍体烟草物种中的同源物的系统发育。我们分别生成了 44 424 个和 65 457 个 N. Benthamiana 和 N. tabacum 基因的系统发育树，每个统称为一个系统发育树。在大多数基因树中，烟草科 Noctiflorae 和 Sylvestres 的成员被认为是最接近本塞姆氏烟草的物种。通过分析系统的基因树，我们：(i) 将产生本塞姆氏烟草的杂交事件定为 4-5 MyA，并且 (ii) 分离了亚基因组。根据系统分析，我们将 1.42 Gbp 的基因组序列分配给 Noctiflorae 部分，将 0.97 Gbp 分配给 Sylvestres 部分。相比之下，供体物种的读图谱未能成功分离本塞姆氏烟草的亚基因组。我们表明本塞姆氏猪笼草的母系祖先是夜花科的成员，并确认西尔维斯特科的成员是父本亚基因组供体。我们还证明，本塞姆氏烟草的长期基因组二倍化的高级阶段反映在其亚基因组组织中。总而言之，我们的结果强调了系统分析对于杂交物种亚基因组表征的有用性。