The Solanaceae family contains many agriculturally important crops, including tomato, potato, pepper, and tobacco, as well as others with growing potential, such as the orphan crops groundcherry, wolfberry, and pepino. Research progress varies greatly among these species, with model crops like tomato far ahead, which limits the broader agricultural application of other solanaceous species. Here, we constructed the interspecies pan-genome for the Solanaceae family and identified distinct patterns of gene retention. We reveal that the activity of specific transposable elements is associated with gene fractionation and transposition. The pan-genome is further resolved at the level of T subgenomes that were generated by Solanaceae specific paleo-hexaploidization (T event). We show the strong fractionation (loss) and divergence of genes resulting from ancient duplications. For example, all the class A and E flower model genes in Solanaceae originally evolved from two tandemly duplicated genes, which further expanded through the γ and T events and then fractionated into ten genes in tomato, acquiring distinct functions critical for fruit development. Based on these results, we developed the Solanaceae Pan-Genome Database (SolPGD, http://www.bioinformaticslab.cn/SolPGD), which integrates various datasets of the inter- and intra-pangenomes of Solanaceae. These findings and valuable resources will further promote studies of solanaceous species, including the orphan crops.
Keywords: Solanaceae; database; fruit; pan-genome; pepper; tomato.
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