Nuclear phylogeny and insights into whole genome duplications and reproductive development of Solanaceae plants.

Solanaceae, the nightshade family, have ∼2700 species including important crops potato and tomato, ornamentals, and medicinal plants. Solanaceae have several sequenced genomes with evidence for whole genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with public databases, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1,700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, and Solanoideae) and the designation of three other subfamilies (Schizanthoideae, Schwenckioideae, and Petunioideae), with the placement of several previously unassigned genera. We placed a Solanaceae-specific whole genome triplication (WGT1) at ∼81 Ma (Million years ago), before the divergence of Schizanthoideae from other Solanaceae subfamilies at ∼73 Ma. In addition, we detected two GDBs (gene duplication bursts) supporting proposed WGD events and four other GDBs. An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene (sub)families found that 21 gene clades have retained gene duplicates, which were likely generated by the Solanaceae WGT1 and could have promoted fleshy fruit development. This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development, providing an improved understanding of Solanaceae evolution.