Adrian F. Powell, Jing Zhang, Duncan Hauser, Julianne Vilela, Alice Hu, Daniel J. Gates, Lukas A. Mueller, Fay-Wei Li, Suzy Strickler, Stacey D. Smith

The tomato family, Solanaceae, is a model clade for a wide range of applied and basic research questions. Currently, reference-quality genomes are available for over 30 species from seven genera, and these include numerous crops as well as wild species (e.g., Jaltomata sinuosa and Nicotiana attenuata). Here we present the genome of the showy-flowered Andean shrub Iochroma cyaneum, a woody lineage from the tomatillo subfamily Physalideae. The assembled size of the genome (2.7Gb) is more similar in size to chilipepper (2.6Gb) than to other sequenced diploid members of the berry clade of Solanaceae (e.g., potato, tomato, and Jaltomata). Our assembly recovers 92% of the conserved orthologous set, suggesting a nearly complete genome for this species. Most of the genomic content is repetitive (69%), with gyspy elements alone accounting for 52% of the genome. Despite the large amount of repetitive content, most of the 12 Iochroma chromosomes are highly syntenic with tomato. Bayesian concordance analysis provides strong support for the berry clade, including Iochroma, but reveals extensive discordance along the backbone, with placement of pepper and Jaltomata being highly variable across gene trees. The Iochroma genome contributes to a growing wealth of genomic resources in Solanaceae and underscores the need for expanded sampling of diverse berry genomes to dissect major morphological transitions.