Genome sequence for the blue‐flowered Andean shrub Iochroma cyaneum reveals extensive discordance across the berry clade of Solanaceae

Abstract

The tomato (Solanum lycopersicum L.) 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 (Miers) Mione and Nicotiana attenuata Torr. ex S. Watson]. Here we present the genome of the showy‐flowered Andean shrub Iochroma cyaneum (Lindl.) M. L. Green, a woody lineage from the tomatillo (Physalis philadelphica Lam.) subfamily Physalideae. The assembled size of the genome (2.7 Gb) is more similar in size to pepper (Capsicum annuum L.) (2.6 Gb) than to other sequenced diploid members of the berry clade of Solanaceae [e.g., potato (Solanum tuberosum L.), 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 Gypsy elements alone accounting for 52% of the genome. Despite the large amount of repetitive content, most of the 12 I. cyaneum chromosomes are highly syntenic with tomato. Bayesian concordance analysis provides strong support for the berry clade, including I. cyaneum, but reveals extensive discordance along the backbone, with placement of chili pepper and Jaltomata being highly variable across gene trees. The I. cyaneum 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.

Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster

“…Using proteomes as input, OrthoFinder separates genes into orthogroups or sets of genes descended from a single gene in the common ancestor of the species under consideration, which includes all orthologs and paralogs. We included 14 sequenced genomes— S. lycopersicum M82_MAS2.0 ( 87 ), S. pimpinellifolium ( 119 ) S. pennellii ( 120 ), S. lycopersicoides ( 121 ), S. tuberosum v6.1 ( 122 ), S. melongena v4.1 ( 123 ), I. cyaneum ( 124 ), Datura stramonium ( 125 ), Lycium barbarum ( 126 ), N. attenuata ( 127 ), P. axillaris ( 128 ), I. trifida ( 129 ), C. canephora ( 130 ), and V. vinifera ( 131 )—and two transcriptomes— S. nigrum ( 55 ) and S. quitoense ( 55 ).…”