Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

Abstract

Premise: Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants. Methods: A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum (Angiosperms353 probe set).

Fruity, sticky, stinky, spicy, bitter, addictive, and deadly: evolutionary signatures of metabolic complexity in the Solanaceae

“…11 A single genusthe Solanumaccounts for nearly half of these species. 12 Nightshades grow in environments ranging from deserts to rainforests, with growth habits that vary from epiphytes to trees. The family includes four major food crops (potato, tomato, pepper, and eggplant), a host of minor food crops (including tomatillo, naranjilla, tamarillo, and groundcherry) as well as the several ornamental crops (including petunia, salpiglossis, schizanthus, and brugmansia) and weed species (Jimson weed and bittersweet).…”

“…[22][23][24][25] In addition, the ability to perform RNA interference (RNAi), virus-induced gene silencing (VIGS), and CRISPR/Cas9 tools in multiple Solanaceae species allows the functional characterization of candidate genes and a more precise connection of genotype and phenotype. [26][27][28][29] The Solanaceae has emerged as a model system for investigating the biosynthesis and evolution of specialized 11,12 Major metabolite classes are mapped to the corresponding clades that produce high amounts of those metabolites and/or act as model species for studying their biosynthesis and evolution. Metabolites may not be distributed solely in the noted phylogenetic group.…”

“…The phylogenetic tree is based upon previously published Solanaceae and Solanum trees. 11,12 . (B) Characteristic acylsugar structures produced by Solanaceae species.…”

“…The Solanaceae family produces specialized metabolites of multiple chemical classes. A simplified phylogeny of the Solanaceae family is shown based on prior determination of phylogenetic relationships 11,12. Major metabolite classes are mapped to the corresponding clades that produce high amounts of those metabolites and/or act as model species for studying their biosynthesis and evolution.…”

A revision of the “spiny solanums” of Tropical Asia (Solanum, the Leptostemonum Clade, Solanaceae)

“…Single country endemics are in bold-face type. Species inclusion in subclades taken from Stern et al (2011), Vorontsova et al (2013), Aubriot et al (2016a) and Gagnon et al (2022). Country-level distribution is presented in Table 2.…”