Complete plastome phylogeny and an update on cox1 intron evolution of Hyoscyameae (Solanaceae)

Within the family Solanaceae, the tribe Hyoscyameae comprises eight genera distributed across Eurasia. Despite a few attempts to understand the relationships within this tribe, the affiliations among most genera remain unresolved. Recently, complete chloroplast genomes from several species of Hyoscyameae were published, enabling phylogenomic inferences. We sequenced the plastome of Scopolia carniolica, the second species of the genus to be reported. Genomic comparisons across the tribe revealed identical gene content and small differences in genome length. Phylogenetic analyses confirmed that Atropa is an early-diverging lineage sister to the rest of the tribe, resolved as two clades. One includes well-supported relationships between Przewalskia, Physochlaina, and Scopolia, and these three genera are sister to Atropanthe. This clade is sister to a second clade composed of Hyoscyamus and Anisodus. The strongly supported phylogenetic affiliations of Atropanthe, Anisodus, and Hyoscyamus represent the major advancements as previous studies were not able to resolve these relationships. Interestingly, the genus Scopolia is paraphyletic in respect to Physochlaina, based on ITS2 sequences. Finally, the evolution of the mitochondrial cox1 intron is reinterpreted. Two independent horizontal acquisitions are inferred, one in the ancestor of Przewalskia, Physochlaina, and S. japonica and another in Hyoscyamus, with no intron losses.

Automated summary

Within the Solanaceae family, the tribe Hyoscyameae consists of eight genera distributed across Eurasia. Recent research using complete chloroplast genomes has helped resolve some phylogenetic relationships within the tribe, but many remain unresolved. Phylogenetic analyses confirm Atropa as an early-diverging lineage, with well-supported relationships between Przewalskia, Physochlaina, and Scopolia in one clade, and Hyoscyamus and Anisodus in another. The paraphyletic relationship between Scopolia and Physochlaina is of note, and new insights have been gained into the evolution of the mitochondrial cox1 intron.