Plastome-based phylogeny and biogeography of L. (Asteraceae) support revised lettuce gene pool categories.

This study generated and analyzed complete plastome and internal transcribed spacer (ITS) data of 46 species, 13 African endemic (AE) species, and 15 species from eight related genera in Lactucinae. The new plastome and nuclear ITS sequences were then used to reconstruct the phylogenetic relationships of species. The whole-plastome data were used to estimate divergence time and ancestral area reconstruction of the identified major lineages. The results showed that species are generally similar in plastome size, Guanine and Cytosine (GC) content, gene structure, and categories, although crop lettuce ( L.) and its gene pool relatives were found to have one unique pseudogene (), and , , , , and showed signs of positive selection. Our phylogenomic analysis demonstrated that is monophyletic after excluding Collett and Hemsl and AE species. AE species are morphologically distinct from core lineage and need to be excluded from . The core species most likely originated from Asia-Temperate W ~6.82 Mya and then dispersed globally and formed nine clades. Finally, the lettuce gene pool concept was amended according to the phylogenetic and historical biogeographic analyses. This study revised the circumscription of , revealed robust phylogenetic relationships within the genus, and provided insights into Lactucinae phylogeny. The lettuce gene pool species could be used as potential genetic resources for lettuce breeding.