Plastid Phylogenomic Insights into the Inter-Tribal Relationships of Plantaginaceae

Simple Summary The current classification of Plantaginaceae divides the family into 12 tribes. However, the inter-tribal relationships of this family remain unresolved, and phylogenetic and comparative studies on Plantaginaceae plastomes are also scarce. In this study, we compared 41 plastomes representing the 11 tribes of Plantaginaceae and uncovered the high conservation of the plastomes in terms of genome structure and gene content. Phylogenetic analyses based on 68 plastid protein-coding genes (PCGs) successfully elucidated the inter-tribal relationships of Plantaginaceae, especially disputed tribes, such as Plantagineae, Digitalideae, Veroniceae, Hemiphragmeae and Sibthorpieae. PhyParts analysis showed a certain extent of conflict between gene trees and species tree, revealing the limitations of phylogenetic analysis of Plantaginaceae using single or multiple plastid DNA sequences. Collectively, our results provide some basic information on the plastomes of the Plantaginaceae taxa and some new insights into the inter-tribal relationships of Plantaginaceae, laying the groundwork for future phylogenetic and taxonomic studies. Plantaginaceae, consisting of 12 tribes, is a diverse, cosmopolitan family. To date, the inter-tribal relationships of this family have been unresolved, and the plastome structure and composition within Plantaginaceae have seldom been comprehensively investigated. In this study, we compared the plastomes from 41 Plantaginaceae species (including 6 newly sequenced samples and 35 publicly representative species) representing 11 tribes. To clarify the inter-tribal relationships of Plantaginaceae, we inferred phylogenic relationships based on the concatenated and coalescent analyses of 68 plastid protein-coding genes. PhyParts analysis was performed to assess the level of concordance and conflict among gene trees across the species tree. The results indicate that most plastomes of Plantaginaceae are largely conserved in terms of genome structure and gene content. In contrast to most previous studies, a robust phylogeny was recovered using plastome data, providing new insights for better understanding the inter-tribal relationships of Plantaginaceae. Both concatenated and coalescent phylogenies favored the sister relationship between Plantagineae and Digitalideae, as well as between Veroniceae and Hemiphragmeae. Sibthorpieae diverged into a separate branch which was sister to a clade comprising the four tribes mentioned above. Furthermore, the sister relationship between Russelieae and Cheloneae is strongly supported. The results of PhyParts showed gene tree congruence and conflict to varying degrees, but most plastid genes were uninformative for phylogenetic nodes, revealing the defects of previous studies using single or multiple plastid DNA sequences to infer the phylogeny of Plantaginaceae.