Plastid Phylogenomic Insights into the Inter-Tribal Relationships of Plantaginaceae

Abstract

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.

Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution

“…Previous studies have revealed that the expansion and contraction of the IR, LSC, and SSC regions are common during evolution and are the main reason for variations in plastome size ( Ravi et al., 2007 ; Downie and Jansen, 2015 ; Daniell et al., 2016 ). Significant contraction of IR region was observed among Linderniaceae species ( Supplementary Figure 2 ), which was also common in Lamiales, such as Gesneriaceae ( Gu et al., 2020 ), Lamiaceae ( Su et al., 2022 ), Oleaceae ( Long et al., 2023 ), Plantaginaceae ( Xie et al., 2023 ), and Scrophulariaceae ( Wang et al., 2022 ). Notably, the IR boundaries did not coincide exactly in the three populations of L. polygonoides , but they had the same plastome size.…”