Phylogenomic discordance among plastid genes in endangered Maltese Limonium

Chloroplast genomes are widely used in plant phylogenetics, yet plastome-wide analyses increasingly reveal heterogeneity among gene trees. Limonium, a genus of over 600 species, centred in the Mediterranean basin, exhibits substantial taxonomic complexity driven by hybridization, apomixis, and polyploidy, but plastome data from its centre of diversity have been lacking. We report the first complete plastomes from Mediterranean Limonium, sequencing the endangered Maltese endemics L. melitense (154,139 bp) and L. zeraphae (154,142 bp), and compare them with seven plastomes from the Irano-Turanian and Chinese-Japanese regions. Genome sizes range from 150,515 to 174,033 bp, with variation primarily associated with inverted repeat (IR) expansion and contraction and differences in repeat content. Highly variable coding genes (ndhF, ycf1, rpl32) and several intergenic regions were identified as candidate molecular markers, and 382 simple sequence repeats were detected across nine plastomes. Structural comparisons revealed IR boundary shifts, repeat variation, and pseudogenization of rpl22 in L. zeraphae. Plastome-wide maximum likelihood analyses strongly supported the monophyly of Limonium and recovered geographically structured clades. To evaluate phylogenetic concordance, we analysed individual plastid protein-coding genes and inferred a species tree under the multispecies coalescent. Gene-tree conflict was localized to specific nodes, particularly involving the placement of L. otolepis and relationships among East Asian taxa, indicating heterogeneous plastome signal despite strong concatenated support. Selection analyses based on Ka/Ks ratios and complementary site-mode approaches identified six genes (ccsA, rpl22, rpoA, rps8, ycf1, ycf2) exhibiting signatures of positive selection. These results demonstrate dynamic plastome evolution and localized phylogenetic discordance within Limonium, refining the evolutionary framework of the genus and informing plastome-based inference in recent plant radiations.