Comparative and Phylogenetic Analyses of Complete Chloroplast Genomes of <i>Scrophularia incisa</i> Complex (Scrophulariaceae).

The <i>Scrophularia incisa</i> complex is a group of closely related desert and steppe subshrubs that includes <i>S. incisa</i>, <i>S. kiriloviana</i> and <i>S. dentata</i>, which are the only <i>S.</i> sect. <i>Caninae</i> components found in Northwest China. Based on earlier molecular evidence, the species boundaries and phylogenetic relationships within this complex remain poorly resolved. Here, we characterized seven complete chloroplast genomes encompassing the representatives of the three taxa in the complex and one closely related species, <i>S. integrifolia</i>, as well as three other species of <i>Scrophularia</i>. Comparative genomic analyses indicated that the genomic structure, gene order and content were highly conserved among these eleven plastomes. Highly variable plastid regions and simple sequence repeats (SSRs) were identified. The robust and consistent phylogenetic relationships of the <i>S. incisa</i> complex were firstly constructed based on a total of 26 plastid genomes from Scrophulariaceae. Within the monophyletic complex, a <i>S. kiriloviana</i> individual from Pamirs Plateau was identified as the earliest diverging clade, followed by <i>S. dentata</i> from Tibet, while the remaining individuals of <i>S. kiriloviana</i> from the Tianshan Mountains and <i>S. incisa</i> from Qinghai-Gansu were clustered into sister clades. Our results evidently demonstrate the capability of plastid genomes to improve phylogenetic resolution and species delimitation, particularly among closely related species, and will promote the understanding of plastome evolution in <i>Scrophularia</i>.