Comparative and Phylogenetic Analyses of Complete Chloroplast Genomes of Scrophularia incisa Complex (Scrophulariaceae)

Abstract

The Scrophularia incisa complex is a group of closely related desert and steppe subshrubs that includes S. incisa, S. kiriloviana and S. dentata, which are the only S. sect. Caninae 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, S. integrifolia, as well as three other species of Scrophularia. 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 S. incisa complex were firstly constructed based on a total of 26 plastid genomes from Scrophulariaceae. Within the monophyletic complex, a S. kiriloviana individual from Pamirs Plateau was identified as the earliest diverging clade, followed by S. dentata from Tibet, while the remaining individuals of S. kiriloviana from the Tianshan Mountains and S. incisa 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 Scrophularia.

Plio-Pleistocene climatic change drives allopatric speciation and population divergence within the Scrophularia incisa complex (Scrophulariaceae) of desert and steppe subshrubs in Northwest China

“…Our preliminary analyses of nuclear ribosomal (nr) and chloroplast (cp) DNA placed this species complex as a monophyletic group embedded in sect. Caninae clade ( Wang, 2015 ). Of those, S. incisa Weinm.…”

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.…”

The chloroplast genome of two medicinal species (Veronica anagallis-aquatica and Veronica unulata) and its comparative analysis with related Veronica species

“…However, geographical and ecological factors may continually change these characteristics in species of the genus Veronica 28, 29 . Recent taxonomy studies have utilized cp genomes to assess the genetic relationship between related species [30][31][32][33] . The basic groups of nine species in this genus range in size variations from 149386 to 152319bp, indicating that each of these species has signi cantly different cp gene sizes [34][35][36][37] .…”