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

Abstract Veronica anagallis-aquatica L and Veronica unulata Wall are widely used ethnomedicinal plants in China. The two species have different clinical efficacies, while their extremely similar morphology and unclear interspecific relationship makes it difficult to accurately identify them, leading to increased instances of mixed usage. This article reports on the complete genome sequence of chloroplasts of these two species and their related veronica species to conduct a comparative genomics analysis and phylogenetic construction. The results showed that the chloroplast (cp) genomes of Veronica exhibited typical circular tetrad structures, with total lengths of 149,386 to 152,319 bp, and GC content of 37.9 to 38.1%, and the number of genes was 129–134. The total number of simple sequence repeats (SSRs) in V. anagallis-aquatica and V. unulata is 37 and 36, while V. arvensis had the highest total number of SSRs (56), mainly consisting of A/T single bases. The vast majority of long repeat sequence types are forward repeats and palindromic repeats. Selective pressureanalysis showed that 3 genes were under positive selection. Sequence differences often occur in the non-coding regions of the large single-copy region (LSC) and small single-copy region (SSC), with the lowest sequence variation in the inverted repeat regions (IR). Seven highly variable regions (trnT-GGU-psbD, rps8-rpl16, trnQ-UUG, trnN-GUU-ndhF, petL, ycf3, and ycf1) were detected, which may be potential molecular markers for identifying V. anagallis-aquatica and V. unulata The phylogenetic tree indicates that there is a close genetic relationship between the genera Veronica and Neopicrorhiza, and V. anagallis-aquatica and V. unulata are sister groups. The chloroplast genome data of nine Veronica species provides important insights into the characteristics and evolution of the chloroplast genome of this genus, as well as the phylogenetic relationship of the genus Veronica.