Background: The plants of the genus Clerodendrum L. have great potential for development as an ornamental and important herbal resource. There is no significant morphological difference among many species of the genus Clerodendrum, which will lead to confusion among the herbs of this genus and ultimately affect the quality of the herbs. The chloroplast genome will contribute to the development of new markers used for the identification and classification of species. Methods and results: Here, we obtained the complete chloroplast genome sequences of Clerodendrum chinense (Osbeck) Mabberley and Clerodendrum thomsoniae Balf.f. using the next generation DNA sequencing technology. The chloroplast genomes of the two species all encode a total of 112 unique genes, including 80 protein-coding, 28 tRNA, and four rRNA genes. A total of 44–42 simple sequence repeats, 19–16 tandem repeats and 44–44 scattered repetitive sequences were identified. Phylogenetic analyses showed that the nine Clerodendrum species were classified into two clades and together formed a monophyletic group. Selective pressure analyses of 77 protein-coding genes showed that there was no gene under positive selection in the Clerodendrum branch. Analyses of sequence divergence found two intergenic regions: trnH-GUG-psbA, nhdD-psaC, exhibiting a high degree of variations. Meanwhile, there was no hypervariable region identified in protein coding genes. However, the sequence identities of these two intergenic spacers (IGSs) are greater than 99% among some species, which will result in the two IGSs not being used to distinguish Clerodendrum species. Analysis of the structure at the LSC (Large single copy) /IR (Inverted repeat) and SSC (Small single copy)/IR boundary regions showed dynamic changes. The above results showed that the complete chloroplast genomes can be used as a super-barcode to identify these Clerodendrum species. The study lay the foundation for the understanding of the evolutionary process of the genus Clerodendrum.

Background: Salvia bowleyana, S. splendens, and S. officinalis are globally distributed and have been widely used to treat coronary heart disease, liver tumors, and viral diseases. To systematically determine their phylogenetic relationship and develop molecular markers for species determination, we sequenced and assembled their chloroplast genomes, and analyzed the genome characteristics. Moreover, we compared the phylogenetic specification and divergence genes fragments of chloroplast genomes from the three Salvia species. Results: The length of S. bowleyana, S. splendens, and S. officinalis chloroplast genomes were 151387 bp, 150604 bp, and 151163 bp, respectively. The sizes of the large-single copy, small-single copy, and inverted repeat regions were 82772 bp, 17573 bp, and 51042 bp for S. bowleyana; 82181 bp, 17857 bp, and 50566 bp for S. splendens; 82429 bp, 17510 bp, and 51224 bp for S. officinalis, respectively. The GC contents of the three chloroplast genomes were 38.01%, 38.04%, 38.04%, partly. In the comparison of chloroplast genomes from Lamiaceae family, the six genes ndhB, rpl2, rpl23, rps7, rps12, and ycf2 were present in the IRs regions of all 41 chloroplast genomes in the Lamiaceae family. We found that one of the gene rpl20 was intact and stably occurred in all 41 species chloroplast genomes, however, another pseudogene one was lost in that of 40 species except the Dracocephalum heterophyllum. For the repeat analysis, 29 tandem repeats, 35, 29, 24 simple-sequence repeats(SSRs), and 47, 49, 40 interspersed repeats were identified in the three Salvia species chloroplast genomes based on the diverse requirements. The three specific intergenic sequences(IGS) of rps16-trnQ-UUG, trnL-UAA-trnF-GAA, and trnM-CAU-atpE were found to discriminate the certain species by comparing 23 Salvia chloroplast genomes. Six genes including rpl22, rps19, rpl2, ycf1, ndhF, and psbA were found in the highly diverse IR boundary regions. The genetic distance analysis of IGS showed the trnL-UAG-ccsA, rps16-trnQ-UUG, ccsA-ndhD, rps15-ycf1, and ndhE-ndhG regions had the higher variability. Furthermore, the phylogenetic tree inferred that the 23 Salvia species formed a monophyletic group. Lastly, two pairs of Genus-specific DNA barcode primers were identified, which can be used to amplify the part sequence of trnM-CAU-atpE and ccsA-ndhD region. Conclusions: We acquired the complete chloroplast genome of the three Salvia species, which will provide a solid foundation to understand their phylogenetic status in Salvia genus. Moreover, the research can provide the probability to discriminate the Salvia species compared with the genomics between the phenotype and the distinction of gene fragments .