Qing Du

Mesosphaerum suaveolens (L.) Kuntze is a single annual herb first described in 1759. It has homotypic synonyms, including Ballota suaveolens L. (Linnaeus 1759), Bystropogon suaveolens (L’Héritier 1...

The two Lamioideae species, Lamium barbatum Siebold & Zucc. 1846, is distributed across Europe, North Africa, Asia, and North America, while Leucas ciliata Hochst. ex Benth. 1829 is found in southern China and Southeast Asia. We sequenced their complete chloroplast genomes using the Illumina platform, obtaining lengths of 150,887 bp and 151,259 bp, respectively. Phylogenetic analysis showed Lamium barbatum is closely related to four other Lamium species, including Lamium takeshimense, Lamium album, Lamium amplexicaule, and Lamium galeobdolon. The Leucas ciliata species clusters with Leucas mollissima. These findings provide valuable data for species identification, evolutionary research, and conservation genetics.

RNA editing sites and functional analysis were firstly predicted and verified in the chloroplast genes of Chelidonium majus. The results found that nine genes have the same number of editing sites, while 40 genes have different numbers of editing sites. There are 28 types of codons and 13 types of amino acid mutations in the chloroplast genes of C. majus, among which serine mutations to leucine (S→L) have the highest number. All the molecular weight, extinction coefficients, and hydropathicity are increasing, while the value of theoretical isoelectric points (PI) are decreasing or constant after RNA editing. The five types of proteins, including ndhF, ndhD, ndhB, psaA, and psaB have more than 11 transmembrane regions, as well as they have the most conserved domains and open reading frames (ORFs). The number of ORFs by each gene is decreasing, whereas the length of ORFs is becoming more longer. The signal peptide was found within one protein of the petA gene. The rpoB protein had the approximate three-dimensional domain of Ricin-type beta-trefoil lectin with one more increase of conserved domain through mutation. After experiment validation, the two new mutated proteins were found within the rpoB protein. These results provide a solid basis for exploring functional expression regulation and the origin of evolution.

Albizia kalkora (Roxb.) Prain 1897, belonging to the family Fabaceae, is not only a landscape tree but also a medicinal plant. At present, few plastomes have been reported from Albizia, which delays the in-depth phylogenomic studies and the development of high-resolution discriminating markers for this genus. Herein, we sequenced the first plastome of A. kalkora by NGS technology. The genome is a circular structure (176,158 bp), containing a large single-copy (LSC) region (91,521 bp), a small copy (SSC) region (5237 bp), and two inverted repeat (IR) regions (39,700 bp each). It has 35.45% GC content and encodes 109 unique genes, which are 76 protein-coding, 4 rRNA, and 29 tRNA genes. The genetic distance analysis of the intergenic spacer regions for A. kalkora, A. odoratissima and A. bracteate shows four intergenic regions with very high K2p values, namely, ccsA-ndhD (15.04), matK-rps16 (10.77), rps11-rpl36 (17.63) and rps3-rps19 (20.08), which can discriminate the three Albizia species. In addition, we identified ten pairs of regions that could be utilized to design primers to discriminate the three Albizia species. The phylogenetic analysis showed Albizia was closely related to Samanea. The results in this study will provide valuable information to elucidate the classification, identification and evolutionary history of Albizia.

We analyzed and compared the three Leonurus species from appearance characteristics, intrinsic gene contents and functions, gene transcribed spacer regions (ITS2) in the nuclear genome, and the process of evolutionary development. The chloroplast genomes of them were found to be common circular structures with the four regions, the length range from 151236bp to 151689bp including the identical number of 37 tRNA and 8 rRNA. The special trans-spliced rps12 genes with two introns and three exons can be caught sight of L. sibiricus. The isoleucine (AUU) and cysteine (UGC) was the most and least abundant amino acid with the codons ending with most bases of A/U. The eleven hotspot divergent regions and four specific CDS genes were systematically counted with the highest nucleotide diversity. We cloned the DNA sequences of the two chosen IGS regions (atpH-atpI and rps15-ycf1) to develop the DNA barcodes, thus found that sixteen specific variable SNP sites and two Indel sites within the three Leonurus species. Furthermore, the ITS2 DNA sequences of 7 Leonurus species were varied after the 57th base in a total of 221 bases. In the aftermath of evolutional analysis, the three Leonurus species were significantly clustered into one great clade, while they were located at the different sub-branch with similar topology and close relationship of Phlomoides rotata based on the sequences of 64 shared nucleotide and ITS2 DNA. Thus above results can directly offer various evidence to better clarify the specific distinction among the three Leonurus species and their evolutionary history.

Two new prenylated flavonoids named sinoflavonoids NJ and NK (1–2), along with ten known compounds were isolated from the fruits of Podophyllum hexandrum Royle. The chemical structures were determined through NMR spectroscopic data and MS analysis. Sinoflavonoid NJ (1) with an unusual 5,11-dioxabenzo[b]fluoren-10-one skeleton was firstly reported from Berberidaceae. The isolated flavonoids were tested with LPS-induced RAW 264.7 mouse macrophages model for their anti-inflammatory activity. Sinoflavonoid NJ (1) showed the most potent inhibition on nitric oxide production with IC₅₀ value as 0.06 μM. Graphical Abstract

To systematically determine their phylogenetic relationships and develop molecular markers for species discrimination of Salvia bowleyana, S. splendens, and S. officinalis, we sequenced their chloroplast genomes using the Illumina Hiseq 2500 platform. The chloroplast genomes length of S. bowleyana, S. splendens, and S. officinalis were 151,387 bp, 150,604 bp, and 151,163 bp, respectively. The six genes ndhB, rpl2, rpl23, rps7, rps12, and ycf2 were present in the IR regions. The chloroplast genomes of S. bowleyana, S. splendens, and S. officinalis contain 29 tandem repeats; 35, 29, 24 simple-sequence repeats, and 47, 49, 40 interspersed repeats, respectively. The three specific intergenic sequences (IGS) of rps16-trnQ-UUG, trnL-UAA-trnF-GAA, and trnM-CAU-atpE were found to discriminate the 23 Salvia species. A total of 91 intergenic spacer sequences were identified through genetic distance analysis. The two specific IGS regions (trnG-GCC-trnM-CAU and ycf3-trnS-GGA) have the highest K2p value identified in the three studied Salvia species. Furthermore, the phylogenetic tree showed that the 23 Salvia species formed a monophyletic group. Two pairs of genus-specific DNA barcode primers were found. The results will provide a solid foundation to understand the phylogenetic classification of the three Salvia species. Moreover, the specific intergenic regions can provide the probability to discriminate the Salvia species between the phenotype and the distinction of gene fragments.

Main conclusion The complete chloroplast genome of Swertia kouitchensis has been sequenced and assembled, compared with that of S. bimaculata to determine the evolutionary relationships among species of the Swertia in the Gentianaceae family. Abstract Swertia kouitchensis and S. bimaculata are from the Gentianaceae family. The complete chloroplast genome of S. kouitchensis was newly assembled, annotated, and analyzed by Illumina Hiseq 2500 platform. The chloroplast genomes of the two species encoded a total of 133, 134 genes, which included 88–89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA genes. One intron was contained in each of the eight protein-coding genes and eight tRNA-coding genes, whereas two introns were found in two genes (ycf3 and clpP). The most abundant codon of the two species was for isoleucine, and the least abundant codon was for cysteine. The number of microsatellite repeat sequences was twenty-eight and thirty-two identified in the chloroplast genomes of S. kouitchensis and S. bimaculata, respectively. A total of 1127 repeat sequences were identified in all the 23 Swertia chloroplast genomes, and they fell into four categories. Furthermore, five divergence hotspot regions can be applied to discriminate these 23 Swertia species through genomes comparison. One pair of genus-specific DNA barcodes primer has been accurately identified. Therefore, the diverse regions cloned by a specific primer may become an effective and powerful molecular marker for the identification of Swertia genus. Moreover, four genes (ccsA, ndhK, rpoC1, and rps12) were positive selective pressure. The phylogenetic tree showed that the 23 Swertia species were clustered into a large clade including four evident subbranches, whereas the two species of S. kouitchensis and S. bimaculata were separately clustered into the diverse but correlated species group.

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 .