Chloroplast Genome Sequences and Phylogenetic Analysis of Eight Newly Sequenced Caryophyllaceae Species.

BACKGROUND: Caryophyllaceae is a big family composed of many economic and medicinal species. However, the phylogeny of the family is insufficient and genome data are lacking for many species. OBJECTIVE: Using next-generation sequencing (NGS) to acquire the chloroplast (cp) genomes of Eremogone acicularis (F.N.Williams) Ikonn., E. brevipetala (Tsui & L.H.Zhou) Sadeghian & Zarre, E. bryophylla (Fernald) Pusalkar & D.K.Singh, E. kansuensis (Maxim.) Dillenb. & Kadereit, Shivparvatia glanduligera (Edgew.) Pusalkar & D.K.Singh, Silene atsaensis (Marq.) Bocquet, S. caespitella Williams, and S. lhassana (Williams) Majumdar. METHODS: Bioinformatic software was used to conduct the comparative genome and phylogeny analysis of these cp genomes. RESULTS: The eight cp genomes were 132 188-151 919 bp in length, containing 130-132 genes. A/T was dominant in simple sequence repeats (SSRs). Forward repeats and palindromic repeats were the most frequent in long terminal repeats (LTRs). Compared with the four species of Eremogone Fenzl, the inverted repeat (IR) boundaries of S. caespitella, S. atsaensis, S. lhassana, and Sh. glanduligera were significantly expanded. Four and one mutational hotspots were identified in the large single copy (LSC) region and small single copy (SSC) region, respectively. The ratio of nonsynonymous substitution to synonymous substitution (Ka/Ks ratio) showed these cp genomes may have undergone strong purifying selection. In the phylogenetic trees, both Silene L. and Eremogone were monophyletic groups. However, Sh. glanduligera was closely related to Amaranthus hypochondriacus. CONCLUSION: These results have provided new evidence and useful information for species identification, evolution, and genetic research on the Caryophyllaceae. HIGHLIGHTS: In this study, eight newly sequenced cp genomes of Caryophyllaceae species were reported for the first time.

Chloroplast Genome Structure and Phylogenetic Analysis of 13 Lamiaceae Plants in Tibet.

BACKGROUND: The chloroplast (cp) genome has unique and highly conserved characteristics and is therefore widely used in species identification and classification, as well as to improve the in-depth understanding of plant evolution. METHODS: In this study, the cp genomes of 13 Lamiaceae plants in the Tibet Autonomous Region of China were sequenced, assembled and annotated using bioinformatics methods. Phylogenetic trees were constructed to reveal the phylogenetic relationship of related species in the Lamiaceae. RESULTS: The results showed that all 13 cp genomes had a typical four-segment structure, including one large single-copy (LSC) region, one pair of inverted repeat (IR) regions and one small single-copy (SSC) region. The sequence lengths of the 13 cp genomes were between 149,081 bp and 152,312 bp, and the average GC content was 37.6%. These genomes contained 131-133 annotated genes, including 86-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. A total of 542 SSR loci were detected using MISA software. The repeat types were mostly single-nucleotide repeats, accounting for 61% of simple repeats. A total of 26,328-26,887 codons were detected in 13 cp genomes. According to the RSCU value analysis, the codons mostly ended with A/T. Analysis of IR boundaries showed that the other species were relatively conserved, except for Nepeta laevigata (D. Don) Hand.-Mazz., which differed in gene type and location on both sides of the boundary. By analysing nucleotide diversity, two highly mutated regions located in the LSC and SSC regions were identified in the 13 cp genomes. CONCLUSIONS: Using the cp genome of Lycium ruthenicum Murray as the outgroup, 97 cp genomes of the Lamiaceae were used to construct an Maximum Likehood (ML) phylogenetic tree, in which these species were divided into eight major clades, corresponding to eight subfamilies based on morphological classification. The phylogenetic results based on monophyletic relationships were consistent with the morphological classification status at the tribe level.

Comparative analyses of five complete chloroplast genomes from the endemic genus Cremanthodium (Asteraceae) in Himalayan and adjacent areas.

Cremanthodium Benth. is an endemic genus in the Himalayas and adjacent areas. Some plants of the genus are traditional medicinal plants in Tibetan medicine. In this study, the chloroplast genomes of five species (Cremanthodium arnicoides (DC. ex Royle) Good, Cremanthodium brunneopilosum S. W. Liu, Cremanthodium ellisii (Hook. f.) Kitam., Cremanthodium nervosum S. W. Liu, and Cremanthodium rhodocephalum Diels) were collected for sequencing. The sequencing results showed that the size of the chloroplast genome ranged from 150,985 to 151,284 bp and possessed a typical quadripartite structure containing one large single copy (LSC) region (83,326-83,369 bp), one small single copy (SSC) region (17,956-18,201 bp), and a pair of inverted repeats (IR) regions (24,830-24,855 bp) in C. arnicoides, C. brunneopilosum, C. ellisii, C. nervosum, and C. rhodocephalum. The chloroplast genomes encoded an equal number of genes, of which 88 were protein-coding genes, 37 were transfer ribonucleic acid genes, and eight were ribosomal ribonucleic acid genes, and were highly similar in overall size, genome structure, gene content, and order. In comparison with other species in the Asteraceae family, their chloroplast genomes share similarities but show some structural variations. There was no obvious expansion or contraction in the LSC, SSC or IR regions among the five species, indicating that the chloroplast gene structure of the genus was highly conserved. Collinearity analysis showed that there was no gene rearrangement. The results of the phylogenetic tree showed that the whole chloroplast genomes of the five species were closely related, and the plants of this genus were grouped into one large cluster with Ligularia Cass. and Farfugium Lindl.

Effective materials and mechanisms study of Tibetan herbal medicine Lagotis integra W. W. Smith treating DSS-induced ulcerative colitis based on network pharmacology, molecular docking and experimental validation.

ETHNOPHARMACOLOGICAL RELEVANCE: Lagotis integra W. W. Smith (L. integra W. W. Smith) is an important origin plant of the famous Tibetan medicine HERBA LAGOTIS. It was documented to treat "Chi Ba" disease clinically, the symptoms of which are similar to ulcerative colitis (UC). AIMS OF THIS STUDY: To screen out the active components and study the mechanisms of L. integra W. W. Smith treating UC. MATERIALS AND METHODS: The components of L. integra W. W. Smith were comprehensively analyzed using UHPLC-Q-TOF/MS method. The mechanisms were investigated using network pharmacology method including target prediction, protein-protein interaction network analysis and gene enrichment analysis. Then, the mechanisms were verified using Dextran Sulfate Sodium (DSS)-induced UC model. Finally, the core active components were further screened out through molecular docking. RESULTS: The results showed that 32 major components were identified including 8 flavonoids, 9 phenylpropanoid glycosides, 13 iridoid glycosides and 1 phenolic acid. 76 potential core therapeutic targets and top 5 key targets, which were AKT serine/threonine kinase 1 (AKT1), vascular endothelial growth factor (VEGFA), tumor necrosis factor-α (TNF-α), epidermal growth factor receptor (EGFR) and caspase-3 (CASP3), were screened out according to network pharmacology analysis. Animal experiments confirmed that those compounds could downregulate the expression levels of the 5 key target proteins in colonic tissue of mice to exert excellent anti-UC effect. Molecular docking results showed that the main active components were echinacoside, hemiphroside B, plantamajoside, plantainoside D, 10-O-trans-isoferuloyl catalpol and scutellarioside II. CONCLUSIONS: For the first time, our study provides insights into the effective materials and molecular mechanisms of L. integra W. W. Smith treating UC, which contributes to the understanding of its pharmacodynamics.

Sequence Analysis of the Plastomes of Two Tibetan Medicinal Plants of the Family Papaveraceae.

BACKGROUND: With the rapid development of next-generation sequencing technology, more plants plastomes have been sequenced, further advancing species identification and phylogenetic studies. However, there are a few studies on the genetic and phylogenetic analysis of the plastomes of Dicranostigma lactucoides Hook. f. et Thoms. and Hypecoum leptocarpum Hook. f. et Thoms. METHODS: In this study, we sequenced and analyzed the plastomes of Dicranostigma lactucoides Hook. f. et Thoms. and Hypecoum leptocarpum Hook. f. et Thoms., and conducted a phylogenetic analysis using 13 related species. RESULTS: The results showed that the plastomes of both D. lactucoides and H. leptocarpum had a typical tetrad structure, with sizes of 166,819 bp and 163,282 bp, respectively. We annotated 133 genes for D. lactucoides and 120 genes for H. leptocarpum. A total of 72 and 43 simple repetitive sequences were detected in D. lactucoides and H. leptocarpum, respectively. Codon preference analysis showed that the relative usage frequency of codons and the relative abundance of synonymous codons used were the same for both plastomes. Nucleotide polymorphism analysis identified seven variant loci with high nucleotide diversity (Pi) values, all located in the large single copy (LSC) region. Inverted repeat (IR) boundary analysis revealed differences in gene types and locations on both sides of the boundary, except for the small single copy/inverted repeat a (SSC/IRa) boundary. The phylogenetic analysis showed the species clustered into two major groups, one with five genera (Hypecoum, Corydalis, Papaver, Meconopsis, and Dicranostigma) and the other with two genera (Coreanomecon; and Hylomecon). CONCLUSIONS: Comparative analysis of the plastome genomic characteristics and phylogeny of D. lactucoides and H. leptocarpum laid the foundation for identifying the above two species and the phylogenetic study and comprehensive exploitation of the Papaveraceae.

Lipskynoids A-G, New Acyclic Diterpenes from the Flowers of Carpesium lipskyi.

Seven new acyclic diterpenes, namely lipskynoids A-G (1-7), were isolated from the flowers of Carpesium lipskyi, a traditional Tibetan herbal medicine with anti-inflammatory and antipyretic-analgesic effects. These new compounds were elucidated by analysis of extensive spectroscopic data including ESI-MS, 1D, 2D NMR, and DP4+ analyses. Biological assays showed that 1-7 display significant inhibitory effects against the NO production in LPS-induced RAW264.7 cells with its IC50 values from 9.9 to 18.47 µM, however, no cytotoxicity effect was observed of these isolates against the growth of HePG2, PC3, DU145, and A549 cells.

Carpelipines C and D, Two Anti-Inflammatory Germacranolides from the Flowers of Carpesium lipskyi Winkl. (Asteraceae).

Two new germacranolides, carpelipine C (1) and carpelipine D (2), together with four known ones (3-6), were isolated from Carpesium lipskyi Winkl. flowers, a folk Tibetan herbal medicine with antipyretic-analgesic and anti-inflammatory effects. The chemical structures of new structure were illuminated by diversified spectroscopic and X-ray crystallographic analyses. Compounds 1 and 3 dramatically suppressed the synthesis of NO and decreased pre-inflammatory protein expression of iNOS and COX-2 in LPS-induced RAW264.7 cells. Furthermore, it was revealed that NF-κB/MAPK signaling pathway were involved in the anti-inflammatory process of 1 and 3, and their effects on reducing oxidative stress by activating Nrf2/HO-1 pathway were also measured. This article indicated that the traditional use of C. lipskyi to treat inflammatory diseases has a certain rationality.

Two Olean-27-carboxylic Acid-Type Triterpenoids as Chemical Markers Isolated from Saxifraga umbellulata.

Two olean-27-carboxylic acid-type triterpenoids (1 and 2) were isolated from Saxifraga umbellulata (Saxifragaceae), representing the first case in the chemical discoveries of genus Saxifraga. Compound 1 was determined to be a new compound named 'Saxifragic acid' based on the comprehensive spectroscopic and X-ray crystallographic analyses. Compound 2 (deacetylated saxifragic acid) is a known compound reported before, but its absolute configuration through X-ray crystallographic analyses was first described here. In addition, their cytotoxicity against five digestive human cancer cell lines (BGC-823, GBC-SD, CCC-9810, HT-29, and HepG2) and hepatoprotective activity against CCl4 -induced L-o2 cell injury in vitro were evaluated. Interestingly, UPLC-QTOFMS analysis showed that these two compounds could be used as chemical markers to discriminate between S. umbellulata and S. tangutica, both of which are used for the treatment of hepatobiliary diseases in traditional Tibetan medicine.

Integrated transcriptomic and metabolomic analyses revealed the molecular mechanism of terpenoid formation for salicylic acid resistance in Pulsatilla chinensis callus.

As a kind of traditional Chinese medicine, Pulsatilla chinensis (Bunge) Regel is well known for its anti-inflammation and anti-cancer activities, which are attributed to its active components including total saponins and monomers. To clarify the synthesis and metabolism mechanisms of class components in callus terpenes of P. chinensis, a certain concentration of salicylic acid (SA) hormone elicitor was added to the callus before being analysed by transcriptomic and metabolomic techniques. Results showed that the content of Pulsatilla saponin B4 in the callus suspension culture was significantly increased up to 1.99% with the addition of SA. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the differentially expressed genes were mainly enriched in 122 metabolic pathways, such as terpenoid metabolism-related pathways: terpenoid skeleton synthesis pathway, monoterpenoid biosynthesis pathways, diterpenoid biosynthesis pathways, and ubiquinone and other terpenoid-quinone biosynthesis pathways. A total of 31 differentially accumulated metabolites were obtained from four differential groups. Amongst 21 kinds of known chemical components in P. chinensis, deoxyloganic acid was the only monoterpenoid; the others are triterpenoids. In summary, this study found that SA elicitors can affect the metabolic changes of terpenoids in P. chinensis callus, which provided a basis for analysing the genetic regulation of terpenoid components of leucons.

The complete chloroplast genome of Mitreola yangchunensis (Loganiaceae).

The complete chloroplast (cp) genome of Mitreola yangchunensis was sequenced and assembled for the first time. The genome is 154,665 bp in length, containing a large single-copy (LSC) region of 85,351 bp, a small single-copy region (SSC) of 18,218 bp and a pair of inverted repeats (IRs) of 25,548 bp. It contains 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content is 37.9%, while the corresponding values of LSC, SSC, and IR regions are 35.9, 32.0, and 43.4%, respectively. Phylogenetic analyses using complete cp genomes showed that M. yangchunensis is most closely related to Mitrasacme pygmaea in Loganiaceae, and Gelsemiaceae and Loganiaceae form a single cluster with high support value.

The complete chloroplast genome of Stephania tetrandra (Menispermaceae).

The complete chloroplast genome of Stephania tetrandra was sequenced and assembled for the first time. The chloroplast genome is 159,974 bp in length, containing a large single-copy (LSC) region of 90,539 bp and a small single-copy region (SSC) of 20,735 bp, separated by a pair of inverted repeats (IRs) of 24,350 bp. The genome contains 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes. Among them, 15 genes have one intron each and three genes contain two introns. The overall GC content is 37.8%, while the corresponding values of LSC, SSC, and IR regions are 35.8, 32.4, and 43.7%, respectively. Phylogenetic analysis showed that S. tetrandra is more closely related to the clade of two species within Stephania, providing new insight into the evolution of Menispermaceae.

The complete chloroplast genome of Turpinia arguta (Staphyleaceae).

The complete chloroplast genome of Turpinia arguta was sequenced and assembled for the first time. The chloroplast genome was 160,139 bp in length, containing a large single-copy region (LSC) of 89,625 bp and a small single-copy region (SSC) of 18,262 bp, separated by a pair of inverted repeats (IRs) of 26,126 bp. The genome contained 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Among them, 15 genes had one intron each and 3 genes containing two introns. The overall GC content was 37.4%, while the corresponding values of LSC, SSC, and IR regions were 35.4%, 31.8%, and 42.8%, respectively. Phylogenetic analysis showed that T. arguta is more closely related to Staphylea trifolia and provided new insight into the evolution of Staphyleaceae.

The complete chloroplast genome of Mitrasacme pygmaea (Loganiaceae).

The complete chloroplast genome of Mitrasacme pygmaea was sequenced and assembled for the first time. The chloroplast genome is 152,611 bp in length, containing a large single-copy (LSC) region of 83,881 bp and a small single-copy region (SSC) of 18,110 bp, separated by a pair of inverted repeats (IRs) of 25,310 bp. The genome contains 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Among them, 15 genes have one intron each and 3 genes contain two introns. The overall GC content is 37.9%, while the corresponding values of LSC, SSC, and IR regions are 36.0%, 31.7%, and 43.4%, respectively. Phylogenetic analysis showed that M. pygmaea is sister to Gentiana tibetica and provided new insight into the evolution of Loganiaceae.

Diuretic and Antidiuretic Activities of Ethanol Extract and Fractions of Lagopsis supina in Normal Rats.

Lagopsis supina is a well-known traditional Chinese medicine and used as an agent for diuresis in China for centuries. This is the first time to evaluate the diuretic activity of the ethanol extract of L. supina (LS) and its four fractions (LSA, LSB, LSC, and LSD) in normal rats. After the administration of LS-H, LS-M, LSB-H, and LSC-L, the urine output of the rats was significantly increased, while the urine excretion was significantly reduced after treatment with LSB-L. The urine Na+ excretion was remarkably increased with LS-H, LS-M, LSA-H, LSA-L, LSB-H, LSC-L, and LSD-L, and the urine K+ excretion was significantly increased after administration of LS-H and LSB-H. Moreover, the urine Na+ and K+ excretion was significantly reduced after treatment with LSC-H and LSD-H. However, the urine pH values and urine and serum Na+-K+-ATPase levels did not show remarkable change after administration of LS or its four fractions in comparison with the control group. On the contrary, LS and its four fractions can suppress the renin-angiotensin-aldosterone system (RAAS), including ADH arrest by LSB-H, LSB-L, LSC-L, LSD-L, and LSD-H and ALD arrest by LSD-L, as well as promote ANP release by LS-M, LSB-H, LSC-H, and LSD-H, while furosemide can suppress only arrest of ADH within 24 h compared with the control group. In addition, LS and its four fractions did not change the urine and serum TNF-α and IL-6 levels in normal rats within 24 h. This study will provide a quantitative basis for explaining the natural medicinal use of LS as a diuretic agent for edema and promoting the diuretic process.

Bioactive Sesquiterpenoids from the Peeled Stems of Syringa pinnatifolia.

Fourteen new sesquiterpenoids, alashanoids A-H (1, 2, and 4-9), (+)-2,9-humuladien-6-ol-8-one (3b), and five pairs of enantiomers (1 and 4-7), along with eight known analogues (3a and 10-16) were isolated from the stems of Syringa pinnatifolia. The structures were established using IR, UV, MS, and NMR data. The absolute configurations of the new compounds were resolved by X-ray diffraction, a modification of Mosher's method, and experimental and calculated ECD data analysis. The new sesquiterpenoids represent three skeletons: a rare 2,2,5,9-tetramethylbicyclo[6.3.0]-undecane (1), a humulane-type (2-8), and a caryophyllene-type (9) skeleton. Compounds 6a, 7, and 11 showed protective effects against hypoxia-induced injury to H9c2 cells at a concentration of 40 µM, and 5-7, 11, and 13 inhibited NO production in LPS-induced RAW264.7 macrophage cells with IC50 values ranging from 13.6 to 70.6 µM. These compounds decreased the TNF-α and IL-6 levels in RAW264.7 cells in a concentration-dependent manner at 20-80 µM.

[Analysis of varieties and standards of Scrophulariaceae plants used in Tibetan medicine].

In this paper, the popular domestic varieties and quality standard of Scrophulariaceae plants used in Tibetan medicine were analyzed. The results showed that there were 11 genera and 99 species (including varieties), as well as 28 medicinal materials varieties of Scrophulariaceae plants were recorded in the relevant literatures. In relevant Tibetan standards arid literatures, there are great differences in varieties, sources, parts, and efficacies of medicinal plant. Among them, about 41.4% (including 41 species) of endemic plants, about 15.2% (including 15 species) of the original plants have medicinal standard legal records, except the medicinal materials of Scrophalaria ningpoensis, Lagotis brevituba, Picrorhiza scrophulariiflora, Veronica eriogyne general, most varieties have not completed quality standard. Consequently it is necessary to reinforce the herbal textual, resources and the use present situation investigation, the effects of the species resources material foundation and biological activity, quality standard, specification the medical terms of the plants, and promote Tibetan medicinal vareties-terminologies-sources such as the criterion and quality standard system for enriching the varieties of Tibetan medicinal materials and Chinese medicinal resources.

[Analysis of varieties and standards of Leguminosae plants used in Tibetan medicine].

In this paper, the domestic varieties and quality standard of Leguminosae medicinal plants used in Tibetan medicine were analyzed. The results showed that there were 36 genera and 142 species (including varieties), as well as 64 medicinal materials varieties of Leguminosae plants were recorded in relevant literatures. In relevant Tibetan standards and literatures, there are great differences in varieties, sources, used parts, and efficacy of medicinal plants. Among them, about 38.0% (including 54 species) of the endemic plants, about 25.4% (including 36 species) of the original plants have medicinal standard legal records, except 9 kinds of traditional Chinese medicine general quality standard more fairly completed, the most varieties have only description about characters, identification, etc. Therefore it is necessary to reinforce study for the herbal textual, resources and the use present situation, chemical components and biological activity, quality standard, medicinal terms specification, to promote establishment of quality standard system for variety-terminologies-sources of Tibetan medicinal plants.

[Traightened on Chinese endemic seed plant species of medicine plants used in Tibetan medicine].

This paper is in order to discussion with the composition and characteristics of Tibetan medicine plant resources, and promote the reasonable protection and utilization of the resources of Tibetan materia medica. Statistical analysis of species, distributions, and others of Chinese endemic seed plant from Tibetan medicine plants and usually used in the clinic of Tibetan medicine. The results showed that there are 523 species (25%) of Chinese endemic seed plant, belonging to 65 families and 162 genera, in about 2 000 varieties of Tibetan medicine plants recorded in relevant literatures. There are 180 Chinese endemic seed plant species (28%) belonging to 42 families and 72 genera from 625 medicine plants usually used in the clinic of Tibetan medicine. Specifically, the most of these Chinese endemic seed plant species are characteristic crude drug used in Tibetan medicine, and mainly or only distributed in Qinghai-Tibet Plateau. And a few species of them were intersected with traditional Chinese medicines (TCM) and other ethnic medicines. In addition, about 10% are listed in China Species Red List. The Qinghai-Tibet Plateau is the most abundant areas of Areal-types of the Chinese endemic seed plant. This is the biological and ecological reason formation the characteristics of Tibetan medicine plant resources. Therefore, strengthen the research of Chinese endemic seed plants used in Tibetan medicine is great significance for the reasonable protection and utilization of Tibetan medicine plant resources.

[Identification of cattail pollen (puhuang), pine pollen (songhuafen) and its adulterants by ITS2 sequence].

DNA barcoding method was conducted for the authentication of pollen materials due to difficulty of discriminating pollen materials bearing morphological similarity. In this study, a specific focus was to identify cattail pollen (Puhuang) and pine pollen (Songhuafen) samples from their adulterants which are frequently mixed-together. Regions of the internal transcribed spacer (ITS2) from 60 samples were sequenced, and new primers for cattail pollen were designed according to the sequence information. The results from the NJ trees showed that the species of pine pollen, Puhuang and their adulterants can be classified as obvious monophyly. Therefore, we propose to adapt DNA barcoding methodology to accurately distinguish cattail pollen, pine pollen and their adulterant materials. It is a great help for drug regulatory agency to supervise the quality of medicinal materials.