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Abies chensiensis Van Tiegh. (Pinaceae) is a rare and endangered endemic conifer in China. In this study, using the Illumina sequencing platform, we firstly characterized its whole plastid genome sequence. Our study revealed that A. chensiensis have a typical plastid genome of 121,498 bp in length, comprised of a large single copy region of 76,484 bp, a small single copy region of 42,654 bp and two inverted repeat regions of 1180 bp. A total of 113 genes, 74 protein-coding genes, 35 tRNA, and 4 rRNA genes were identified. The phylogenetic analysis indicated that A. chensiensis was placed as a sister to the congeneric A. sibirica.

Background: Transfer RNAs can participate in a variety of vital life activities. The gymnosperms with important ecological and economic values were the dominant and constructive species in the forest ecosystems in the North hemisphere. However, evolution and structural changes of chloroplast tRNA in gymnosperms remain largely unclear.Results: In this study, the nucleotide evolution, phylogenetic relationships and structural variations of 1,779 chloroplast tRNAs in gymnosperms were determined. The number and types of tRNA genes contained in the chloroplast genome of different gymnosperms were not much different, the average amount of tRNA contained was 33, and the occurrence frequency of various types of tRNA in gymnosperms was generally consistent. Nearly half of the anti-codons were absent. Molecular sequence variation analysis revealed the conservative secondary structure of tRNA. About a quarter of the tRNA genes were found to contain precoded 3’ CCA tails. A few tRNAs underwent novel structural changes that were closely related to their minimum free energy, these structural changes affected the stability of tRNA. Phylogenetic analysis showed that tRNAs have evolved from multiple common ancestors and tRNALeu was the most primitive type of tRNA. The transition rate of chloroplast tRNAs was higher than the transversion rate in gymnosperms. The tRNAs continuously have experienced more loss than duplication events during the evolutionary process. Conclusions: These findings provided novel insights into the molecular evolution and biological characteristics of the chloroplast tRNA in gymnosperms.

Acer davidii Franch. and A. morrisonense Hayata are two important forest tree species (Aceraceae) endemic to mainland China and the Taiwan area, respectively. To investigate population structure and interspecific differentiation between them, we characterized a set of novel microsatellite markers using Illumina sequencing technology. The cross-species amplification analysis showed that 11 out of 21 polymorphic SSR primers of A. davidii also exhibited polymorphisms in A. morrisonense. At the species level, A. davidii has a slightly higher genetic diversity (mean observed heterozygosity, HO = 0.180) than A. morrisonense (HO = 0.119). AMOVA showed that most of the variations in A. davidii occurred among individuals within populations and within individuals. Bayesian clustering analyses demonstrated that the two maple species formed two clear genetic lineages. PCoA showed that A. davidii and A. morrisonense were significantly divided into two genetic groups. In addition, asymmetrical weaker gene flow was detected among the two forest tree species. These results suggest that the long term geographic isolation between the mainland and Taiwan may have resulted in a high level of genetic differentiation between these two important maple species.

The complete chloroplast (cp) genome of Bupleurum boissieuanum was assembled from high-throughput Illumina sequencing data. The cp genome is 156,108 bp in length, and comprises a pair of 26,303-bp inverted repeat (IR) regions, which are separated by one small single-copy (SSC) region of 17,495 bp and one large single-copy (LSC) region of 86,007 bp. It contains 112 unique genes, with 17 of them being duplicated within the IR. The overall G+C content of the whole genome is 37.7%, and the corresponding values of the LSC, SSC and IR regions are 35.8, 31.4 and 42.8%, respectively. Phylogenetic analysis was conducted to assess inter-relationships among the major clades of Apiaceae, and suggested that B. boissieuanum is closely related to the congeneric B. falcatum.

Polygala tenuifolia Willd. is an important traditional Chinese medicinal herb. In the present study, inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic variability in 20 natural populations of P. tenuifolia. The genetic diversity was low at the population level (PPB = 29.95%, h = 0.0795, I = 0.1261), but substantially higher at the species level (PPB = 90.91%, h = 0.3100, I = 0.4620). The hierarchical analysis of molecular variance (AMOVA) revealed pronounced genetic differentiation among populations (ΦST = 0.6803), in line with the high gene differentiation coefficient (GST = 0.7448) and limited among-population gene flow (Nm = 0.1713). Both Bayesian assignment analysis and Principal Coordinates Analysis (PCoA) supported the grouping of the sampled populations (excluding MX and NS) into three genetic clusters, corresponding to three geographic groups; moderate genetic differentiation occurred among the geographic groups (ΦST = 0.1500). The isolation-by-distance pattern revealed by Mantel test (r = 0.5336, P = 0.0001, 9999 permutations) indicated a clear geographic tendency in the distribution of genetic diversity in this species. Considering the low within-population but relatively higher intraspecific genetic diversities and the pronounced among-population genetic differentiation, we suggest that in situ conservation measures be taken to preserve maximum genetic variability in this species and that a possibly maximum number of populations be conserved.

Euphorbia kansui is a threatened perennial herb endemic to China, and a good knowledge of its population genetics would be essential to the formulation of effective conservation and management strategies. In this study, 12 novel microsatellite markers were developed for E. kansui using Illumina sequencing technology. The number of alleles varied between 2 and 11, with an average of 4.1 alleles per locus. The expected (H E) and observed heterozygosity (H O) ranged from 0.0950 to 0.7875 and from 0.0500 to 0.9500, with an average of 0.4050 and 0.4083, respectively. Following the false discovery rate controlling procedure, significant deviations from Hardy–Weinberg equilibrium was only detected in a single locus (Ek1073). These informative microsatellite markers can be readily used for genetic analyses of this threatened plant.

Orchidaceae is the 3rd largest family of angiosperms, an evolved young branch of monocotyledons. This family contains a number of economically-important horticulture and flowering plants. However, the limited availability of genomic information largely hindered the study of molecular evolution and phylogeny of Orchidaceae. In this study, we determined the evolutionary characteristics of whole chloroplast (cp) genomes and the phylogenetic relationships of the family Orchidaceae. We firstly characterized the cp genomes of four orchid species: Cremastra appendiculata, Calanthe davidii, Epipactis mairei, and Platanthera japonica. The size of the chloroplast genome ranged from 153,629 bp (C. davidi) to 160,427 bp (E. mairei). The gene order, GC content, and gene compositions are similar to those of other previously-reported angiosperms. We identified that the genes of ndhC, ndhI, and ndhK were lost in C. appendiculata, in that the ndh I gene was lost in P. japonica and E. mairei. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in orchid species. E. mairei had the highest number of repeats (81), while C. davidii had the lowest number (57). The total number of Simple Sequence Repeats is at least 50 in C. davidii, and, at most, 78 in P. japonica. Interestingly, we identified 16 genes with positive selection sites (the psbH, petD, petL, rpl22, rpl32, rpoC1, rpoC2, rps12, rps15, rps16, accD, ccsA, rbcL, ycf1, ycf2, and ycf4 genes), which might play an important role in the orchid species’ adaptation to diverse environments. Additionally, 11 mutational hotspot regions were determined, including five non-coding regions (ndhB intron, ccsA-ndhD, rpl33-rps18, ndhE-ndhG, and ndhF-rpl32) and six coding regions (rps16, ndhC, rpl32, ndhI, ndhK, and ndhF). The phylogenetic analysis based on whole cp genomes showed that C. appendiculata was closely related to C. striata var. vreelandii, while C. davidii and C. triplicate formed a small monophyletic evolutionary clade with a high bootstrap support. In addition, five subfamilies of Orchidaceae, Apostasioideae, Cypripedioideae, Epidendroideae, Orchidoideae, and Vanilloideae, formed a nested evolutionary relationship in the phylogenetic tree. These results provide important insights into the adaptive evolution and phylogeny of Orchidaceae.

Anatomical, histochemical and phytochemical methods were used to investigate the structure, localization and dynamic changes of total saponin and senegenin of vegetative organs in Polygala tenuifolia Willd. Histochemical localization results showed that saponin accumulated mainly in parenchyma cells of vegetative organs. The phytochemical results also showed that the saponin accumulated in the vegetative organs of P. tenuifolia, with higher content in roots and lower content in the aerial parts that included stems and leaves. The saponin content and dry weight of the vegetative organs of P. tenuifolia had dynamic variance at the developmental stages and all reached the highest level in the post-fruit period. Hence, the roots and aerial parts should be gathered in August to make full use of the plant. As the root is the main medicinal organ of P. tenuifolia, the content of total saponin and senegenin of different aged and different parts of the root were determined. The content of total saponin and senegenin exhibited a sustained decreasing trend with increasing root age; therefore, the annual roots had high quality. The content of total saponin and senegenin in different parts of the root showed obvious variation. The content in the "skin areas" was much higher than that of xylem. The results offer a theoretical basis for determining the appropriate harvesting stage and a reasonable harvest of P. tenuifolia.

To study the pharmacokinetic effect of different combined administration with monarch drug Ziziphi Spinosae Semen on its main components in rats. Sprague-Dawley (SD) rats were randomly divided into Ziziphi Spinosae Semen group, Ziziphi Spinosae Semen-Fructus Schisandrae Chinensis group, Ziziphi spinosae Semen-Salviae Miltiorrhize Radix et Rhizoma group and Zaoren Ansheng prescription group. After oral administration, HPLC was eluted with the mobile phase of acetonitrle-0.03% phosphate acid water in a gradient mode. The detection wavelength was 280 nm. The pharmacokinetic parameters of spinosin and ferulic acid were calculated by DAS 2. 0 software. Compared with Ziziphi Spinosae Semen group, Ziziphi Spinosae Semen-Fructus Schisandrae Chinensis group, Ziziphi Spinosae Semen-Salviae miltiorrhizae Radix et Rhizoma group showed a lower maximum plasma concentration (C(max)) and area under curve (AUC(0-t)) for spinosin and ferulic acid but higher clearance speed (CL/F); whereas the Zaoren Ansheng prescription group showed higher maximum plasma concentration (C(max)) and area under curve (AUC(0-t)) for spinosin and ferulic acid but lower clearance speed (CL/F). Compared with Ziziphi Spinosae Semen group, prescription group showed slower metabolism of spinosin and ferulic

Juniperus pingii (Ping's juniper) is a threatened conifer species endemic to China, and a good knowledge of its population genetics would be essential to formulate effective conservation strategies. In this study, ten polymorphic microsatellite loci were isolated, and characterized for their utility using 58 individuals from two geographically distinct populations. In population XGLL, the number of alleles per locus (N (A)) ranged from four to 11, with an average of 6.2 per locus; the observed (H (O)) and expected heterozygosity (H (E)) ranged from 0.205 to 0.854 and from 0.423 to 0.754, with an average of 0.347 and 0.527, respectively. In population BM, N (A), H (O) and H (E) ranged from four to eight, from 0.198 to 0.454 and from 0.339 to 0.853, with an average of 5.8, 0.294 and 0.556, respectively. Following the sequential Bonferroni correction, only one locus (Jp07) was found to deviate significantly from Hardy-Weinberg equilibrium within population XGLL, and no significant linkage disequilibrium was detected in any of these loci within either population. These polymorphic microsatellite loci would be useful for population genetic studies of this conifer species.

The complete nucleotide sequence of the Taiwan red pine Pinus taiwanensis Hayata chloroplast genome (cpDNA) is determined in this study. The genome is composed of 119,741 bp in length, containing a pair of very short inverted repeat (IRa and IRb) regions of 495 bp, which was divided by a large single-copy (LSC) region of 65,670 bp and a small single-copy (SSC) region of 53,080 bp in length. The cpDNA contained 115 genes, including 74 protein-coding genes (73 PCG species), 4 ribosomal RNA genes (four rRNA species) and 37 tRNA genes (22 tRNA species). Out of these genes, 12 harbored a single intron, and one (rps12) contained a couple of introns. The overall AT content of the Taiwan red pine cpDNA is 61.5%, while the corresponding values of the LSC, SSC and IR regions are 62.2%, 60.6% and 63.6%, respectively. A maximum parsimony phylogenetic analysis suggested that the genus Pinus, Picea, Abies and Larix were strongly supported as monophyletic, and the cpDNA of P. taiwanensis is closely related to that of P. thunbergii.

The effects of enhanced ultraviolet-B (UV-B) radiation on chemical compositions of radix, stem and leaf of Scutellaria baicalensis Georgi were studied via FTIR Results showed that alcohols and phenolic substances in the radix and leaf of S. baicalensis Georgi were increased by UV-B radiation as well as the content of flavonoids and flavonoids glycosides. The terpenoids content in radix and protein content in leaf were increased by supplementary UV-B radiation. Contrary to the circumstance in radix and leaf, contents of alcohols and phenolic, flavonoids, unsaturated fat and lactone in stem were decreased by UV-B radiation. These results indicated that there is a trade-off in distribution of the metabolites in radix, stem and leaf of different parts. More information could be revealed for the result of FTIR spectral analysis via FTIR second derivative spectrum, especially the information of the combination between flavonoids and glycosides. The effects of UV-B radiation on chemical composition in radix, stem and leaf of S. baicalensis Georgi could be examined simply and rapidly via the method of FTIR. Thus, it can be used as a prior method before the further analysis of chemical composition.

Anatomical, histochemical and phytochemistry methods were used to investigate the structure of vegetative organs, and saponins localization and dynamic changes in Polygala sibirica L. The root consisted of developed periderm and secondary vascular. The secondary phloem was thick, and mainly composed of parenchyma. There were well-developed vessels and fibers in the secondary xylem. The stem was composed of epidermis, cortex and vascular bundle. The ring of sclerenchymatous cells lied between cortex and phloem might be the apoplastic protective screen which could protect the stem from drought. The leaf was bifacial one. The root and stem possessed characteristics adapting to arid environment. Histochemical localization results showed that saponins distributed in secondary phloem and phelloderm of root, in epidermis, cortex and phloem of stem, mainly in mesophyll of leaf. It displayed that saponins accumulated mainly in parenchyma cells of vegetative organs, among of which, the secondary phloem was the main storage site. The HPLC results also showed that the saponins accumulated in all the vegetative organs of Polygala sibirica L., with higher content in roots and lower content in the aerial part that included stems and leaves. The study indicated the aerial part of Polygala sibirica L. also had medicinal value. The saponins content had dynamic variance at the developmental stage, the crude drug should be gathered at period from April to May.

To establish an HPLC-ESI-MS(n) method for analyzing the chemical ingredients in the water soluble extracts of Fructus Choerospondiatis.Water-solvable extracts of Fructus Choerospondiatis are obtained by heating recirculation. Multi-stage reaction mode (MRM) of the HPLC-ESI-MS(n) was used to determine the content of Gallic acid, the MS(n) technology was used to obtain the information of characteristic multistage fragment ions so as to identify the chemical structure of peaks in the total current spectrum.Eleven compounds were identified, and one of them is a new unknown ingredient.The method, which has high recovery and specificity, can offer the experimental evidences for the further research of the chemical ingredients extracted from the Fructus Choerospondiatis.