Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume.

Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine-cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.

Veronicastrum wulingense (Plantaginaceae), a new species from Southwestern Hubei, China.

BACKGROUND: The genus Veronicastrum Heist. ex Fabr. are mainly distributed in East Asia, and only Veronicastrum virginicum (L.) Farw. is disjunctively distributed in eastern North America. The south area of China (extending to Taiwan Island) is the richest in Veronicastrum species. It is of medicinal importance in China as traditional herbs used to treat ascites diseases that caused by schistosomiasis. During field investigation of plant resources in Pingbaying National Forest Park, Southwestern Hubei, China, an unknown flowering population of Veronicastrum was discovered from thick humus layers adjacent to rocks under broad-leaved forests by walkways. They were collected and morphological characters assesed for further taxonomic treatment. Molecular analysis was also conducted to ascertain its phylogenetic position in the genus Veronicastrum. RESULTS: This species is similar to Veronicastrum liukiuense (Ohwi) T.Yamaz. from the Ryukyu Islands, but can be distinctly differed by its axillary inflorescences (versus terminal on short leafy branches), pedicels up to 2.5 mm (versus sessile), corollas purple to purple-red (versus white tinged with pale purple) and florescence June to July (versus September to October). Also, phylogenetic studies showed the species was an independent clade in the genus Veronicastrum based on the maximum likelihood (ML) analyses using two different matrix sequences of concatenated molecular markers. The plastid genome of this new species is also reported in this study for the first time. CONCLUSION: The morphological and molecular evidences support the recognition of Veronicastrum wulingense as a new species.

Morphological Characteristics and Comparative Chloroplast Genome Analyses between Red and White Flower Phenotypes of Pyracantha fortuneana (Maxim.) Li (Rosaceae), with Implications for Taxonomy and Phylogeny.

Pyracantha fortuneana (Maxim.) Li (Rosaceae), commonly known as Chinese firethorn, is an evergreen shrub with high nutritional, medicinal, and horticultural importance. This species typically has white flowers, but a rare red flower phenotype has been found in very few wild populations in western Hubei, China, showing great ornamental potential. In this study, the complete chloroplast genome of the red flower phenotype of P. fortuneana was reported for the first time, using high-throughput sequencing technology. The complete chloroplast genome was 160,361 bp in length and showed a typical quadripartite structure with a pair of inverted repeat (IR) regions (26,350 bp) separated by a large single-copy (LSC) region (88,316 bp) and a small single-copy (SSC) region (19,345 bp). A total of 131 functional genes were annotated in this chloroplast genome, including 86 protein-coding genes (PCGs), eight rRNA genes, and 37 tRNA genes. Comparative chloroplast genome analyses revealed that high genome similarity existed not only between red and white flower phenotypes of P. fortuneana, but also among Pyracantha species. No evidence for positive selection was found in any PCG, suggesting the evolutionary conservation of Pyracantha chloroplast genomes. Furthermore, four mutational hotspots (trnG-trnR-atpA, psbZ-trnG-trnfM-rps14, ycf3-trnS-rps4, and ndhF-rpl32) with π > 0.004 were identified as potential molecular markers for Pyracantha species. Phylogenomic analysis strongly supported that the red flower phenotype of P. fortuneana was nested within the common white flower phenotype. Based on both morphological and molecular evidence, we suggest that the red flower phenotype of P. fortuneana could be considered as a new forma. Overall, the availability of these genetic resources will not only offer valuable information for further studies on molecular taxonomy, phylogeny, and population genetics of Pyracantha species but also could be used as potential genetic resources for Chinese firethorn breeding.

Traditional Uses, Phytochemistry, and Pharmacological Properties of the Genus Blechnum-A Narrative Review.

Blechnum L. is a genus belonging to the Blechnaceae family with 236 accepted species that grow in intertropical, subtropical, and southern temperate regions. Several species of the genus have long been used in folk medicines to treat a broad spectrum of ailments, including typhoid, urinary infections, influenza, wounds, pulmonary complaints, blisters, boils, and antihelmintic-related complications. So far, about 91 chemical compounds have been isolated from different parts of 20 Blechnum species. Among these metabolites, phenolic compounds, sterols, and fatty acids are the main constituents. Modern pharmacological investigations revealed several isolated compounds and extracts to exhibit exceptional biological properties including the antioxidant, antimicrobial, anti-inflammatory, anticancer, insecticidal, antitrematocidal and wound healing. In various tests, both quercetin-7',3',4'-trimethoxy and phytol metabolites showed potential antioxidant and antitrematocidal properties, while ponasterone exhibited insecticidal activity. Despite having a broad range of traditional medicinal benefits and biological properties, understanding the scientific connotations based on the available data is still challenging. This article presents a comprehensive review of the traditional uses, phytochemical compounds, and pharmacological aspects of the Blechnum species.

Comparative and Phylogenetic Analysis Based on the Chloroplast Genome of Coleanthus subtilis (Tratt.) Seidel, a Protected Rare Species of Monotypic Genus.

Coleanthus subtilis (Tratt.) Seidel (Poaceae) is an ephemeral grass from the monotypic genus Coleanthus Seidl, which grows on wet muddy areas such as fishponds or reservoirs. As a rare species with strict habitat requirements, it is protected at international and national levels. In this study, we sequenced its whole chloroplast genome for the first time using the next-generation sequencing (NGS) technology on the Illumina platform, and performed a comparative and phylogenetic analysis with the related species in Poaceae. The complete chloroplast genome of C. subtilis is 135,915 bp in length, with a quadripartite structure having two 21,529 bp inverted repeat regions (IRs) dividing the entire circular genome into a large single copy region (LSC) of 80,100 bp and a small single copy region (SSC) of 12,757 bp. The overall GC content is 38.3%, while the GC contents in LSC, SSC, and IR regions are 36.3%, 32.4%, and 43.9%, respectively. A total of 129 genes were annotated in the chloroplast genome, including 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The accD gene and the introns of both clpP and rpoC1 genes were missing. In addition, the ycf1, ycf2, ycf15, and ycf68 were pseudogenes. Although the chloroplast genome structure of C. subtilis was found to be conserved and stable in general, 26 SSRs and 13 highly variable loci were detected, these regions have the potential to be developed as important molecular markers for the subfamily Pooideae. Phylogenetic analysis with species in Poaceae indicated that Coleanthus and Phippsia were sister groups, and provided new insights into the relationship between Coleanthus, Zingeria, and Colpodium. This study presents the initial chloroplast genome report of C. subtilis, which provides an essential data reference for further research on its origin.

Morphological and genomic evidence for a new species of Corallorhiza (Orchidaceae: Epidendroideae) from SW China.

Corallorhiza sinensis, a new species of mycoheterotrophic orchid from western Sichuan, China, is described and illustrated based on molecular and morphological evidence. It is morphologically similar to Corallorhiza trifida, but can be distinguished by bigger flowers, both sepals and petals with 3 veins, and longer lateral lobes of lip. To distinguish the new Corallorhiza species and explore its phylogenetic position within subtribe Calypsoinae, this study employed sequences of the nuclear ribosomal DNA (nrDNA) and whole plastome assembled from the genome skimming approach. The plastome is 148,124 bp in length, including a pair of inverted repeats (IRs) of 26,165 bp, a large single-copy region (LSC) of 82,207 bp, and a small single-copy region (SSC) of 13,587 bp. Further, phylogenetic analyses were performed using nrDNA sequence and 79 coding sequences (CDSs) from 26 complete plastomes of subtribe Calypsoinae. The phylogenetic tree based on nrDNA sequence suggested that Corallorhiza is a monophyletic group, and strongly support C. sinensis as sister to the rest species of Corallorhiza. The plastid tree showed that 10 Corallorhiza species grouped into two clades and C. sinensis is most closely related to the North American C. striata and C. bentleyi instead of Oreorchis foliosa and O . angustata in the same clade. The plastid tree and nrDNA tree indicate Oreorchis is a paraphyletic. Although the topological conflicts are displayed between plastome and nrDNA phylogenies of C. sinensis, it is still the most closely related to Corallorhiza. Comparative analysis showed that C. sinensis populations are characteristic of the intermediate morphological traits between Corallorhiza and Oreorchis. The finding of this new species from China shed new light on the phylogeny of Oreorchis and Corallorhiza.

Outcomes of Interferon/Ribavirin Therapy in Patients with HCV Defined by Expression of Plasma Soluble Human Leukocyte Antigen-G but Not IL-37.

BACKGROUND Chronic hepatitis C virus (HCV) infection leads to life-threatening complications worldwide. Immunomodulation signals the response to virus clearance. The immune-suppressive molecule human leukocyte antigen-G (HLA-G) has been shown to function in inhibiting both innate and adaptive immune responses. The objective of this study was to investigate the expression of HLA-G and IL-37 in sustained virological response (SVR) and non-SVR HCV-positive patients before and after complete treatment with a combination of pegylated interferon (IFN) and ribavirin (RBV). MATERIAL AND METHODS Our study included 132 chronic hepatitis C patents who received combined therapy with IFN-a and RBV. Both SVR and non-SVR patients were included. The end-of-treatment response was defined as undetectable HCV RNA at week 48. Patients with end-of-treatment response were detected by HCV RNA at 24 weeks after therapy. The expression levels of HLA-G and IL-37 at the end and 24 weeks after treatment were detected by ELISA. RESULTS Plasma HLA-G and IL-37 were significantly increased in HCV-infected patients compared with healthy individuals before treatment. Furthermore, HLA-G in SVR patients was noticeably decreased after treatment, while HLA-G in non-SVR patients had no changes after treatment. Additionally, both in SVR and non-SVR patients, the expression of IL-37 was remarkably reduced compared with baseline after treatment. CONCLUSIONS These findings suggest that elevation of HLA-G and IL-37 in HCV may play an important role in response to combined therapy with IFN-a and RBV. Monitoring the expression of HLA-G during therapy could contribute to adjusting the treatment program of HCV-infected patients.

Resistant mutants induced by adefovir dipivoxil in hepatitis B virus isolates.

AIM: To investigate the loci of adefovir dipivoxil (ADV)-induced resistance in hepatitis B virus (HBV) isolates and optimize the management of ADV-treated patients. METHODS: Between June 2008 and August 2010, a cross-sectional control study was conducted comprising 79 patients with chronic HBV infection-related liver disease who had been administered ADV monotherapy. Patients underwent liver imaging. Serum DNA extracts were analyzed for HBV DNA levels, genotypes, and serology markers, and deep sequencing of the HBV P gene was performed. RESULTS: ADV-resistant patients were found either with a single mutated locus, or with coexisting mutated loci. The most prevalent mutations were rtA181T, rtV214A, and rtN236T. Twenty-six patients had more than two mutated loci. The mutants were distributed among the patients without any significant affinity for gender, age, end-stage of liver disease, complications of non-alcoholic fatty liver disease, or HBV DNA levels. Patients with the rtA181T mutant were primarily infected with genotype C and e-antigen negative HBV, while patients with the rtN236T mutant were primarily infected by genotype B HBV (χ(2) = 6.004, 7.159; P = 0.023, 0.007). The duration of treatment with ADV was shorter in the single mutant group compared with the multi-mutant group (t = 2.426, P = 0.018). CONCLUSION: Drug-resistant HBV mutants are complex and diverse. Patients should receive the standard and first-line antiviral treatment, strictly comply with medication dosage, and avoid short-term withdrawal.

[Clinical analysis of hepatitis B virus mutations related to adefovir dipivoxil among patients with chronic hepatitis B virus infection in eastern Zhejiang province].

OBJECTIVE: To explore the clinical characteristics of hepatic B virus (HBV) mutations related to adefovir dipivoxil (ADV) among patients with chronic HBV infection in eastern Zhejiang province and provide some reference values on normative usage of antiviral drugs. METHODS: The data of chronic HBV-infected patients with HBV mutations related to ADV (n = 88) and non-mutation (n = 202) from June 2008 to August 2010 were analyzed retrospectively. The gene resistance mutations of HBV P region were analyzed by gene sequencing. And the HBV genotypes, HBV serum markers, HBV DNA levels and liver imaging findings were also analyzed. RESULTS: There were 9 cases with pre-existing mutations in 88 patients. The mutated sites were multiple and complicated. And the mutated sites related to other antiviral drugs were all accompanied by ADV-related mutations. The single mutated site was mostly at rtA181T (46.59%) and at rtV214A (11.36%). There were 27 cases (30.68%) with ≥ two mutated sites. The constituent ratios of males, end-stage liver diseases, complicated nonalcoholic fatty liver disease (NAFLD) and HBV genotype C infection in the mutation group were higher than those in the non-mutation group (P < 0.01, < 0.01, 0.019, 0.045). The average ages in the mutation group were also higher than those in the non-mutation group (P < 0.001). But the constituent ratios of HBeAg positivity and the levels of HBV DNA were lower (P = 0.002, 0.02). CONCLUSION: There may be some cases with pre-existing ADV-related mutations in ADV treatment-naive patients. The mutated sites occur at multiple loci, mostly at rtA181T and rtV214A. The male patients and those with a longer history of HBV infection, HBeAg negativity, HBV genotype C infection, illness progression and complicated NAFLD may be more susceptible to mutation. It is important for patients to accept and implement standardized regimens of antiviral drugs so as to prevent resistance and avoid salvage therapy.

Elevation of plasma soluble human leukocyte antigen-G in patients with chronic hepatitis C virus infection.

The subversion of immune responses that hepatitis C virus (HCV) uses to escape immune surveillance and to establish persistent infection has been poorly understood. The immune-suppressive molecule human leukocyte antigen-G (HLA-G) has been supposed to play important roles in viral infection. In the current study, HCV genotype was analyzed in 67 chronic HCV-infected (CHC) patients. Plasma soluble sHLA-G (including sHLA-G1 and HLA-G5), interleukin-10 (IL-10), and interferon-γ (IFN-γ) levels were determined in these CHC patients and in healthy subjects by enzyme-linked immunosorbent assay, and the sHLA-G isoforms present in plasma were determined by Western blot. Data showed that HCV 1b was the predominant genotype, with a prevalence of 64.2%. sHLA-G was dramatically increased in CHC patients (median: 85.54 U/ml, range: 19.40-204.07) over that in normal controls (median: 9.13 U/ml, range: 5.07-69.56) (p < 0.001). Western blotting revealed that plasma sHLA-G was derived from sHLA-G1 and HLA-G5. IL-10 and IFN-γ levels were also significant higher in CHC patients than in normal controls (median: 16.3 pg/ml vs 1.8 pg/ml, p < 0.001, and 1025.3 pg/ml vs 858.3 pg/ml, p = 0.03, respectively). No significant association was observed for the HCV genotype and viral RNA load with the levels of sHLA-G, IL-10, and IFN-γ in CHC patients. These results indicate that elevation of sHLA-G expression in HCV patients was independent of viral genotype and viral RNA load. Given its immunotolerant property, an increase in sHLA-G may play a role in the persistency of HCV infection.

[Study of the effect and mechanism of spastic paraplegia 21 protein on the replication of hepatitis B virus].

OBJECTIVE: To study the effect of human spastic paraplegia 21 protein (SPG21) on the replication of hepatitis B virus(HBV) and its regulatory mechanism. METHODS: HBV infectious clone pHBV1.3 and its promoter pHBV-Luc were transfected respectively into HepG2 cells with SPG21 of different concentrations, HBsAg and HBeAg in the supernatants were measured by enzyme linked immunosorbent assay (ELISA), expression of HBV core mRNA and protein were detected by RT-PCR and western blot, covalently closed circular DNA(ccc DNA) levels were measured by real-time PCR, and HBV promoter activity was measured by luminometer fluorescence detector. RESULTS: Expression of HBsAg, HBeAg, HBV core protein and cccDNA were upregulated by SPG21 as well as HBV promoter activity in a dose-dependent approach. The activity of HBV promoter increased to 1.63, 3.09 and 4.66 times in HepG2 cells treated with 50mug/ml, 100mug/ml and 200mug/ml SPG21 respectively during 48 hour-treated ( P less than 0.05), as compared to the control group. CONCLUSIONS: SPG21 can enhance the replication of HBV in HepG2 cells.

[Effect of hepatitis B virus X gene on the expression of spastic paraplegia 21].

OBJECTIVE: To investigate the effect of hepatitis B virus(HBV) X gene on the expression of SPG21. METHODS: The expressions of SPG21 mRNA and protein in HepG2 and HepG2.2.15 cells were tested by RT-PCR and western blot. HepG2 cells were co-transfected with reporter plasmid pGL3-SPG21 and plasmids carrying individual genes of HBV, the luciferase activity was measured and the expressions of SPG21 were detected by RT-PCR and western blot. RESULTS: The expressions of SPG21 mRNA and protein were higher in HepG2.2.15 cells than in HepG2 cells (0.36+/-0.06 vs 0.21+/-0.05, P value is less than 0.05). The activity of SPG21 in HepG2 cells transfected with pCMV-X was higher (875+/-27 vs 67+/-12, P value is less than 0.01) as compared to blank control group (transfected with pCMV-tag2B). HBV X gene enhanced SPG21 gene promoter activity, SPG21 mRNA expression and SPG21 protein production in HepG2 cells in a dose-dependent manner. CONCLUSION: HBV X gene can specially activate SPG21 expression.