Development and evaluation of real-time quantitative PCR assays for detection of Phellinus noxius causing brown root rot disease.

Brown root rot disease (BRRD) is a highly destructive tree disease. Early diagnosis of BRRD has been challenging because the first symptoms and signs are often observed after extensive tissue colonization. Existing molecular detection methods, all based on the internal transcribed spacer (ITS) region, were developed without testing against global Phellinus noxius isolates, other wood decay fungi, or host plant tissues. This study developed SYBR Green real-time quantitative PCR (qPCR) assays for P. noxius. The primer pair Pn_ITS_F/Pn_ITS_R targets the ITS, and the primer pair Pn_NLR_F/Pn_NLR_R targets a P. noxius-unique group of homologous genes identified through a comparative genomics analysis. The homologous genes belong to the nucleotide-binding-oligomerization-domain-like receptor (NLR) superfamily. The new primer pairs and a previous primer pair G1F/G1R were optimized for qPCR conditions and tested for specificity using 61 global P. noxius isolates, five other Phellinus species, and 22 non-Phellinus wood decay fungal species. While all three primer pairs could detect as little as 100 fg (about 2.99 copies) of P. noxius genomic DNA, G1F/G1R had the highest specificity and Pn_NLR_F/Pn_NLR_R had the highest efficiency. To avoid false positives, the cutoff Cq values were determined as 34 for G1F/G1R, 29 for Pn_ITS_F/Pn_ITS_R, and 32 for Pn_NLR_F/Pn_NLR_R. We further validated these qPCR assays using Ficus benjamina seedlings artificially inoculated with P. noxius, six tree species naturally infected by P. noxius, rhizosphere soil, and bulk soil. The newly developed qPCR assays provide sensitive detection and quantification of P. noxius, which is useful for long-term monitoring of BRRD status.

Phylogeography of the wide-host range panglobal plant pathogen Phytophthora cinnamomi.

Various hypotheses have been proposed regarding the origin of the plant pathogen Phytophthora cinnamomi. P. cinnamomi is a devastating, highly invasive soilborne pathogen associated with epidemics of agricultural, horticultural and forest plantations and native ecosystems worldwide. We conducted a phylogeographic analysis of populations of this pathogen sampled in Asia, Australia, Europe, southern and northern Africa, South America, and North America. Based on genotyping-by-sequencing, we observed the highest genotypic diversity in Taiwan and Vietnam, followed by Australia and South Africa. Mating type ratios were in equal proportions in Asia as expected for a sexual population. Simulations based on the index of association suggest a partially sexual, semi-clonal mode of reproduction for the Taiwanese and Vietnamese populations while populations outside of Asia are clonal. Ancestral area reconstruction provides new evidence supporting Taiwan as the ancestral area, given our sample, indicating that this region might be near or at the centre of origin for this pathogen as speculated previously. The Australian and South African populations appear to be a secondary centre of diversity following migration from Taiwan or Vietnam. Our work also identified two panglobal, clonal lineages PcG1-A2 and PcG2-A2 of A2 mating type found on all continents. Further surveys of natural forests across Southeast Asia are needed to definitively locate the actual centre of origin of this important plant pathogen.

Tuber elevatireticulatum sp. nov., a new species of whitish truffle from Taiwan.

BACKGROUND: There are estimated 180-220 species of Tuber described in the world, but the diversity of the genus in Taiwan is poorly known, with only two species recorded, i.e., Tuber formosanum and T. furfuraceum. During our survey of hypogenous fungi in Taiwan, a whitish truffle belongs to Puberulum clade was collected from roots of Keteleeria fortunei var. cyclolepis in central Taiwan and appeared to differ from the two recorded species. RESULTS: The whitish truffle is herein described as a new species Tuber elevatireticulatum, which is distinguished from closely resembled Asian whitish truffles species like Tuber thailandicum, T. panzhihuanense, T. latisporum and T. sinopuberulum by the association with Keteleeria host, small light brown ascocarps with a dark brown gleba, dark brownish and elliptical ascospores ornamented with a prominently raised alveolate reticulum. Molecular phylogenetic analyses of both ITS and LSU loci clearly supports T. elevatireticulatum as a new species without any significant incongruence. CONCLUSIONS: The whitish truffle is herein described as a new species T. elevatireticulatum based on the evidence from morphology and DNA sequences. T. elevatireticulatum is the first scientific record of whitish truffle in Taiwan.

The Genetic Structure of Phellinus noxius and Dissemination Pattern of Brown Root Rot Disease in Taiwan.

Since the 1990s, brown root rot caused by Phellinus noxius (Corner) Cunningham has become a major tree disease in Taiwan. This fungal pathogen can infect more than 200 hardwood and softwood tree species, causing gradual to fast decline of the trees. For effective control, we must determine how the pathogen is disseminated and how the new infection center of brown root rot is established. We performed Illumina sequencing and de novo assembly of a single basidiospore isolate Daxi42 and obtained a draft genome of ~40 Mb. By comparing the 12,217 simple sequence repeat (SSR) regions in Daxi42 with the low-coverage Illumina sequencing data for four additional P. noxius isolates, we identified 154 SSR regions with potential polymorphisms. A set of 13 polymorphic SSR markers were then developed and used to analyze 329 P. noxius isolates collected from 73 tree species from urban/agricultural areas in 14 cities/counties all around Taiwan from 1989 to 2012. The results revealed a high proportion (~98%) of distinct multilocus genotypes (MLGs) and that none of the 329 isolates were genome-wide homozygous, which supports a possible predominant outcrossing reproductive mode in P. noxius. The diverse MLGs exist as discrete patches, so brown root rot was most likely caused by multiple clones rather than a single predominant strain. The isolates collected from diseased trees near each other tend to have similar genotype(s), which indicates that P. noxius may spread to adjacent trees via root-to-root contact. Analyses based on Bayesian clustering, FST statistics, analysis of molecular variance, and isolation by distance all suggest a low degree of population differentiation and little to no barrier to gene flow throughout the P. noxius population in Taiwan. We discuss the involvement of basidiospore dispersal in disease dissemination.

MicroRNA-like small RNAs prediction in the development of Antrodia cinnamomea.

Antrodia cinnamomea, a precious, host-specific brown-rot fungus that has been used as a folk medicine in Taiwan for centuries is known to have diverse bioactive compounds with potent pharmaceutical activity. In this study, different fermentation states of A. cinnamomea (wild-type fruiting bodies and liquid cultured mycelium) were sequenced using the next-generation sequencing (NGS) technique. A 45.58 Mb genome encoding 6,522 predicted genes was obtained. High quality reads were assembled into a total of 13,109 unigenes. Using a previously constructed pipeline to search for microRNAs (miRNAs), we then identified 4 predicted conserved miRNA and 63 novel predicted miRNA-like small RNA (milRNA) candidates. Target prediction revealed several interesting proteins involved in tri-terpenoid synthesis, mating type recognition, chemical or physical sensory protein and transporters predicted to be regulated by the miRNAs and milRNAs.

Genomic and transcriptomic analyses of the medicinal fungus Antrodia cinnamomea for its metabolite biosynthesis and sexual development.

Antrodia cinnamomea, a polyporus mushroom of Taiwan, has long been used as a remedy for cancer, hypertension, and hangover, with an annual market of over $100 million (US) in Taiwan. We obtained a 32.15-Mb genome draft containing 9,254 genes. Genome ontology enrichment and pathway analyses shed light on sexual development and the biosynthesis of sesquiterpenoids, triterpenoids, ergostanes, antroquinonol, and antrocamphin. We identified genes differentially expressed between mycelium and fruiting body and 242 proteins in the mevalonate pathway, terpenoid pathways, cytochrome P450s, and polyketide synthases, which may contribute to the production of medicinal secondary metabolites. Genes of secondary metabolite biosynthetic pathways showed expression enrichment for tissue-specific compounds, including 14-α-demethylase (CYP51F1) in fruiting body for converting lanostane to ergostane triterpenoids, coenzymes Q (COQ) for antroquinonol biosynthesis in mycelium, and polyketide synthase for antrocamphin biosynthesis in fruiting body. Our data will be useful for developing a strategy to increase the production of useful metabolites.

Ophiodiaporthe cyatheae gen. et sp. nov., a diaporthalean pathogen causing a devastating wilt disease of Cyathea lepifera in Taiwan.

The scaly tree fern, Cyathea lepifera, in Taiwan has been devastated by an ascomycetous pathogen in recent years. This fungus resembles species of Diaporthe, but unlike anamorphs of Diaporthe that produce two types of conidia, its anamorph produces one conidium type. It is described herein as Ophiodiaporthe cyatheae gen. et sp. nov. Through pathogenicity tests, O. cyatheae was demonstrated to be the causal agent of the C. lepifera wilt disease. Of interest, sporulating structures of O. cyatheae have not been found on C. lepifera plants but in culture thus far. The mating system is homothallic. Phylogenetic analyses based on combined sequences of nSSU-rDNA, nLSU-rDNA, EF1-α-1 and RPB2 placed O. cyatheae in Diaporthaceae. Combined sequences of EF1-α-2 and TUB indicated that O. cyatheae had its origin within Diaporthe.

Recent research and development of Antrodia cinnamomea.

Medicinal mushrooms have attracted much attention recently owing to their potent therapeutic activity, especially as chemopreventive and immunomodulatory agents. Antrodia cinnamomea is a treasured Taiwanese mushroom that has been used by aboriginal tribes for centuries to treat food intoxication and to enhance liver functions. It was included in Asian folk medicine in the last few decades with remarkable results in treating inflammatory disorders, cancers, hypertension and hepatitis. This myriad of therapeutic activities encouraged several research groups to subject A. cinnamomea to intensive biological and phytochemical investigation, leading to the isolation of different classes of pharmacologically active secondary metabolites. The in vitro and in vivo biological results of the mushroom extracts and its active components revealed their potent cytotoxic, anti-inflammatory and hepatoprotective activities. The aim of this study is to review recent reports on the biological activities of A. cinnamomea extracts and its active components; quality control protocols; synthetic methodologies for the preparation of active components; developed culture techniques; phylogenetic analysis and gene cloning. This study also tackles major challenges facing future expansion of A. cinnamomea production.

Evaluation of dazomet as fumigant for the control of brown root rot disease.

BACKGROUND: Brown root rot disease caused by Phellinus noxius is widespread in approximately 216 tree and plant species in tropical and subtropical countries. No direct means of protection against P. noxius infection have thus far been developed. Therefore, in this field survey, a method was developed for preventing and controlling brown root rot disease using fumigation with dazomet. RESULTS: Tracers were used to monitor the effect of dazomet fumigation. The results from field surveys and phytotoxicity tests showed that dazomet is able to kill P. noxius without any side effects on plants. CONCLUSION: The use of an environmentally friendly agent to control brown root rot disease is needed, and prevention of the disease is more important than treatment. Hence, chemical fumigation with 60 g m(-2) of 98% dazomet may be a possible means of preventing P. noxius incursion in agriculture, gardening and agroforestry.

Cloning and characterization of the lanosterol 14alpha-demethylase gene from Antrodia cinnamomea.

Sterol 14alpha-demethylase (CYP51) is one of the key enzymes for sterol biosynthesis in fungi; it is widely distributed in all members of the cytochrome P450 superfamily. In this study, AcCyp51, encoding a cytochrome P450 sterol 14alpha-demethylase, was obtained from the sequences of EST libraries of Antrodia cinnamomea by using 5' RACE and genome walking methods. The open reading frame of AcCyp51 is 1635 bp and encodes 544 amino acids. The recombinant protein of AcCYP51 fused with glutathione-S-transferase from Escherichia coli revealed the demethylating activity by using lanosterol as substrate and GC-MS analysis. Gene expression levels of AcCYP51 were higher in natural basidiomes than in other cell types. Transcription of AcCYP51 increased in various culture conditions including adding squalene, lanosterol, itroconazole, and oleic acid as inducers. These reveal the important functions of AcCYP51 in basidiomatal formation and suggest that it might participate in other biological processes.

Fructification of Antrodia cinnamomea was strain dependent in malt extract media and involved specific gene expression.

Antrodia cinnamomea is an expensive medicinal fungus that grows only inside the rotten trunk of Cinnamomum kanehirae . In vitro culture of A. cinnamomea fruiting body is difficult and, therefore, of value for further investigation. To study whether the fructification of A. cinnamomea is strain dependent in artificial media, we grew four different A. cinnamomea strains on malt extract agar (MEA) media. The standard MEA and a series of dilution of the MEA nutrient components were made to culture A. cinnamomea. The formation of fruiting body was determined by visual and microscopic observation on A. cinnamomea's porous morphogenesis and HPLC analysis. All A. cinnamomea strains cultured grew best in 50% MEA, but carried different capabilities of fructification. In addition, we studied four antioxidation- or senescence-related genes, including a cytochrome P450, a glutathione-S-transferase, a peroxiredoxin, and a manganese superoxide dismutase. We found both cytochrome P450 and glutathione-S-transferase were expressed 3.66- and 2.75-fold in fruiting body compared with mycelium, respectively, and perxoiredoxin and manganese superoxide dismutase were found with similar expressions in both fruiting body and mycelium.

A triterpenoid methyl antcinate K isolated from Antrodia cinnamomea promotes dendritic cell activation and Th2 differentiation.

Dendritic cells (DC) play a central role in the initiation and regulation of immune responses. Increasing evidence has indicated that manipulation of DC can serve as a therapeutic mechanism for immunomodulation. In this study we tested some unique compounds isolated from Antrodia cinnamomea, a medicinal fungus in Taiwan, on mouse bone marrow-derived DC activation. A triterpenoid methyl antcinate K (me-AntK) promoted DC maturation by enhancing the expression of MHC class II, CD86, and reducing the endocytosis. TNF-alpha, MCP-1, and MIP-1beta were secreted by DC after me-AntK treatment, indicating augmentation of innate immunity by me-AntK. Interestingly, the me-AntK-activated DC induced Ag-specific T-cell proliferation and facilitated Th2 differentiation. Examining signaling responses, we found that me-AntK treatment uniquely activated JNK and ERK in DC. Our results demonstrate that me-AntK is the first natural triterpenoid to promote the ability of DC to prime Th2 responses. This suggests that me-AntK can potentially be applied to enhance immune responses and modulate DC function in immunotherapy.

Molecular characterization and expression analysis of Acmago and AcY14 in Antrodia cinnamomea.

Mago nashi (Mago) and Y14 proteins, highly conserved among eukaryotes, participate in mRNA localization and splicing, and as such play important roles in oogenesis, embryogenesis and germ-line sex determination during animal development. Here we identified mago (Acmago) and Y14 (AcY14) homologues derived from Antrodia cinnamomea. Acmago encodes 149 amino acids and AcY14 encodes 168 amino acids. Multiple amino acid sequence alignment as well as secondary and tertiary structure prediction showed that AcMago and AcY14 have similar protein structure to the reported crystal structures of other Mago and Y14 proteins. During fungal development both Acmago and AcY14 genes were abundantly expressed in natural basidiomes. This is the first report of the molecular characterization and expression analysis of the mago and Y14 genes from fungi.

Lanostanes from Phellinus igniarius and their iNOS inhibitory activities.

Four new lanostanol-type triterpenoids, igniarens A - D ( 1- 4), were isolated from the fruit body of Phellinus igniarius together with two known triterpenoids, and two known ergostanes. These four new compounds were identified by spectroscopic analysis as 22 R-hydroxy-24-methylene-29-norlanost-7, 9(11)-dien-3-one (1), 3alpha,22 R-dihydroxy-24-methylene-29-norlanost-7, 9(11)-diene (2), 3alpha,22 R-dihydroxy-24-methylene-29-norlanost-8-ene ( 3), and 3alpha,22 R-dihydroxy-24-methylenelanost-8-ene ( 4). Their effects on NO production in lipopolysaccharide (LPS)-activated macrophages were assessed. Compounds 1- 8 inhibited NO production in activated RAW 264.7 cells to various degrees. The most potent compound 5alpha,8alpha-epidioxy-22 E-ergosta-6,22-dien-3beta-ol ( 7) significantly inhibited LPS-induced NO production in a concentration-dependent manner without affecting the cellular viability, with an IC (50) of 37.57 +/- 1.38 microM.

Compound MMH01 possesses toxicity against human leukemia and pancreatic cancer cells.

MMH01 is a compound isolated from Antrodia cinnamomea. MMH01 markedly inhibited growth of human leukemia U937 and pancreatic cancer BxPC3 cells. It resulted in distinct patterns of cell cycle distribution in U937 (G2/M, sub-G1 and polyploidy) and BxPC3 cells (G0/G1 and sub-G1). The modes of cell death in U937 cells include apoptosis and mitotic catastrophe, whereas apoptosis-associated events or necrosis in BxPC3 cells. Neither mitochondrial membrane permeabilization nor caspase dependence was noted. Proteins involving mitotic catastrophe-associated cell death such as cyclin B1 and checkpoint kinase 2 were activated in U937 cells. Only slight to moderate viability inhibition was noted to human monocytes, the normal counterpart of these myeloid leukemic cells. In conclusion, MMH01 possesses cytotoxicity against human leukemia and pancreatic cancer cells.

Lanostane-triterpenoids from the fungus Phellinus gilvus.

Triterpenoids gilvsins A-D (1-4), with oxygenated lanostane skeletons, were isolated from the fruiting body of Phellinus gilvus, together with two known compounds, 24-methylenelanost-8-ene-3beta, 22-diol and 5alpha-ergosta-7,22-diene-3-one. The structures of 1-4 were deduced from analysis of spectroscopic data. The absolute configuration at C-22 of 1 was determined by the modified Mosher's method and the structure of 1 was confirmed by X-ray analysis. The hypoglycemic activities of the crude extract of P. gilvus and the isolated compounds were also evaluated, but were not promising for further investigation.

Antifungal activity of essential oil and its constituents from Calocedrus macrolepis var. formosana Florin leaf against plant pathogenic fungi.

Resistance to conventional fungicides causes the poor disease control of agriculture. Natural products from plants have great potential as novel fungicide sources for controlling pathogenic fungi. In this study antipathogenic activity of the leaf essential oil and its constituents from Calocedrus macrolepis var. formosana Florin were evaluated in vitro against six plant pathogenic fungi. Chemical analysis of leaf oil by GC/MS allowed identification of alpha-pinene (44.2%), limonene (21.6%), beta-myrcene (8.9%), beta-caryophyllene (8.2%), caryophyllene oxide (2.4%), alpha-cadinol (1.6%), beta-pinene (1.2%), and T-muurolol (1.1%) as main components. Sesquiterpenoid components of the oil were more effective than monoterpenoid components of the oil. In particular, T-muurolol and alpha-cadinol strongly inhibited the growth of Rhizoctonia solani and Fusarium oxysporum, with the IC(50) values < 50 microg ml(-1). These compounds also efficiently inhibited the mycelial growths of Colletotrichum gloeosporioides, P. funerea, Ganoderma australe and F. solani. These results showed that T-muurolol and alpha-cadinol possess antifungal activities against a broad spectrum of tested plant pathogenic fungi and could be used as potential antifungal agents for the control of fungal diseases in plants.

Isolation and analysis of genes specifically expressed during basidiomatal development in Antrodia cinnamomea by subtractive PCR and cDNA microarray.

cDNAs specifically expressed at the basidiome stage were isolated by using PCR-selected cDNA subtraction in order to study gene regulation during porous-hymenium basidiomatal formation in Antrodia cinnamomea. blastx results suggested that most of the expressed sequence tags (52.4-69.5%) had no significant protein homology to genes from other published living things. cDNAs particularly expressed at different growing conditions were identified using cDNA microarray analysis. Reverse transcriptase PCR analyses confirmed that the clone putative to P-type ATPase, various cytochrome P450s and some unknown genes were abundant at natural basidiomes while endoglucanase was abundant at the tissue from artificial medium.

Anti-inflammatory ergostanes from the basidiomata of Antrodia salmonea.

Three new anti-oxidative ergostanes, methyl antcinate L (1), antcin M (2), and methyl antcinate K (3), together with nine additional known compounds, 3-ketodehydrosulphurenic acid, sulphurenic acid, dehydrosulphurenic acid, 3beta,15alpha-dihydroxylanosta-7,9(11),24-trien-21-oic acid, zhankuic acid A, zhankuic acid B, zhankuic acid C, antcin C, and antcin K were isolated from the basidiomata of Antrodia salmonea, a newly identified species of Antrodia (Polyporaceae) in Taiwan. These three new compounds were identified as methyl 3alpha,7alpha,12alpha-trihydroxy-4alpha-methylergosta-8,24(29)-dien-11-on-26-oate (1), 3alpha,12alpha-dihydroxy-4alpha-methylergosta-8,24(29)-dien-11-on-26-oic acid (2), and methyl 3alpha,4beta,7beta-trihydroxy-4alpha-methylergosta-8,24(29)-dien-11-on-26-oate (3) by spectroscopic analysis. We studied their antioxidative potential on the production of reactive oxygen species and nitric oxide (NO) in neutrophils and microglial cells, respectively. Compounds 1-3 displayed potent antioxidative activity with IC50 values of around 2.0-8.8 microM that was partially due to inhibition (6-67%) of NADPH oxidase activity but not through direct radical-scavenging properties. Compounds 1-3 also inhibited NO production with IC50 values of around 1.7-16.5 microM and were more potent than a non-specific NOS inhibitor. We conclude that these three new compounds 1, 2, and 3 exhibit anti-inflammatory activities in activated inflammatory cells.

New lanostanes and naphthoquinones isolated from Antrodia salmonea and their antioxidative burst activity in human leukocytes.

Four new compounds were isolated from the basidiomata of the fungus Antrodia salmonea, a newly identified species of Antrodia (Aphyllophorales) in Taiwan. These new compounds are named as lanosta-8,24-diene-3beta,15alpha,21-triol (1), 24-methylenelanost-8-ene-3beta,15alpha,21-triol (2), 2,3-dimethoxy-5-(2',5'-dimethoxy-3',4'-methylenedioxyphenyl)-7-methyl-[1,4]-naphthoquinone (3), and 2,3-dimethoxy-6-(2',5'-dimethoxy-3',4'-methylenedioxyphenyl)-7-methyl-[1,4]-naphthoquinone (4), respectively. Their structures were elucidated by spectroscopic methods. An in vitro cellular functional assay was performed to evaluate their anti-oxidative burst activity in human leukocytes. They showed inhibitory effects against phorbol 12-myristate-13-acetate (PMA), a direct protein kinase C activator, induced oxidative burst in neutrophils (PMN) and mononuclear cells (MNC) with 50 % inhibitory concentration (IC(50)) ranging from 3.5 to 25.8 microM. The potency order of these compounds in PMA-activated leukocytes was as 1 > 3 > 4 > 2. They were relatively less effective in formyl-Met-Leu-Phe (fMLP), a G-protein coupled receptor agonist, induced oxidative burst, except for compounds 3 and 4 in fMLP-activated PMN. These results indicated that three (1, 3, and 4) of these four newly identified compounds displayed anti-oxidative effect in human leukocytes with different potency and might confer anti-inflammatory activity to these drugs.