Screening for differentially expressed genes in Anoectochilus roxburghii (Orchidaceae) during symbiosis with the mycorrhizal fungus Epulorhiza sp

PKC-SWI6 signaling regulates asexual development, cell wall integrity, stress response, and lifestyle transition in the nematode-trapping fungus Arthrobotrys oligospora

Predatory fungi possess intricate signal transduction systems that regulate their development and support successful infection of the host. Herein, we characterized three components of the cell wall integrity-controlling pathway, namely protein kinase C (AoPKC), SLT2-MAPK (AoSLT2), and SWI6 (AoSWI6), in a representative nematode-trapping fungus Arthrobotrys oligospora, using gene disruption and multi-omics approaches. The phenotypic traits (such as mycelia development, conidiation, stress response, and trap morphogenesis) and metabolic profiles of ΔAopkc and ΔAoswi6 mutants were similar but differed from those of the ΔAoslt2 mutants. Transcriptomic analysis indicated that the genes differentially expressed in the absence of Aoswi6 were involved in DNA replication, repair, and recombination during trap formation. Moreover, the yeast two-hybrid assay showed that AoPKC interacted with AoSWI6, suggesting that in A. oligospora, PKC can directly regulate SWI6, bypassing the SLT2 signaling cascade. Conclusively, our findings deepen our understanding of the regulatory mechanism of asexual development and lifestyle switching in nematode-trapping fungi.

Establishment of In Vitro Regeneration Protocol for Sabah’s Jewel Orchid, Macodes limii J.J. Wood & A.L. Lamb

Habitat disturbance and excessive collection of wild orchids from their natural habitat have threatened many orchids species at risk of extinction. In this study, the in vitro regeneration protocol for Macodes limii, a jewel orchid endemic to Sabah was established. The effects of explant source and plant growth regulators (PGRs) including naphthaleneacetic acid, picloram, 2,4-dichlorophenoxyacetic acid, 6-benzylaminopurine, kinetin, and thidiazuron on the in vitro regeneration capacity of M. limii plantlets were examined. Both factors showed a significant interaction in promoting axillary shoot formation. Nodal explants from the third and fourth positions cultured with 1.0 mg/L TDZ, induced 95% of shoot regeneration, with an average of three shoots/explant (1.6–1.8 cm of shoot length) after 90 days of culture. The well-developed plantlets went through an acclimatization phase for 60 days with a 60% of survival rate. An inter simple sequence repeat (ISSR) marker analysis confirmed the genetic stability of the in vitro regenerated plants to the mother plant. The successfully acclimatized plantlets were finally transferred to Poring Orchid Conservation Centre for reintroduction. The established protocol provides the means for large-scale production of this endemic jewel orchid, as well as a basis for further research aimed at the conservation and genetic improvement of this plant.

Beneficial Effects of Endophytic Fungi from the Anoectochilus and Ludisia Species on the Growth and Secondary Metabolism of Anoectochilus roxburghii

Endophytic fungi possess favorable effects on their host plants, including disease-resistance improvement, secondary metabolite induction, and growth promotion. It is therefore a promising and sustainable strategy to utilize endophytic fungi for the quality improvement of medicinal herbs or important crops. In our study, a collection of 277 strains of endophytic fungi were isolated from Anoectochilus and Ludisia orchids. Two strains J162 and J211 can be symbiotically cocultured with the tissue culture seedlings of Anoectochilus roxburghii, a popular medicinal and edible plant in southern China. Both strains can significantly enhance the biomass of A. roxburghii and induce the biosynthesis and accumulation of its active ingredients, including flavonoids, kinsenoside, and polysaccharides. J162 and J211 were further identified as Chaetomium globosum and Colletotrichum gloeosporioides based on multilocus phylogenetic analysis. Immunocytochemical staining indicated that J162 and J211 mainly colonized the intercellular gap of xylem parenchyma cells of A. roxburghii roots without obvious harm. In addition, quantitative real-time polymerase chain reaction showed that the expression of three growth-related genes, namely, uracil phosphoribosyl transferase, amino acid transmembrane transporter, and maturase K, were significantly altered in A. roxburghii plants when treated with J162 and J211. In conclusion, the two strains are highly beneficial microbial resources for the growth and accumulation of active ingredients of A. roxburghii in agricultural cultivation.

Rapid detection of adulteration in Anoectochilus roxburghii by near-infrared spectroscopy coupled with chemometric methods

To determine the authenticity of Anoectochilus roxburghii, this study presents an application of near-infrared spectroscopy and chemometric methods for evaluating adulteration of A. roxburghii with two cheaper adulterants, i.e. C. Goodyera schlechtendaliana and Ludisia discolor. Partial least squares discriminant analysis models were built for the accurate classification of authentic A. roxburghii and A. roxburghii adulterated at 5-100% (w/w) levels. Partial least squares regression models were used to predict the level of adulteration in the A. roxburghii. After by compared different spectral pretreatment methods, and using interval PLS and synergy interval PLS for variable selection, optimum models were developed. These results show that the NIR spectroscopy combined with chemometric methods offers a simple, fast, and reliable method for classifying and quantifying the adulteration of A. roxburghii.

Deep sequencing-based comparative transcriptional profiles of Cymbidium hybridum roots in response to mycorrhizal and non-mycorrhizal beneficial fungi

Background

The Orchidaceae is one of the largest families in the plant kingdom and orchid mycorrhizae (OM) are indispensable in the life cycle of all orchids under natural conditions. In spite of this, little is known concerning the mechanisms underlying orchid- mycorrhizal fungi interactions. Our previous work demonstrated that the non-mycorrhizal fungus Umbelopsis nana ZH3A-3 could improve the symbiotic effects of orchid mycorrhizal fungus Epulorhiza repens ML01 by co-cultivation with Cymbidium hybridum plantlets. Thus, we investigated the C. hybridum transcript profile associated with different beneficial fungi.

Results

More than 54,993,972 clean reads were obtained from un-normalized cDNA library prepared from fungal- and mock- treated Cymbidium roots at four time points using RNA-seq technology. These reads were assembled into 16,798 unique transcripts, with a mean length of 1127 bp. A total of 10,971 (65.31%) sequences were annotated based on BLASTX results and over ninety percent of which were assigned to plant origin. The digital gene expression profiles in Cymbidium root at 15 days post inoculation revealed that 1674, 845 and 1743 genes were sigificantly regulated in response to ML01, ZH3A-3 and ML01+ ZH3A-3 treatments, respectively. Twenty-six genes in different regulation patterns were validated using quantitative RT-PCR. Our analysis showed that general defense responses were co- induced by three treatments, including cell wall modification, reactive oxygen species detoxification, secondary biosynthesis and hormone balance. Genes involved in phosphate transport and root morphogenesis were also detected to be up-regulated collectively. Among the OM specifically induced transcripts, genes related to signaling, protein metabolism and processing, defense, transport and auxin response were identifed. Aside from these orchid transcripts, some putative fungal genes were also identified in symbiotic roots related to plant cell wall degradation, remodeling the fungal cell wall and nutrient transport.

Conclusion

The orchid root transcriptome will facilitate our understanding of orchid - associated biological mechanism. The comparative expression profiling revealed that the transcriptional reprogramming by OM symbiosis generally overlapped that of arbuscular mycorrhizas and ectomycorrhizas. The molecular basis of OM formation and function will improve our knowledge of plant- mycorrhzial fungi interactions, and their effects on plant and fungal growth, development and differentiation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-747) contains supplementary material, which is available to authorized users.

Screening for differentially expressed genes in endophytic fungus strain 39 during co-culture with herbal extract of its host Dioscorea nipponica Makino

Strain 39 is an endophytic fungus which was isolated from Dioscorea nipponica Makino (DNM). After Strain 39 co-cultured with ethanol extract of DNM rhizomes for several days, the content of saponins in this culture mixture would be obviously increased. To analyze the mechanism of this microbial transformation, we used the differential display reverse transcription polymerase chain reaction (DDRT-PCR) method to compare the transcriptomes between Strain 39 cultured in normal PD medium and in PD medium which added ethanol extract of DNM rhizomes. We amplified 29 DDRT-PCR bands using 12 primer combinations of three anchored primers and five random primers, and six bands were re-amplified. Analysis of real-time PCR and sequence alignment showed that three clones were up-regulated in sample group: squalene epoxidase, squalene synthase, and catalase, one clone was expressed only in sample group. The possible roles and origins of the above genes were discussed, and the molecular mechanism of Strain 39 biotransformation was speculated. This study is the first report of the molecular biotransformation mechanism of saponins production by endophytic fungus of DNM.