MicroRNAs (miRNAs) are small non-coding RNA molecules that function as diverse endogenous gene regulators at the post-transcriptional level. In the past two decades, as research effort on miRNA identification, function and evolution has soared, so has the demand for miRNA databases. However, the current plant miRNA databases suffer from several typical drawbacks, including a lack of entries for many important species, uneven annotation standards across different species, abundant questionable entries, and limited annotation. To address these issues, we developed a knowledge-based database called Plant miRNA Encyclopedia (PmiREN, http://www.pmiren.com/), which was based on uniform processing of sequenced small RNA libraries using miRDeep-P2, followed by manual curation using newly updated plant miRNA identification criteria, and comprehensive annotation. PmiREN currently contains 16,422 high confidence novel miRNA loci in 88 plant species and 3,966 retrieved from miRBase. For every miRNA entry, information on precursor sequence, precursor secondary structure, expression pattern, clusters and synteny in the genome, potential targets supported by Parallel Analysis of RNA Ends (PARE) sequencing, and references is attached whenever possible. PmiREN is hierarchically accessible and has eight built-in search engines. We believe PmiREN is useful for plant miRNA cataloguing and data mining, therefore a resource for data-driven miRNA research in plants.

MYC2 is a core transcription factor in the plant response to jasmonates. It also functions in secondary metabolism and various processes for growth and development. However, the knowledge about its role in Salvia miltiorrhiza is still very limited. We determined that the biosynthesis of salvianolic acid B (Sal B) was strongly induced in 2-month-old transgenic plants that over-expressed SmMYC2. In the roots of transgenic line 12 that over-expressed SmMYC2 (OEM-12), the Sal B concentration was as high as 5.95 ± 0.07 mg g-1, a level that was 1.88-fold higher than that in control plants that had been transformed with an empty vector. Neither tanshinone IIA nor cryptotanshinone was detected by high-performance liquid chromatography in any of the genotypes. Global transcriptomic analysis using RNA sequencing revealed that most enzyme-encoding genes for the phenylpropanoid biosynthesis pathway were up-regulated in the overexpression lines. Furthermore, both the phenylalanine and tyrosine biosynthesis pathways were activated in those transgenics. Our data demonstrate that overexpression of SmMYC2 promotes the production of phenolic acids by simultaneously activating both primary and secondary pathways for metabolism in S. miltiorrhiza.

Jasmonates (JAs) are integral to various defense responses and induce biosynthesis of many secondary metabolites. MYC2, a basic helix-loop-helix (bHLH) transcription factor (TF), acts as a transcriptional activator of JA signaling. MYC2 is repressed by the JASMONATE ZIM-domain (JAZ) proteins in the absence of JA, but de-repressed by the protein complex SCFCOI1 on perception of JA. We previously reported that overexpression of SmMYC2 promotes the production of salvianolic acid B (Sal B) in Salvia miltiorrhiza. However, the responsible molecular mechanism is unclear. Here, we showed that SmMYC2 binds to and activates the promoters of its target genes SmTAT1, SmPAL1, and SmCYP98A14 to activate Sal B accumulations. SmbHLH37, a novel bHLH gene significantly up-regulated by constitutive expression of SmMYC2, was isolated from S. miltiorrhiza for detailed functional characterization. SmbHLH37 forms a homodimer and interacts with SmJAZ3/8. Overexpression of SmbHLH37 substantially decreased yields of Sal B. SmbHLH37 binds to the promoters of its target genes SmTAT1 and SmPAL1 and blocks their expression to suppress the pathway for Sal B biosynthesis. These results indicate that SmbHLH37 negatively regulates JA signaling and functions antagonistically with SmMYC2 in regulating Sal B biosynthesis in S. miltiorrhiza.

Lentinula edodes, one of the most important edible mushrooms in China, is affected heavily by the infection of green mold that overgrows mushroom mycelia. We collected the diseased samples from main L. edodes cultivation regions in China to characterize the pathogen and to study the effect of Trichoderma spp. on L. edodes species. We identified six Trichoderma species, that is, T. harzianum, T. atroviride, T. viride, T. pleuroticola, T. longibrachiatum, and T. oblongisporum based on the internal transcribed spacer or tef1‐α sequences and morphology characteristics. In confrontation cultures on Petri plates or in tubes, and in L. edodes cultures in a medium containing Trichoderma metabolites, L. edodes mycelia were not only distorted and swollen, but also inhibited by Trichoderma isolates. It is not possible that adjusting pH value or temperature is used for controlling L. edodes green disease, because the growth of most of Trichoderma isolates and L. edodes shared similar pH and temperature conditions.

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Transcription factors that include myeloblastosis (MYB), basic helix-loop-helix (bHLH), and tryptophan-aspartic acid (WD)-repeat protein often form a ternary complex to regulate the phenylpropanoid pathway. However, only a few MYB and bHLH members involved in the biosynthesis of salvianolic acid B (Sal B) have been reported, and little is known about Sal B pathway regulation by the WD40 protein transparent testa glabra 1 (TTG1)-dependent transcriptional complexes in Salvia miltiorrhiza. We isolated SmTTG1 from that species for detailed functional characterization. Enhanced or reduced expression of SmTTG1 was achieved by gain- or loss-of-function assays, respectively, revealing that SmTTG1 is necessary for Sal B biosynthesis. Interaction partners of the SmTTG1 protein were screened by yeast two-hybrid (Y2H) assays with the cDNA library of S. miltiorrhiza. A new R2R3-MYB transcription factor, SmMYB111, was found through this screening. Transgenic plants overexpressing or showing reduced expression of SmMYB111 upregulated or deregulated, respectively, the yields of Sal B. Both Y2H and bimolecular fluorescent complementation experiments demonstrated that SmMYB111 interacts with SmTTG1 and SmbHLH51, a positive regulator of the phenolic acid pathway. Our data verified the function of SmTTG1 and SmMYB111 in regulating phenolic acid biosynthesis in S. miltiorrhiza. Furthermore, ours is the first report of the potential ternary transcription complex SmTTG1-SmMYB111-SmbHLH51, which is involved in the production of Sal B in that species.

As part of a program to develop transgenic highbush blueberry (Vaccinium corymbosum L.) cultivars, studies were conducted to determine optimum conditions for high efficiency shoot regeneration from leaf explants of shoots propagated in vitro. The effects on shoot organogenesis of age of explant source, length of dark treatment, the addition of either thidiazuron (TDZ) at 1 or 5 μm, or zeatin riboside at 20 μm to the regeneration medium, and a photosynthetic photon flux (PPF) of either 18 ± 5 or 55 ± 5 μmol·m–2·s–1 were investigated. A maximum of 13.0, 13.0, 12.6, and 4.6 shoots regenerating per explant for cultivars Duke, Georgiagem, Sierra, and Jersey, respectively, occurred on regeneration medium with zeatin riboside and under a PPF of 55 ± 5 μmol·m–2·s–1. `Duke' regenerated equally well on medium with either zeatin riboside or 1 μm TDZ, whereas the number of shoots per explant for `Georgiagem' and `Sierra' was significantly higher on zeatin riboside. Regeneration of `Duke', `Jersey', and `Sierra' on zeatin riboside was significantly better under a PPF of 55 ± 5 μmol·m–2·s–1 than under 18 ± 5 μmol·m–2·s–1, but the higher PPF inhibited regeneration of `Duke' on 5 μm TDZ. There were no significant differences in percentage of regeneration or the number of shoots per explant from leaf explants derived from either 1-, 2-, or 3-week-old shoot cultures, or when either 1 week or 2 weeks of darkness preceded light treatments. Chemical names used: 1-phenyl-3-(1,2,3-thiadiazol-5-yl)urea (thidiazuron, TDZ); 9-(-β-ribofuranosyl)-6-(4-hydroxy-3-methyl-but-2-enylamino)purine (zeatin riboside).

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