Codon usage bias is an important characteristic of genetic information transfer in organisms. Analysis of codon usage bias of different species is important for understanding the rules on genetic information transfer. The previous method for analysis of codon usage bias is mainly based on genomic data. However, this method is greatly limited, because the genome sequences of higher organisms are still not available up to now. In this study, we found that we could obtain the same optimal codons of Ganoderma lucidum (Curtis: Fr.) P. Karst based on its whole genomic data or large-scale transcriptomic data from its liquid-cultured hyphae, primordium and fruiting body, separately. This result indicated the feasibility to understand the codon usage bias based on the large-scale transcriptomic data. By calculating the proportion of rare codons of Escherichia coli and Saccharomyces cerevisiae in 26 terpene synthases (TS) of G. lucidum, we found that the rare codons of S. cerevisiae have a higher proportion in TS genes, while the rare codons of E. coli have relatively lower, suggesting that the TS genes of G. lucidum are possibly more difficult to be expressed in S. cerevisiae than in E. coli. Chemical synthesis of TS genes according to the yeast optimal codons will be an effective way to solve the problem on the mismatch of gene codon bias between the foreign genes and the host strain.

Salvia miltorrhiza Bge. is a perennial deciduous flowering plant. Its medicinal root and rhizomes part is widely used in the treatment of various diseases. In this study, bioinformatics analysis was performed to identify 4832 genome SSR loci with length longer than or equal to 40 bp from the draft genome assembly of S. miltorrhiza. The re-sults showed that the dinucleotide repeat motifs and trinucleotide repeat motifs constitute the main types of genome SSR loci, accounting for 37.3% and 61.3% respectively. SSR types enriched with A/T bases showed significantly higher abundance than other types, including AT/TA AAT/ATT, ATA/TAT, TAA/TTA, accounting for 30.5%, 21.6%, 17.1%, 20.4% of the total number of SSR loci, respectively. 1079 primer pairs were designed for these genome SSR loci. These primers can be used for genomic diversity analysis, genetic map construction, genetic marker screening. These data could lay the foundation for population genetics and genomics research of S. miltorrhiza.

Cytochrome P450 (CYP450) is a key element in the Ganoderma triterpenoid biosynthetic pathway. The catalytic reaction process for CYP450 requires NADPH / NADH for electron transfer. After searching the genome dataset of Ganoderma lucidum, the unique sequence encoding CYP450 and NADPH were discovered, separately. The open reading frames of GLCYP450 and GLNADPH were cloned separately using RT-PCR strategy from G lucidum. The appropriate restriction enzyme cutting sites were introduced at the 5' and 3' ends of gene sequence. The genes of GLCYP450 and GLNADPH were recombined into the yeast expression vector pESC-URA, leading to the formation of the yeast expression plasmid pESC-GLNADPH-GLCYP450. This study provides a foundation for researching Ganoderma triterpene biosynthesis using the approach of synthetic biology.

Glycyrrhizin is the major bioactive compound in Glycyrrhiza uralensis. Farnesyl-diphosphate synthase (FPS) is one of the major enzymes involved in the glycyrrhizin biosynthetic. We cloned the full length of FPS coding sequence based on the transcriptome data of G. uralensis. The FPS gene of G. uralensis (GlyurFPS) is 1029 bp, coding 342 amino acid. The homology between the sequence of its protein and that of the FPS in Cicer arietinum, Medicago sativa, Medicago truncatula, Glycine max, Lotus japonicus was of 94%, 94%, 93%, 93% and 92%, respectively. Plant FPS gene is very conservative, therefore the phylogenetic tree is same with the plant classification consistent.

The transcript encoding 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) was discovered from the transcriptome data of Huperzia serrata. The transcript contained an open reading frame with length of 1,440 bp and coded 479 amino acids. The full length of HsDXR1 had been cloned using RT-PCR method. Ac-cording the bioinformatic analysis, the molecular weight of HsDXR1 protein was 51.4961 kDa and the pI was 6.44. No signal peptide and transmembrane site was discovered in HsDXR1, and the protein was most likely to be located in chloroplast. HsDXR1 had the same domain similar to the DXR protein of Arabidopsis and Oryza sativa. The expression level of HsDXR1 was most abundantly in H. serrata stem, followed by root and leaf. This study cloned and analyzed HsDXR1 gene from H. serrata for the first time. The result will provide a foundation for exploring the mechanism of terpene biosynthesis in H. serrata plants.

3-Hydroxy-3-methylglutaryl coenzyme-A reductase (HMGR), the first enzyme of mavalonic acid pathway, is one of the key devices involved in ginsenoside biosynthesis based on synthetic biology approach. The open reading frame of a novel HMGR gene from Panax ginseng (PgHMGR2) was cloned and analyzed in this study. PgHMGR2-encoding protein showed 71.6% sequence similarity to a P. ginseng HMGR in GenBank. The full-length cDNA sequence of PgHMGR2 containing 1 770 bp, which encodes 589 amino acids, was cloned by RT-PCR strategy from P. ginseng. The bioinformatic analysis showed that PgHMGR2-encoding protein contained two transmembrane regions and the HMG_CoA_reductase domain, without signal peptide. The protein sequence of PgHMGR2 had the highest sequence similarity (99%) with Panax quinquefolius HMGR (GenBank accession No. ACV65036). The expression level of PgHMGR2 was the highest in flower based on a real-time PCR analysis, followed by leaf and root, and the lowest was in stem. The result will provide a foundation for exploring the molecular function of PgHMGR2 involved in ginsenoside biosynthesis based on synthetic biology approach in P. ginseng plants.

Research on medicinal model organism is one of the core technologies to promote the modernization of traditional Chinese medicine (TCM). The research progress of Salvia miltiorrhiza as medicinal model plant is summarized in this paper. The genome of S. miltiorrhiza is small and its life cycle is short, as well as this plant can be stably genetically transformed. Because S. miltiorrhiza possesses the important medicinal and economic values, recently the transcriptome and genome of S. miltiorrhiza have been significantly recovered. The research prospect of S. miltiorrhiza as medicinal model plant in TCM was discussed, including biosynthesis of active components and their genetic regulation, relationship between quality of TCM and ecological environments, and selective breeding of good quality lines. Furthermore, as medicinal model plant, the construction of mutant library for S. miltiorrhiza, the genome map with high quality, and the functional genome should be investigated. Accompanying modern investigation of life sciences, the platform for medicinal model plant, S. miltiorrhiza, will be promoted to be established. It is important to develop the ethnopharmacology and new drugs around the world.

The medicinal fungi, which are of great importance in traditional medicine, are facing the problems of wild resources scarcity and low concentration of bioactive compounds. Velvet family and LaeA global regulator play a vital role in secondary metabolism and developmental programs, which are found in a wide variety of fungi ranging from Chytridiomycota to Basidiomycota. This review elaborates the structures and functions between Velvet family and LaeA protein. The Velvet family which shares the Velvet protein domain, including VeA (Velvet), VelB (Velvet like B), VosA (viability of spores A) and VelC (Velvet like C), acts on the regulation function is secondary metabolism and developmental programs such as asexual and sexual development. Furthermore, the function is affected by environmental factors such as light and temperature. LaeA protein which owns S-adenosylmethionine-dependent methyltransferase domain, coordinately regulates development and secondary metabolism by regulating and modifying the Velvet proteins. The regulation of LaeA is mediated by light receptor proteins. Therefore, clarifying the mechanism of Velvet and LaeA proteins in medicinal fungi will pave the way for nurturing medicinal fungi and improving production of bioactive compounds.

Background::Studies suggest seasonal fluctuations of symptoms in Parkinson’s disease (PD) patients in Western countries. However, the association between seasonal change and variation in nonmotor symptoms (NMS) in Chinese PD patients is unclear. Here, we studied whether there is a change rule with annual cycle with severity of NMS for patients with PD in Southeast China.Methods::We studied 1005 PD patients between April 2008 and October 2020. Patients were classified into four seasons according to the 24 Chinese solar terms, based on assessment date. We compared comprehensive NMS scales and polysomnography parameters among groups and conducted further analysis of disease severity.Results::Among the 1005 patients studied, the mean age was 64.2 ± 9.7 years and 569 (56.6%) of them were men. Relative to the summer group, patients assessed during winter had higher Scales for Outcomes in Parkinson’s disease-Autonomic Dysfunction (SCOPA-AUT) scores ( P = 0.045). The sleep efficiency factor scores of Pittsburgh Sleep Quality Index in patients were higher during spring than summer ( P = 0.009). Among patients who completed polysomnography during the same period ( n = 135), compared with summer follow-ups, we observed a higher percentage of NREMS1 in winter and spring follow-ups ( P = 0.042, P = 0.011), a higher NREMS1 time in spring follow-ups ( P = 0.0024), a lower NREMS2 time in winter follow-ups ( P = 0.007), and a higher percentage of phasic rapid eye movement (REM)-sleep without atonia in autumn and winter follow-ups ( P = 0.026 and P = 0.020, respectively). In a subset of patients with PD and REM sleep behavior disorder (RBD; n = 182), those visited during winter had higher scores for RBD questionnaire-Hong Kong and its factor 1 (dream-related sub-score) than those visited during summer ( P = 0.034, P = 0.020). We observed similar findings for SCOPA-AUT and sleep efficiency factor scores in early stage patients in subgroup analysis. Conclusions::PD patients assessed for follow-up during summer showed less severe symptoms of autonomic dysfunction and RBD symptoms than those assessed in winter, and less sleep disturbance than those in spring and winter, suggesting that seasonal change and NMS fluctuation are related, especially in patients with early stage PD.

Objective To assess scoliosis in adolescence and adults by three-dimensional ( 3-D ) ultrasound imaging . Methods A commercial available ultrasound instrument with a magnetic sensor system was used for long distance 3-D ultrasound imaging .Specific phantoms were imaged to evaluate the precision of this imaging system . Twenty healthy adults and 20 patients with scoliosis were imaged by 3-D ultrasonography and radiography . The deformity angle of the patients with scoliosis was measured on the reconstructed coronal plane ( C plane) of 3-D ultrasound imaging . The relevance between the curvature measured by ultrasound and the Cobb angles originated by radiography were evaluated . Results There was no significant difference between the angles of the phantom measured by the 3-D ultrasound imaging system and that measured by an angle gauge ( P = 0 .479) . The transverse process ,vertebral arch and acoustic shadow of the central spinous process of spines in healthy adults can be displayed on the reconstructed C plane by 3-D ultrasound imaging . The morphology of scoliosis in all the twenty patients can be observed on the reconstructed C planes ( multi-layers) by 3-D ultrasound imaging ,which accorded well with that observed on radiograph . In 9 patients ,part of the spinal segment could not be totally displayed on one single coronal plane and no additional measurement was carried out . In 11 patients ,all the segments of the spine could be clearly displayed on a single coronal plane and the curvature of scoliosis was then measured . There were no significant differences between the angle measured on 3-D ultrasound imaging and the Cobb angle measured on radiograph( P =0 .974) and the two measurement methods have high correlation( r =0 .991 , P <0 .0001) . Conclusions The commercial available 3-D ultrasound imaging system applied in this study offers a viable method to assess scoliosis in adolescence and adults in a reliable and radiation-free manner .