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The characteristics of codon usage and the influencing factors of the transcriptomic coding sequence in Ziziphi Spinosae Semen were investigated. The optimal codon was determined by analyzing 5,045 CDS samples using the Perl program and Codon W 1.4.2 software. The average content of GC, GC1, GC2 and GC3 of CDS ranged from 38.53–48.82%. The ENC-plot, bias, and neutral analyses showed that the codon preference is affected by mutation under selection. A total of 28 optimal codons were obtained, including UCC, UGC, UCG, etc. These were identified by the gene high expression screening codon methods, most of which end with C and G, and only CGU ends with U. Selection pressure has a great impact on the codon usage preference in Ziziphi Spinosae Semen CDS, and the mutation pressure also has some effects. The results of this study will provide a theoretical basis for the carrier selection for saponins and flavonoid synthesis and the evolution and contribution to the increased production of this medicinal plant species.

Background: Retrieve Curative effect of Six Gentlemen Modified Decoction (SGMD) in treating with coronavirus disease ( COVID-19 ) by network pharmacology and verify its authenticity by molecular docking. Methods: The chemical constituents, effective components, and action targets were screened using TCMSP. COVID-19 related targets were retrieved by the GeneCards and NCBI databases, and drug targets and disease targets were mapped by Venny to obtain potential targets for treatment. The regulatory network of traditional Chinese medicine (TCM) compounds was established with Cytoscape to obtain the key components, and the PPI network and its network topology were established with the Bisogenet and CytoNCA plug-ins to obtain the core targets. Bioconductor was used for GO function analysis and KEGG pathway analysis to obtain the relevant functions and pathways. Results: 173 effective components, 253 targets, and 348 targets related to COVID-19 were obtained after screening, 50 cross targets were shown, and the key components of the top 15 are flavonoids such as quercetin, luteolin, kaempferol, naringenin, licochalcone A, etc. The top 28 core targets include TP53, EGFR, SRC, AR, ABL1, and others. Biological processes such as the responses to metal ions, molecules of bacterial origin, lipopolysaccharide, toxic substances, and oxidative stress were involved. The main pathway involved the AGE−RAGE signaling pathway in diabetic complications as well as the TNF and IL-17 signaling pathways. The average binding energies of the first three core components connected with 6LU7 and 1R42 were -4.16 kJ/mol and -4.12 kJ/mol, respectively.Conclusion: The core compounds of SGMD can spontaneously combine with SARS-CoV-2 3CL hydrolase and ACE2 to treat COVID-19.

A single recessive powdery mildew resistance gene Pm61 from wheat landrace Xuxusanyuehuang was mapped within a 0.46-cM genetic interval spanning a 1.3-Mb interval of the genomic region of chromosome arm 4AL. Epidemics of powdery mildew incited by the biotrophic fungus Blumeria graminis f. sp. tritici (Bgt) have caused significant yield reductions in many wheat (Triticum aestivum)-producing regions. Identification of powdery mildew resistance genes is required for sustainable improvement of wheat for disease resistance. Chinese wheat landrace Xuxusanyuehuang was resistant to several Bgt isolates at the seedling stage. Genetic analysis based on the inoculation of Bgt isolate E09 on the F1, F2, and F2:3 populations produced by crossing Xuxusanyuehuang to susceptible cultivar Mingxian 169 revealed that the resistance of Xuxusanyuehuang was controlled by a single recessive gene. Bulked segregant analysis and simple sequence repeat (SSR) mapping placed the gene on chromosome bin 4AL-4-0.80-1.00. Comparative genomics analysis was performed to detect the collinear genomic regions of Brachypodium distachyon, rice, sorghum, Aegilops tauschii, T. urartu, and T. turgidum ssp. dicoccoides. Based on the use of 454 contig sequences and the International Wheat Genome Sequence Consortium survey sequence of Chinese Spring wheat, four EST-SSR and seven SSR markers were linked to the gene. An F5 recombinant inbred line population derived from Xuxusanyuehuang × Mingxian 169 cross was used to develop the genetic linkage map. The gene was localized in a 0.46-cM genetic interval between Xgwm160 and Xicsx79 corresponding to 1.3-Mb interval of the genomic region in wheat genome. This is a new locus for powdery mildew resistance on chromosome arm 4AL and is designated Pm61.

Astragalus membranaceus is an important medicinal plant widely cultivated in East Asia. MicroRNAs (miRNAs) are endogenous regulatory molecules that play essential roles in plant growth, development, and the response to environmental stresses. Cold is one of the key environmental factors affecting the yield and quality of A. membranaceus, and miRNAs may mediate the gene regulation network under cold stress in A. membranaceus. To identify miRNAs and reveal their functions in cold stress response in A. membranaceus, small RNA sequencing was conducted followed by bioinformatics analysis, and quantitative real time PCR (qRT-PCR) analysis was performed to profile the expression of miRNAs under cold stress. A total of 168 conserved miRNAs belonging to 34 families and 14 putative non-conserved miRNAs were identified. Many miRNA targets were predicted and these targets were involved in diversified regulatory and metabolic pathways. By using qRT-PCR, 27 miRNAs were found to be responsive to cold stress, including 4 cold stress-induced and 17 cold-repressed conserved miRNAs, and 6 cold-induced non-conserved miRNAs. These cold-responsive miRNAs probably mediate the response to cold stress by regulating development, hormone signaling, defense, redox homeostasis, and secondary metabolism in A. membranaceus. These cold-corresponsive miRNAs may be used as the candidate genes in further molecular breeding for improving cold tolerance of A. membranaceus.

Background Ammopiptanthus nanus is a rare broad-leaved shrub that is found in the desert and arid regions of Central Asia. This plant species exhibits extremely high tolerance to drought and freezing and has been used in abiotic tolerance research in plants. As a relic of the tertiary period, A. nanus is of great significance to plant biogeographic research in the ancient Mediterranean region. Here, we report a draft genome assembly using the Pacific Biosciences (PacBio) platform and gene annotation for A. nanus. Findings A total of 64.72 Gb of raw PacBio sequel reads were generated from four 20-kb libraries. After filtering, 64.53 Gb of clean reads were obtained, giving 72.59× coverage depth. Assembly using Canu gave an assembly length of 823.74 Mb, with a contig N50 of 2.76 Mb. The final size of the assembled A. nanus genome was close to the 889 Mb estimated by k-mer analysis. The gene annotation completeness was evaluated using Benchmarking Universal Single-Copy Orthologs; 1,327 of the 1,440 conserved genes (92.15%) could be found in the A. nanus assembly. Genome annotation revealed that 74.08% of the A. nanus genome is composed of repetitive elements and 53.44% is composed of long terminal repeat elements. We predicted 37,188 protein-coding genes, of which 96.53% were functionally annotated. Conclusions The genomic sequences of A. nanus could be a valuable source for comparative genomic analysis in the legume family and will be useful for understanding the phylogenetic relationships of the Thermopsideae and the evolutionary response of plant species to the Qinghai Tibetan Plateau uplift.

Powdery mildew, caused by the biotrophic para-sitic fungus Blumeria graminis f. sp. tritici ( Bgt ), is a prevalent disease in many wheat ( Triticum aestivum L.)–producing regions throughout the world. To reduce yield losses and avoid environ-mental pollution caused by fungicide application, growing resistant cultivars is the preferred means for managing wheat powdery mildew. ‘Zhongmai 155’, a commercial winter wheat cultivar released in 2012, was resistant to 92 of the 115 Bgt isolates originating from northern China. Using segregat-ing F 2 and F 2:3 populations derived from Zhong-mai 155 × ‘Han 4564’ cross, genetic analysis indicated that a single dominant resistance gene, tentatively designated PmZ155 , was responsible for the resistance of Zhongmai 155 to the Bgt isolate E09. The gene was subsequently local-ized on chromosome 5DS on the basis of the results of molecular marker analysis. The flanking markers SCAR203 and Xcfd8 are linked to gene PmZ155 at genetic distances of 0.3 and 4.9 cM, respectively, and were physically mapped to the deletion bin 5DS-1-0-0.63; therefore

Astragalus membranaceus is an important medicinal plant widely cultivated in East Asia. MicroRNAs (miRNAs) are endogenous regulatory molecules that play essential roles in plant growth, development, and the response to environmental stresses. Cold is one of the key environmental factors affecting the yield and quality of A. membranaceus, and miRNAs may mediate the gene regulation network under cold stress in A. membranaceus. To identify miRNAs and reveal their functions in cold stress response in A. membranaceus, small RNA sequencing was conducted followed by bioinformatics analysis, and quantitative real time PCR (qRT-PCR) analysis was performed to profile the expression of miRNAs under cold stress. A total of 168 conserved miRNAs belonging to 34 families and 14 putative non-conserved miRNAs were identified. Many miRNA targets were predicted and these targets were involved in diversified regulatory and metabolic pathways. By using qRT-PCR, 27 miRNAs were found to be responsive to cold stress, including 4 cold stress-induced and 17 cold-repressed conserved miRNAs, and 6 cold-induced non-conserved miRNAs. These cold-responsive miRNAs probably mediate the response to cold stress by regulating development, hormone signaling, defense, redox homeostasis, and secondary metabolism in A. membranaceus. These cold-corresponsive miRNAs may be used as the candidate genes in further molecular breeding for improving cold tolerance of A. membranaceus.

The effectiveness of wheat cultivar Liangxing 99 against powdery mildew was shown to be controlled by a single dominant gene located on a new locus of chromosome 2BL in the bin 2BL2-0.35-0.50. Liangxing 99, one of the most widely grown commercial cultivars in the winter wheat (Triticum aestivum) producing regions in northern China, was shown to provide a broad spectrum of resistance to Blumeria graminis f. sp. tritici (Bgt) isolates originating from that region. Using an F2 population and F2:3 lines derived from a cross of Liangxing 99 × Zhongzuo 9504, genetic analysis demonstrated that a single dominant gene, designated MlLX99, was responsible for the resistance of Liangxing 99 to Bgt isolate E09. The results of molecular analysis indicated that this gene is located on chromosome 2BL and flanked by the SSR marker Xgwm120 and EST-STS marker BE604758 at genetic distances of 2.9 and 5.5 cM, respectively. Since the flanking markers of MlLX99 were previously mapped to the bin 2BL2-0.36-0.50, MlLX99 must be located in this chromosomal region. MlLX99 showed a different resistance reaction pattern to 60 Bgt isolates from Pm6, Pm33, and PmJM22, which were all previously mapped on chromosome 2BL, but differed in their positions from MlLX99. Due to its unique position on chromosome 2BL, MlLX99 appears to be a new locus for resistance to powdery mildew. Liangxing 99 has shown superior yield performance and wide adaptation to different agricultural conditions, which has resulted in its extensive use as a wheat cultivar in China. The identification of resistance gene MlLX99 facilitates the use of this cultivar in the protection of wheat from damage caused by powdery mildew.