Additional file 3 of Creating a novel petal regeneration system for function identification of colour gene of grape hyacinth

Additional file 3. Cellular features of grape hyacinth petals in vitro and in vivo

Additional file 2 of Creating a novel petal regeneration system for function identification of colour gene of grape hyacinth

Additional file 2. List of primers used in this study

DataSheet1_TaqMan Probe-Based Quantitative Real-Time PCR to Detect Panax notoginseng in Traditional Chinese Patent Medicines.docx

Background: There has been global concern about the safety and accuracy of traditional Chinese patent medicines (TCPMs). Panax notoginseng, also known as sanqi, is an important constituent of TCPMs. However, identifying the species contained in TCPMs is challenging due to the presence of multiple ingredients and the use of various preparation processes.Objective: To detect P. notoginseng in TCPMs.Methods: A TaqMan probe-based qPCR assay was constructed and validated with DNA extracted from P. notoginseng and adulterants. In total, 75 samples derived from 25 batches of TCPMs were tested using the constructed qPCR method.Results: A TaqMan probe-based qPCR assay targeting P. notoginseng was established. The constructed qPCR assay could specifically discriminate P. notoginseng from Panax ginseng, Panax quinquefolium and Curcuma aromatica Salisb. cv. Wenyujin. The sensitivity study showed that the detectable DNA template concentration of P. notoginseng for this qPCR assay was 0.001 ng/μl. All 75 samples from TCPMs were confirmed to contain P. notoginseng by the qPCR assay.Conclusions: The qPCR method can accurately identify P. notoginseng in TCPMs and is promising as a powerful tool for quality control and market regulation.</p

Additional file 1 of Creating a novel petal regeneration system for function identification of colour gene of grape hyacinth

Additional file 1. Effect of explant age and 6-BA concentration on flower petal regeneration of grape hyacinth

Experimental design.

The experiment mainly consisted of NH4-N pulse phase and releasing of NH4-N dosing phase. During NH4-N pulse phase, three NH4-N loading patterns were applied to plants, namely, Pattern I - high NH4-N (4 mg L−1) loading with low pulse frequency; Pattern II - moderate NH4-N (2 mg L−1) loading with moderate pulse frequency; Pattern III - low NH4-N (1 mg L−1) loading with high pulse frequency. CK: without NH4-N loading. During release of NH4-N loading phase, water in the experiment was refreshed with tap water in 23 June. Plant samples were collected in morning every four days.</p

Percentage (%) of explained variance based on three-way ANOVA for change in biomass, height, branch number, root length, and total branch length of <i>M</i>. <i>spicatum</i> in NH₄-N pulse patterns under high and low light during NH₄-N pulse and release of NH₄-N loading phases.

Boldface type indicates significant difference at the level of P < 0.05.</p

Data_Sheet_1_Analysis of Whole-Genome facilitates rapid and precise identification of fungal species.docx

Fungal identification is a cornerstone of fungal research, yet traditional molecular methods struggle with rapid and accurate onsite identification, especially for closely related species. To tackle this challenge, we introduce a universal identification method called Analysis of whole GEnome (AGE). AGE includes two key steps: bioinformatics analysis and experimental practice. Bioinformatics analysis screens candidate target sequences named Targets within the genome of the fungal species and determines specific Targets by comparing them with the genomes of other species. Then, experimental practice using sequencing or non-sequencing technologies would confirm the results of bioinformatics analysis. Accordingly, AGE obtained more than 1,000,000 qualified Targets for each of the 13 fungal species within the phyla Ascomycota and Basidiomycota. Next, the sequencing and genome editing system validated the ultra-specific performance of the specific Targets; especially noteworthy is the first-time demonstration of the identification potential of sequences from unannotated genomic regions. Furthermore, by combining rapid isothermal amplification and phosphorothioate-modified primers with the option of an instrument-free visual fluorescence method, AGE can achieve qualitative species identification within 30 min using a single-tube test. More importantly, AGE holds significant potential for identifying closely related species and differentiating traditional Chinese medicines from their adulterants, especially in the precise detection of contaminants. In summary, AGE opens the door for the development of whole-genome-based fungal species identification while also providing guidance for its application in plant and animal kingdoms.</p

Growth parameters (mean ± SE, <i>n</i> = 4) including biomass, height, branch number, root length, and total branch length of <i>M</i>. <i>spicatum</i> in different sampling times under the high light treatment (○---) and low light treatment (●—) in different patterns of NH₄-N pulse.

Initial values are shown at time 0. Values during NH4-N pulse phase and release of NH4-N loading phase are shown in the first–fourth time and the fifth–seventh time, respectively. The F and P values of one-way ANOVA between high and low light treatments in the two phases are also shown.</p

Growth parameters (mean ± SE, <i>n</i> = 4) including biomass, height, branch number, root length, and total branch length of <i>M</i>. <i>spicatum</i> in response to different patterns of NH₄-N pulse under high and low light on June 23 (the sixteenth day during NH₄-N pulse phase) and July 5 (the thirteenth day during release of NH₄-N loading phase).

Growth parameters (mean ± SE, n = 4) including biomass, height, branch number, root length, and total branch length of M. spicatum in response to different patterns of NH4-N pulse under high and low light on June 23 (the sixteenth day during NH4-N pulse phase) and July 5 (the thirteenth day during release of NH4-N loading phase).</p

Percentage (%) of explained variance based on three-way ANOVA for change in biomass, height, branch number, root length, leaf number, and total branch number of <i>P</i>. <i>maackianus</i> treated with NH₄-N pulse patterns under high and low light during NH₄-N pulse phase and release of NH₄-N loading phase. Boldface type indicates significant difference at the level of P < 0.05.

Percentage (%) of explained variance based on three-way ANOVA for change in biomass, height, branch number, root length, leaf number, and total branch number of P. maackianus treated with NH4-N pulse patterns under high and low light during NH4-N pulse phase and release of NH4-N loading phase. Boldface type indicates significant difference at the level of P < 0.05.</p