Additional file 4 of Integrative analyses of targeted metabolome and transcriptome of Isatidis Radix autotetraploids highlighted key polyploidization-responsive regulators

Additional file 4: Table S4. Polyploidy-responsive genes in Isatidis Radix

Additional file 8 of Integrative analyses of targeted metabolome and transcriptome of Isatidis Radix autotetraploids highlighted key polyploidization-responsive regulators

Additional file 8: Figure S1. The morphological characterization of I. indigotica autotetraploid seedling and its diploid progenitor. A The I. indigotica seedling of autotetraploid (4x) and its diploid (2x). B Chromosomes of I. indigotica autotetraploid and diploid root tips. C The comparison of stomata between autotetraploid and diploid leaf. D Isatidis Radix autotetraploid and diploid

Additional file 5 of Integrative analyses of targeted metabolome and transcriptome of Isatidis Radix autotetraploids highlighted key polyploidization-responsive regulators

Additional file 5: Table S5. Correlation analysis of polyploidy-responsive genes and metabolites in Isatidis Radix

Additional file 7 of Integrative analyses of targeted metabolome and transcriptome of Isatidis Radix autotetraploids highlighted key polyploidization-responsive regulators

Additional file 7: Table S7. I. indigotica transcriptional factors acted as key regulators of lignan synthesis in Isatidis Radix

Additional file 1 of Integrative analyses of targeted metabolome and transcriptome of Isatidis Radix autotetraploids highlighted key polyploidization-responsive regulators

Additional file 1: Table S1. Quality statistics of the filtered RNAseq reads

Additional file 2 of Integrative analyses of targeted metabolome and transcriptome of Isatidis Radix autotetraploids highlighted key polyploidization-responsive regulators

Additional file 2: Table S2.qRT-PCR primers of Isatidis Radix genes

Additional file 6 of Integrative analyses of targeted metabolome and transcriptome of Isatidis Radix autotetraploids highlighted key polyploidization-responsive regulators

Additional file 6: Table S6. Correlation analysis of transcriptional factors and metabolites in Isatidis Radix

Additional file 3 of Integrative analyses of targeted metabolome and transcriptome of Isatidis Radix autotetraploids highlighted key polyploidization-responsive regulators

Additional file 3:Table S3. Metabolomic profiling of Isatidis Radix

Table_1_Authenticating the geographic origins of Atractylodes lancea rhizome chemotypes in China through metabolite marker identification.xlsx

IntroductionAtractylodes lancea is widely distributed in East Asia, ranging from Amur to south-central China. The rhizome of A. lancea is commonly used in traditional Chinese medicine, however, the quality of products varies across different regions with different geochemical characteristics.MethodThis study aimed to identify the chemotypes of A. lancea from different areas and screen for chemical markers by quantifying volatile organic compounds (VOCs) using a targeted metabolomics approach based on GC–MS/MS.ResultsThe A. lancea distributed in Hubei, Anhui, Shaanxi, and a region west of Henan province was classified as the Hubei Chemotype (HBA). HBA is characterized by high content of β-eudesmol and hinesol with lower levels of atractylodin and atractylon. In contrast, the Maoshan Chemotype (MA) from Jiangsu, Shandong, Shanxi, Hebei, Inner Mongolia, and other northern regions, exhibited high levels of atractylodin and atractylon. A total of 15 categories of VOCs metabolites were detected and identified, revealing significant differences in the profiles of terpenoid, heterocyclic compound, ester, and ketone among different areas. Multivariate statistics indicated that 6 compounds and 455 metabolites could serve as candidate markers for differentiating A. lancea obtained from the southern, northern, and Maoshan areas.DiscussionThis comprehensive analysis provides a chemical fingerprint of selected A. lancea. Our results highlight the potential of metabolite profiling combined with chemometrics for authenticating the geographical origin of A. lancea.</p

Table_1_Drought stress modifies the community structure of root-associated microbes that improve Atractylodes lancea growth and medicinal compound accumulation.xlsx

Atractylodes lancea is an important medicinal plant in traditional Chinese medicine, its rhizome is rich of volatile secondary metabolites with medicinal values and is largely demanded in modern markets. Currently, supply of high-yield, high-quality A. lancea is mainly achieved via cultivation. Certain soil microbes can benefit plant growth, secondary metabolism and induce resistance to environmental stresses. Hence, studies on the effects of soil microbe communities and isolates microorganisms on A. lancea is extremely meaningful for future application of microbes on cultivation. Here we investigated the effects of the inoculation with an entire soil microbial community on the growth, resistance to drought, and accumulation of major medicinal compounds (hinesol, β-eudesmol, atractylon and atractylodin) of A. lancea. We analyzed the interaction between A. lancea and the soil microbes at the phylum and genus levels under drought stress of different severities (inflicted by 0%, 10% and 25% PEG6000 treatments). Our results showed that inoculation with soil microbes promoted the growth, root biomass yield, medicinal compound accumulation, and rendered drought-resistant traits of A. lancea, including relatively high root:shoot ratio and high root water content under drought. Moreover, our results suggested drought stress was more powerful than the selectivity of A. lancea in shaping the root-associated microbial communities; also, the fungal communities had a stronger role than the bacterial communities in protecting A. lancea from drought. Specific microbial clades that might have a role in protecting A. lancea from drought stress were identified: at the genus level, the rhizospheric bacteria Bacillus, Dylla and Actinomadura, and rhizospheric fungi Chaetomium, Acrophialophora, Trichoderma and Thielava, the root endophytic bacteria Burkholderia-Caballeronia-Paraburkholderia, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Dylla and Actinomadura, and the root endophytic fungus Fusarium were closely associated with A. lancea under drought stress. Additionally, we acquired several endophytic Paenibacillus, Paraburkholderia and Fusarium strains and verified they had differential promoting effects on the medicinal compound accumulation in A. lancea root. This study reports the interaction between A. lancea and soil microbe communities under drought stress, and provides insights for improving the outcomes in A. lancea farming via applying microbe inoculation.</p