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Objective: Plant hormones act as chemical messengers in the regulation of plant development and metabolism. The production of ginsenosides in Panax hybrid is promoted by auxins that are transported and accumulated by PIN-FORMED (PIN) and PIN-LIKES (PILS) auxin transporters. However, genome-wide studies of PIN/PILS of ginseng are still scarce. In current study, identification and transcriptional profiling of PIN/PILS gene families, as well as their potential relationship with ginsenoside biosynthesis in Panax ginseng were investigated. Methods: PIN/PILS genes in P. ginseng was identified via in silico genome-wide analysis, followed by phylogenetic relationships, gene structure, and protein profiles investigation. Moreover, previously reported RNA-sequence data from various tissues and roots after infection were utilized for PIN/PILS genes expression pattern analysis. The Pearson's correlation analysis of specific PIN/PILS genes expression level and main ginsenoside contents were taken to reveal the potential relationship between auxin transports and ginsenoside biosynthesis in P. ginseng. Results: A genome-wide search of P. ginseng genome for homologous auxin transporter genes identified a total of 17 PIN and 11 PILS genes. Sequence alignment, putative motif organization, and sub-cellular localization indicated redundant and complementary biological functions of these PIN/PILS genes. Most PIN/PILS genes were differentially expressed in a tissue-specific manner, and showed significant correlations with ginsenoside content correspondingly. Eight auxin transporter genes, including both PIN and PILS subfamily members, were positively correlated with ginsenoside content (cor > 0.60; P-value <0.05). The expression levels of eleven auxin transporter genes were increased dramatically in the early stage (0–0.5 DPI) after Cylindrocarpon destructans infection, accompanied with various overall expression patterns, implying the dynamic auxin transport in response to biotic stress. Conclusion: Based on the results, we speculate that the accumulation or depletion in temporal or spatial manner of auxin by PIN/PILS transporters involved in the regulation of HMGR activity and subsequent ginsenoside biosynthesis.
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Ginseng ( C.A. Meyer) is one of the best-selling herbal medicines, with ginsenosides as its main pharmacologically active constituents. Although extensive chemical and pharmaceutical studies of these compounds have been performed, genome-wide studies of the basic helix-loop-helix (bHLH) transcription factors of ginseng are still limited. The bHLH transcription factor family is one of the largest transcription factor families found in eukaryotic organisms, and these proteins are involved in a myriad of regulatory processes. In our study, 169 bHLH transcription factor genes were identified in the genome of , and phylogenetic analysis indicated that these PGbHLHs could be classified into 24 subfamilies. A total of 21 RNA-seq data sets, including two sequencing libraries for jasmonate (JA)-responsive and 19 reported libraries for organ-specific expression analyses were constructed. Through a combination of gene-specific expression patterns and chemical contents, 6 PGbHLH genes from 4 subfamilies were revealed to be potentially involved in the regulation of ginsenoside biosynthesis. These 6 PGbHLHs, which had distinct target genes, were further divided into two groups depending on the absence of MYC-N structure. Our results would provide a foundation for understanding the molecular basis and regulatory mechanisms of bHLH transcription factor action in .
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Ginseng is the dried root and rhizome of Panax ginseng.The lack of genomic data has restricted the development of ginseng industry and basic research.The genome size of P.ginseng was estimated to be 3.42 Gb by using the genome data of Oryza sativa ssp.Nipponbare and Glycine max (L.) Merrill as the reference and the flow cytometric analysis.Meanwhile,shotgun libraries with the insert size of 250 bp and 500 bp were constructed,and sequenced for double terminal PE 150 by using Illumina Hiseq X Ten platform.Totally,183.82 Gb high quality data was obtained after filtering the raw data.The genome size of P.ginseng was 3.35 Gb and the sequencing depth was 54.87 X by K-mer analysis.In this study,flow cytometry and K-mer analysis were used to identify the genome size of ginseng,which provided basic data for the further whole genome sequencing and herbgenomics studies.
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This study aimed at investigating the drug preparation of precise powder decoction pieces (PPDP) system,Fallopia multiflora radix preparata (FMRP) was employed in this study.Different specifications of PPDP were prepared,their extract rates were in contrast with the original pieces.Compared the quality uniformity of three batches between FMRP original slices and its PPDP extraction,the similarity of the chemical fingerprints was evaluated,and the contents of common peaks and quality uniformity were compared by relative peak areas.ITS2 sequence was taken as a DNA barcode to identify F.multiflora radix (FMR).As a result,the extract rate of PPDP was 2.5 times as much as the original slices.The average content of stilbene glucoside from the three original slices and the PPDP extraction were 3.56 ± 2.61 and 13.23 ± 0.37 mg·g-1,respectively;while the RSD were 73.28％ and 2.82％.The similarity of the fingerprints of the PPDP extraction was almost the same as that of the original slices,but the content and the uniformity of the common peaks of the PPDP extraction were significantly improved.Thus,FMR was accurately identified using ITS2 sequences.It was concluded that the PPDP considerably improve the decocting rate and quality uniformity,indicating that PPDP could save resources and improve the clinical efficacy.
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This study aimed at evaluating the quality of precise powder decoction pieces (PPDP) of E.Folium (EF) compared with the traditional commercial slices by chemical fingerprint methods and DNA molecular identification technology.Different specifications of PPDP were prepared,and their dry extract contents were in contrast with that of commercial slices.The slices of EF were identified using ITS2 and psbA-trnH sequences.Three batches of commercial slices were collected,and the content uniformity,fingerprint and similarity evaluation before and after the mixing and pulverization were detected by HPLC-DAD and DNA sequence alignment.It was found that the paste rate of PPDP was slightly higher than that of the traditional commercial slices.The dissolution of chlorogenic acid of PPDP was higher than that of the traditional commercial slices.RSD of inter-assay dissolutions of chlorogenic acid of commercial slices was 15.56％,which was reduced to 6.82％ after mixing and preparing into PPDP.The fingerprints showed that the similarity of the PPDP of EF was elevated with the inceases of 10 marketed common peaks.The PPDP of EF was accurately identified by ITS2 and psbA-trnH sequences.In conclusion,compared with traditional commercial slices of EF,the PPDP apparently improved the dissolution rate and the quality uniformity,demonstrated that the boiled powder of CRP achieved obvious clinic advantages.
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This study aimed at comparing the precise powder decoction pieces and market raw TCM slices of P.cacumen over the decocting quality.ITS2 sequence was adopted as a DNA barcode to identify P.cacumen.The chemical composition of the medicinal materials was characterized by HPLC fingerprints for the evaluation of the similarity of precise powder decoction pieces and market TCM slices.The concentrations of quercitrin were determined using UPLC,and the characteristic common peaks were identified.In addition,the extraction efficiency between the market TCM slices and the precise powder decoction pieces was also compared by standard decoction method.It was found that P.cacumen was accurately identified by ITS2 sequences.HPLC fingerprints showed that the extraction efficiency and similarity of the precise powder decoction pieces increased compared with the market TCM slices.However,the extraction yield rate of the precise powder decoction pieces was improved by 20％ increased in accordance with the standard decoction method,while the contents of the index component,quercitrin,presented rare increase and the decocting rates of the other chemical components little change in the study.In conclusion,it was indicated that precise powder decoction pieces improved the extraction efficiency and uniformity in comparison with TCM slices.
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Background: The pangolin is a Pholidota mammal with large keratin scales protecting its skin. Two pangolin species ( Manis pentadactyla and Manis javanica ) have been recorded as critically endangered on the International Union for Conservation of Nature Red List of Threatened Species. Optical mapping constructs high-resolution restriction maps from single DNA molecules for genome analysis at the megabase scale and to assist genome assembly. Here, we constructed restriction maps of M. pentadactyla and M. javanica using optical mapping to assist with genome assembly and analysis of these species. Findings: Genomic DNA was nicked with Nt.BspQI and then labeled using fluorescently labeled bases that were detected by the Irys optical mapping system. In total, 3,313,734 DNA molecules (517.847 Gb) for M. pentadactyla and 3,439,885 DNA molecules (504.743 Gb) for M. javanica were obtained, which corresponded to approximately 178X and 177X genome coverage, respectively. Qualified molecules (≥150 kb with a label density of >6 sites per 100 kb) were analyzed using the de novo assembly program embedded in the IrysView pipeline. We obtained two maps that were 2.91 Gb and 2.85 Gb in size with N50s of 1.88 Mb and 1.97 Mb, respectively. Conclusions: Optical mapping reveals large-scale structural information that is especially important for non-model genomes that lack a good reference. The approach has the potential to guide de novo assembly of genomes sequenced using next-generation sequencing. Our data provide a resource for Manidae genome analysis and references for de novo assembly. This note also provides new insights into Manidae evolutionary analysis at the genome structure level.
