Integration of small RNAs, degradome, and transcriptome sequencing provides insights into the differences between Shizhu
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ORIGINAL ARTICLE
Integration of small RNAs, degradome, and transcriptome sequencing provides insights into the differences between Shizhu ginseng and Yuan ginseng Mengyuan Peng1 • Yanlin Chen1 • Wenjuan Wang1 • Zhihua He1 • Wangqiang Dai1 • Zhiyun Lin1 Zemin Yang3 • Mengjuan Gong1 • Yongqin Yin1 • Bin Han1 • Yu Zeng1 • Yingfang Wang1,2
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Received: 10 September 2019 / Accepted: 21 September 2020 Ó The Author(s) 2020
Abstract Panax ginseng is one of the most popular herbs which have been used as an important traditional Chinese medicine since ancient times. Yuan ginseng and Shizhu ginseng,which belong to P. ginseng, are widely used as substitutes for wild ginseng in clinical practice. Clinical practice has proved that the clinical efficacy of Shizhu ginseng is better than Yuan ginseng. However, current research cannot completely explain this phenomenon. Considering that small RNA may be one of the pharmacodynamic substances of P. ginseng, it is challenging to investigate differential miRNAs between Shizhu ginseng and Yuan ginseng. In this study, the transcriptome, small RNAome and degradome of P. ginseng were studied by high-throughput sequencing. A total of 63,875 unigenes and 43,950,137 small RNA clean reads were obtained from the roots of P. ginseng. Among 3206 differentially expressed genes, 1190 genes were up-regulated in Yuan ginseng when compared with Shizhu ginseng. 24 known differential miRNAs and 7 novel differential miRNAs were obtained. The 304 targets of 24 differentially expressed miRNA (17 known and 7 novel) families are mainly related to energy metabolism, biotic stress and disease immunity in ginseng itself. Through the association analysis of mRNA and miRNA, our work gives a better understanding of the difference between Yuan ginseng and Shizhu ginseng. Considering the cross-kingdom regulation of plant miRNAs, our results may provide a foundation for understanding the miRNA-dependent clinical efficacy in P. ginseng. Keywords Yuan ginseng Shizhu ginseng miRNA Target gene High-throughput sequencing Abbreviations miRNA microRNA UTR Untranslated region SRA Sequence read archive
NCBI
1
School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
2
Guangdong Engineering and Technology Research Center of Topical Precise Drug Delivery System, Guangzhou 510006, China
NR KOG KEGG GO FPKM DEGs FC TPM DEMs qRT-PCR RIN TIR1 GRF GATLA LDLRAP1
3
School of Basic Courses, Guangdong Pharmaceutical University, Guangzhou 510006, China
EVs
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13562-020-00613-5) contains supplementary material, which is available to authorized users. & Yingfang Wang [email protected]
National Center for Biotechnology Information NCBI non-redundant EuKaryotic Orthologous Groups Kyoto Encyclopedia of Genes and Genomes Gene ontology Reads per kb per million reads Differentially expressed genes Fold change Transcript per million Differentially expressed miRNAs Quantitative real-time PCR RNA
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