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Characteristics of RNA alternative splicing and its potential roles in ginsenoside biosynthesis in a single plant of ginseng, Panax ginseng C.A. Meyer

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Abstract

RNA alternative splicing (AS) is prevalent in higher organisms and plays a paramount role in biology; therefore, it is crucial to have comprehensive knowledge on AS to understand biology. However, knowledge is limited about how AS activates in a single plant and functions in a biological process. Ginseng is one of the most widely used medicinal herbs that is abundant in a number of medicinal bioactive components, especially ginsenosides. In this study, we sequenced the transcripts of 14 organs from a 4-year-old ginseng plant and quantified their ginsenoside contents. We identified AS genes by analyzing their transcripts with the ginseng genome and verified their AS events by PCR. The plant had a total of 13,863 AS genes subjected to 30,801 AS events with five mechanisms: skipped exon, retained intron, alternative 5′splice site, alternative 3′ splice site, and mutually exclusive exon. The genes that were more conserved, had more exons, and/or expressed across organs were more likely to be subjected to AS. AS genes were enriched in over 500 GO terms in the plant even though the number of AS gene-enriched GO terms varied across organs. At least 24 AS genes were found to be involved in ginsenoside biosynthesis. These AS genes were significantly up-enriched and more likely to form a co-expression network, thus suggesting the functions of AS and correlations of the AS genes in the process. This study provides comprehensive insights into the molecular characteristics and biological functions of AS in a single plant; thus, helping better understand biology.

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Data availability

The data analyzed for this study are available at SRA database of NCBI (SRP066368) and included within the article or supplementary files. The plant material is available through the corresponding authors, upon request.

References

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  Google Scholar 

  • Breitbart RE, Andreadis A, Nadal-Ginard B (1987) Alternative splicing: a ubiquitous mechanism for the generation of multiple protein isoforms from single genes. Annu Rev Biochem 56:467–495

    Article  CAS  Google Scholar 

  • Bryant DM, Johnson K, DiTommaso T, Tickle T, Couger MB, Payzin-Dogru D, Lee TJ, Leigh ND, Kuo T-H, Davis FG, Bateman J, Bryant S, Guzikowski AR, Tsai SL, Coyne S, Ye WW, Freeman RM Jr, Peshkin L, Tabin CJ, Regev A, Haas BJ, Whited JL (2017) A Tissue-mapped axolotl De Novo transcriptome enables identification of limb regeneration factors. Cell Rep 18:762–776

    Article  CAS  Google Scholar 

  • Dong C, He F, Berkowitz O, Liu J, Cao P, Tang M, Shi H, Wang W, Li Q, Shen Z, Whelan J, Zheng L (2018) Alternative splicing plays a critical role in maintaining mineral nutrient homeostasis in rice (Oryza sativa). Plant Cell 30:2267–2285

    Article  CAS  Google Scholar 

  • Eckardt NA (2013) The plant cell reviews alternative splicing. Plant Cell 25:3639

    Article  CAS  Google Scholar 

  • Ewels P, Magnusson M, Lundin S, Kaller M (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32:3047–3048

    Article  CAS  Google Scholar 

  • Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong W-K, Mochler TC (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20:45–58

    Article  CAS  Google Scholar 

  • Gilbert WJN (1978) Why genes in pieces? Nature 271:501

    Article  CAS  Google Scholar 

  • Jin Y, Cui R, Zhao L, Fan J, Li B (2019) Mechanisms of Panax ginseng action as an antidepressant. Cell Prolif 52:e12696

    PubMed  PubMed Central  Google Scholar 

  • Kiegle EA, Garden A, Lacchini E, Kater MM (2018) A genomic view of alternative splicing of long non-coding RNAs during rice seed development reveals extensive splicing and lncRNA gene families. Front Plant Sci 9:115

    Article  Google Scholar 

  • Kim N-H, Jayakodi M, Lee SC, Choi BS, Jang W, Lee J, Kim HH, Waminal NE, Lakshmanan M, van Nguyen B, Lee YS, Park HS, Koo HJ, Park JY, Perumal S, Joh HJ, Lee H, Kim J, Kim IS, Kim K, Koduru L, Kang KB, Sung SH, Yu Y, Park DS, Choi D, Seo E, Kim S, Kim YC, Hyun DY, Park YI, Kim C, Lee TH, Kim HU, Soh MS, Lee Y, In JG, Kim HS, Kim YM, Yang DC, Wing RA, Lee DY, Paterson AH, Yang TJ (2018) Genome and evolution of the shade-requiring medicinal herb Panax ginseng. Plant Biotech J 16:1904–1917

    Article  CAS  Google Scholar 

  • Kim D, Paggi JM, Park C, Bennett C, Salzberg SL (2019) Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotech 37:907–915

    Article  CAS  Google Scholar 

  • Kolde R, Kolde MR (2019) Package ‘pheatmap’. R Package 1(7):790

  • Lee BY, Kim HS, Choi BS, Hwang DS, Choi AY, Han J, Won E-J, Choi I-Y, Lee S-H, Om A-S, Park HG, Lee J-S (2015) RNA-seq based whole transcriptome analysis of the cyclopoid copepod Paracyclopina nana focusing on xenobiotics metabolism. Comp Biochem Physiol Part D Genomics Proteomics 15:12–19

    Article  CAS  Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079

    Article  Google Scholar 

  • Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550

    Article  Google Scholar 

  • Mao S, Zhang S, Zhou Z, Shi X, Huang T, Feng W, Yao C, Gu X, Yu B (2018) Alternative RNA splicing associated with axon regeneration after rat peripheral nerve injury. Exp Neurol 308:80–89

    Article  CAS  Google Scholar 

  • Marquez Y, Brown JW, Simpson C, Barta A, Kalyna M (2012) Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res 22:1184–1195

    Article  CAS  Google Scholar 

  • Otasek D, Morris JH, Bouças J, Pico AR, Demchak B (2019) Cytoscape automation: empowering workflow-based network analysis. Genome Biol 20:185

    Article  Google Scholar 

  • Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413–1415

    Article  CAS  Google Scholar 

  • Park JW, Tokheim C, Shen S, Xing Y (2013) Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS. Methods Mol Biol 1038:171–179

    Article  CAS  Google Scholar 

  • Park YJ, Lee JH, Kim JY, Park CM (2019) Alternative RNA splicing expands the developmental plasticity of flowering transition. Front Plant Sci 10:606

    Article  Google Scholar 

  • Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C (2017) Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14:417–419

    Article  CAS  Google Scholar 

  • Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotech 33:290–295

    Article  CAS  Google Scholar 

  • Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL (2016) Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11:1650–1667

    Article  CAS  Google Scholar 

  • Ruan J, Guo F, Wang Y, Li X, Wan S, Shan L, Peng Z (2018) Transcriptome analysis of alternative splicing in peanut (Arachis hypogaea L.). BMC Plant Biol 18:139

    Article  Google Scholar 

  • Shen S, Park JW, Huang J, Dittmar KA, Lu ZX, Zhou Q, Carstens RP, Xing Y (2012) MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res 40:e61

    Article  CAS  Google Scholar 

  • Shen S, Park JW, Lu ZX, Lin L, Henry MD, Wu YN, Zhou Q, Xing Y (2014a) rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci USA 111:E5593-5601

    Article  CAS  Google Scholar 

  • Shen Y, Zhou Z, Wang Z, Li W, Fang C, Wu M, Ma Y, Liu T, Kong L-A, Peng D-L, Tian Z (2014b) Global dissection of alternative splicing in paleopolyploid soybean. Plant Cell 26:996–1008

    Article  CAS  Google Scholar 

  • Sun Y, Hou H, Song H, Lin K, Zhang Z, Hu J, Pang E (2018) The comparison of alternative splicing among the multiple tissues in cucumber. BMC Plant Biol 18:5

    Article  Google Scholar 

  • Wang L, Wang S, Li W (2012) RSeQC: quality control of RNA-seq experiments. Bioinformatics 28:2184–2185

    Article  CAS  Google Scholar 

  • Wang K, Jiang S, Sun C, Lin Y, Yin R, Wang Y, Zhang MP (2015) The spatial and temporal transcriptomic landscapes of ginseng, Panax ginseng C.A. Meyer. Sci Rep 5:18283

    Article  CAS  Google Scholar 

  • Xu L, Xu J, Shi G, Xiao S, Dai R, Wu S, Sun B, Zhang X, Zhao Y (2020) Optimization of flash extraction, separation of ginsenosides, identification by HPLC-FT-ICR-MS and determination of rare ginsenosides in mountain cultivated ginseng. RSC Adv 10:44050

    Article  CAS  Google Scholar 

  • Yang R, Li P, Mei H, Wang D, Sun J, Yang C, Hao L, Cao S, Chu C, Hu S, Song X, Cao X (2019a) Fine-tuning of MiR528 accumulation modulates flowering time in rice. Mol Plant 12:1103–1113

    Article  CAS  Google Scholar 

  • Yang Z, Yang Z, Yang C, Wang Z, Chen D, Xie Y, Wu Y (2019b) Identification and genetic analysis of alternative splicing of long non-coding RNAs in tomato initial flowering stage. Genomics 112:897–907

    Article  Google Scholar 

  • Zhang G, Guo G, Hu X, Zhang Y, Li Q, Li R, Zhuang R, Lu Z, He Z, Fang X, Chen L, Tian W, Tao Y, Kristiansen K, Zhang X, Li S, Yang H, Wang J, Wang J (2010) Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res 20:646–654

    Article  CAS  Google Scholar 

  • Zhang MP, Liu Y-H, Chang C-S, Zhi H, Wang S, Xu W, Smith CW, Zhang H-B (2019b) Quantification of gene expression while taking into account RNA alternative splicing. Genomics 111:1517–1528

    Article  CAS  Google Scholar 

  • Zhang H, Mao R, Wang Y, Zhang L, Wang C, Lv S, Liu X, Wang Y, Ji W (2019a) Transcriptome-wide alternative splicing modulation during plant-pathogen interactions in wheat. Plant Sci 288:110160

    Article  CAS  Google Scholar 

  • Zhang MP, Liu Y-H, Xu W, Smith CW, Murray SC, Zhang H-B (2020) Analysis of the genes controlling three quantitative traits in three diverse plant species reveals the molecular basis of quantitative traits. Sci Rep 10:10074

    Article  CAS  Google Scholar 

  • Zhao M, Lin Y, Wang YF, Li X, Han Y, Wang K, Sun C, Wang Y, Zhang MP (2019) Transcriptome analysis identifies strong candidate genes for ginsenoside biosynthesis and reveals its underlying molecular mechanism in Panax ginseng C.A. Meyer. Sci Rep 9:615

    Article  Google Scholar 

Download references

Funding

This research was supported by awards from China 863 Project (2013AA102604-3), the Bureau of Science and Technology of Jilin Province (20200801063GH, 20190201264JC, 20190103104JC, 20180414077GH, and 20180101027JC), and the Development and Reform Commission of Jilin Province (2018C047-3).

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Authors and Affiliations

  1. College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China

    Yilai Han, Lei Zhu, Li Li, Mingzhu Zhao, Kangyu Wang, Chunyu Sun, Jing Chen, Lingyu Liu, Ping Chen, Jun Lei, Yi Wang & Meiping Zhang

  2. Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, 130118, Jilin, China

    Yanfang Wang, Mingzhu Zhao, Kangyu Wang, Chunyu Sun, Yi Wang & Meiping Zhang

  3. College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China

    Yanfang Wang

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  1. Yilai Han
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  2. Lei Zhu
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  3. Li Li
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  12. Yi Wang
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  13. Meiping Zhang
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Contributions

MPZ and YW designed, conceived, and supervised this study. YLH performed the bioinformatics analysis, conducted PCR, and wrote the manuscript. WYF, LZ, LL ZMZ, LLY, PC, and JL extracted and measured the contents of ginsenosides. KW, CS, JC, and LL helped prepare the tables and figures. MPZ edited and revised the manuscript. All the authors read and approved the final version of the manuscript.

Corresponding authors

Correspondence to Yi Wang or Meiping Zhang.

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The authors declare that they have no conflict of interest.

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This study does not contain any studies with human participants performed by any of the authors.

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Communicated by Stefan Hohmann.

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Han, Y., Zhu, L., Li, L. et al. Characteristics of RNA alternative splicing and its potential roles in ginsenoside biosynthesis in a single plant of ginseng, Panax ginseng C.A. Meyer. Mol Genet Genomics 296, 971–983 (2021). https://doi.org/10.1007/s00438-021-01792-z

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  • DOI: https://doi.org/10.1007/s00438-021-01792-z

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