Flavonoid accumulation and identification of flavonoid biosynthesis genes in Dimocarpus longan lour. by transcriptome sequencing

  • Wei ZHENG Harbin University of Commerce, School of Pharmacy, Research Center of Pharmaceutical Engineering Technology, No. 138, Tongda Street, Daoli District, Harbin, 150076
  • Ziwei ZHANG Harbin University of Commerce, School of Pharmacy, Research Center of Pharmaceutical Engineering Technology, No. 138, Tongda Street, Daoli District, Harbin, 150076
  • Xuefei YU Harbin University of Commerce, Library, No. 1, Xuehai Street, Songbei District, Harbin, 150028
  • Xueming DONG Harbin University of Commerce, School of Pharmacy, Research Center of Pharmaceutical Engineering Technology, No. 138, Tongda Street, Daoli District, Harbin, 150076
  • Qiuying ZHANG Harbin University of Commerce, School of Pharmacy, Research Center of Pharmaceutical Engineering Technology, No. 138, Tongda Street, Daoli District, Harbin, 150076
Keywords: flavonoid; gene expression; LC-MS; D. longan; transcriptome sequencing


Dimocarpus longan Lour. (D. longan) is widely cultivated and is very popular around the world. Its by-products such as roots and leaves have been used as traditional Chinese medicines due to their content of important secondary metabolites, especially flavonoids. However, the economic value and application of D. longan roots and leaves are limited because they accumulate relatively low levels of flavonoids. Therefore, it is important to find key genes that regulate the accumulation of the predominant flavonoid compounds in D. longan roots and leaves. Here, we have used RNA-sequencing to describe the transcriptome of D. longan. We obtained 75,229,529 raw reads and 15.04 GB of clean data, generating 56,055 unigenes (N50 = 1,583 nt, mean length = 829.61 nt). Next, we annotated these unigenes using the various available bioinformatics databases. By this approach, we identified 6,684 genes differentially expressed between root and leaf tissues, of which thirteen were identified as flavonoid biosynthesis genes. Of these, eight genes were much highly expressed in roots (DlC4H, DlHCT, DlDFR, DlANS, DlANR, DlCHS, DlF3′H, and DlF3H), and two were much highly expressed in leaves (DlLAR and DlFLS). The contents of thirteen flavonoids in D. longan roots and leaves were measured by LC-MS, and epicatechin was found to be the predominant flavonoid in both tissues, which was significantly higher than the other flavonoids measured in the study. Its contents were 213,773.65 ng/g in roots and 22,388.71 ng/g in leaves. Our findings will facilitate efforts to increase the economic value and expand the applications of D. longan roots and leaves by means of genetic engineering.


Metrics Loading ...


Azuma A, Yakushiji H, Koshita Y, Kobayashi S (2012). Flavonoid biosynthesis-related genes in grape skin are differentially regulated by temperature and light conditions. Planta 236(4):1067-1080.

Chang JJ, Hsu MJ, Huang HP, Chung DJ, Chang YC, Wang CJ (2013). Mulberry anthocyanins inhibit oleic acid induced lipid accumulation by reduction of lipogenesis and promotion of hepatic lipid clearance. Journal of Agricultural and Food Chemistry 61(25):6069-6076.

Conesa A, Gotz S (2008). Blast2GO: A comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics 2008:619832-619843.

Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005). Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674-3676.

Dastmalchi M, Dhaubhadel S (2015). Proteomic insights into synthesis of isoflavonoids in soybean seeds. Proteomics 15(10):1646-1657.

Deng Y, Li C, Li H, Lu S (2018). Identification and characterization of flavonoid biosynthetic enzyme genes in Salvia miltiorrhiza (Lamiaceae). Molecules 23(6):1467-1486.

Dixon RA, Pasinetti GM (2010). Flavonoids and isoflavonoids: from plant biology to agriculture and neuroscience. Plant Physiology 154:453-457. https://doi.org/10.1104/pp.110.161430

Fang J (2014). Bioavailability of anthocyanins. Drug Metabolism Reviews 46(4):508-520. https://doi.org/10.3109/03602532.2014.978080

Ferrer JL, Austin MB, Stewart CJ, Noel JP (2008). Structure and function of enzymes involved in the biosynthesis of phenylpropanoids. Plant Physiology and Biochemistry 46(3):356-370.

Galperin MY, Kristensen DM, Makarova KS, Wolf YI, Koonin EV (2019). Microbial genome analysis: the COG approach. Briefings in Bioinformatics 20(4):1063-1070. https://doi.org/10.1093/bib/bbx117

Glenn TC (2011). Field guide to next-generation DNA sequencers. Molecular Ecology Resources 11(5):759-769.

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, … Regev A (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29(7):644-652.

Han Y, Vimolmangkang S, Soria-Guerra RE, Korban SS (2012). Introduction of apple ANR genes into tobacco inhibits expression of both CHI and DFR genes in flowers, leading to loss of anthocyanin. Journal of Experimental Botany 63(7):2437-2447.

Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, … Xie Z (2008). Single-molecule DNA sequencing of a viral genome. Science 320(5872):106-109.

Hernández Y, Bernstein R, Pagan P, Vargas L, McCaig W, Ramrattan G, … Qiu WG (2018). BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines. BMC Bioinformatics 19(1):76. https://doi.org/10.1186/s12859-018-2074-9

Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH Waterston RH (2009). Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Research 19(4):657-666.

Hou R, Bao Z, Wang S, Su H, Li Y, Du H, … Hu X (2011). Transcriptome sequencing and de novo analysis for Yesso scallop (Patinopecten yessoensis) using 454 GS FLX. PLoS One 6(6):e21560.

Jennings A, Welch AA, Fairweather-Tait SJ, Kay C, Minihane AM, Chowienczyk P, … Cassidy A (2012). Higher anthocyanin intake is associated with lower arterial stiffness and central blood pressure in women. American Journal of Clinical Nutrition 96(4):781-788.

Jordon-Thaden IE, Chanderbali AS, Gitzendanner MA, Soltis DE (2015). Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta. Applications in Plant Sciences 3(5):1400105. https://doi.org/10.3732/apps.1400105

Lei Z, Zhou C, Ji X, Wei G, Huang Y, Yu W, … Qiu Y (2018). Transcriptome analysis reveals genes involved in flavonoid biosynthesis and accumulation in Dendrobium catenatum from different locations. Scientific Reports 8(1):6373-6388.

Li B, Dewey CN (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323. https://doi.org/10.1186/1471-2105-12-323

Li C, Wang Y, Huang X, Li J, Wang H (2013). De novo assembly and characterization of fruit transcriptome in Litchi chinensis Sonn and analysis of differentially regulated genes in fruit in response to shading. BMC Genomics 14 (552):552-567.

Lin Y, Li N, Lin H, Lin M, Chen Y, Wang H, …Lin Y (2020). Effects of chitosan treatment on the storability and quality properties of longan fruit during storage. Food Chemistry 306(125627):125627-125636.

Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, … Wang J (2010). De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 20(2):265-272.

Liu YY, Chen XR, Wang JP, Cui WQ, Xing XX, Chen XY, … Li YH (2019). Transcriptomic analysis reveals flavonoid biosynthesis of Syringa oblata Lindl. in response to different light intensity. BMC Plant Biology 19(1):487-502.

Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, … Matz MV (2009). Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 10(219):219-235.

Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007). KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Research 35:W182-W185.

Myhre S, Tveit H, Mollestad T, Laegreid A (2006). Additional gene ontology structure for improved biological reasoning. Bioinformatics 22(16):2020-2027.

Ni J, Dong L, Jiang Z, Yang X, Chen Z, Wu Y, Xu M (2018). Comprehensive transcriptome analysis and flavonoid profiling of Ginkgo leaves reveals flavonoid content alterations in day-night cycles. PLoS One 13(3):e0193897.

Park SJ, Park DH, Kim DH, Lee S, Yoon BH, Jung WY, … Ryu JH (2010). The memory-enhancing effects of Euphoria longan fruit extract in mice. Journal of Ethnopharmacology 128(1):160-165.

Petrussa E, Braidot E, Zancani M, Peresson C, Bertolini A, Patui S, Vianello A (2013). Plant flavonoids-biosynthesis, transport and involvement in stress responses. International Journal of Molecular Sciences 14(7):14950-14973.

Ronaghi M, Uhlen M, Nyren P (1998). A sequencing method based on real-time pyrophosphate. Science 281(5375):363-365.

Saito K, Yonekura-Sakakibara K, Nakabayashi R, Higashi Y, Yamazaki M, Tohge T, Fernie AR (2013). The flavonoid biosynthetic pathway in Arabidopsis: structural and genetic diversity. Plant Physiology and Biochemistry 72:21-34.

Schmittgen TD, Livak KJ (2008). Analyzing real-time PCR data by the comparative C(T) method. Nature Protocols 3(6):1101-1108.

Shanmugam B, Shanmugam KR, Ravi S, Subbaiah GV, Ramakrishana C, Mallikarjuna K, Reddy KS (2017). Exploratory studies of (-)-epicatechin, a bioactive compound of Phyllanthus niruri, on the antioxidant enzymes and oxidative stress markers in D-galactosamine-induced hepatitis in rats: a study with reference to clinical prospective. Pharmacognosy Magazine 13(1):S56-S62. https://doi.org/10.4103/0973-1296.203973

Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, … Richardson PM (2008). Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Research 18(10):1638-1642.

Tang NP, Zhou B, Wang B, Yu RB, Ma J (2009). Flavonoids intake and risk of lung cancer: a meta-analysis. Japanese Journal of Clinical Oncology 39(6):352-359.

Tang YY, He XM, Sun J, Li CB, Li L, Sheng JF, … Ling DN (2019). Polyphenols and alkaloids in byproducts of longan fruits (Dimocarpus Longan Lour.) and their bioactivities. Molecules 24(6):1186-1201.

Tan L, Wang M, Kang Y, Azeem F, Zhou Z, Tuo D, …Pan Z (2018). Biochemical and Functional characterization of anthocyanidin reductase (ANR) from Mangifera indica L. Molecules 23(11):2876-2895. doi: 10.3390/molecules23112876

Thitiratsakul B, Anprung P (2014). Prebiotic activity score and bioactive compounds in longan (Dimocarpus longan Lour.): influence of pectinase in enzyme-assisted extraction. Journal of Food Science and Technology 51(9):1947-1955.

Tohge T, de Souza LP, Fernie AR (2017). Current understanding of the pathways of flavonoid biosynthesis in model and crop plants. Journal of Experimental Botany 68(15):4013-4028.

Tseng HC, Wu WT, Huang HS, Wu MC (2014). Antimicrobial activities of various fractions of longan (Dimocarpus longan Lour.Fen Ke) seed extract. International Journal of Food Sciences and Nutrition 65(5)589-593.

Vogt T (2010). Phenylpropanoid biosynthesis. Molecular Plant 3(1):2-20.

Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, … Li Y (2010). De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genomics 11:726-739.

Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D … Zhang X (2011). Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12:451-463.

Wilson RT, Wang J, Chinchilli V, Richie JP, Virtamo J, Moore LE, Albanes D (2009). Fish, vitamin D, and flavonoids in relation to renal cell cancer among smokers. American Journal of Epidemiology 170(6):717-729.

Xie F, Burklew CE, Yang Y, Liu M, Xiao P, Zhang B, Qiu D (2012). De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome. Planta 236(1):101-113.

Yang C, He N, Ling X, Ye M, Zhang C, Shao W, … Li Q (2008). The isolation and characterization of polysaccharides from longan pulp. Separation and Purification Technology 63(1):226-230. https://doi.org/10.1016/j.seppur.2008.05.004

Yang K, Chan CB (2018). Epicatechin potentiation of glucose-stimulated insulin secretion in INS-1 cells is not dependent on its antioxidant activity. Acta Pharmacologica Sinica 39:893-902.

Yao Q, Lin MT, Zhu YD, Xu HL, Zhao YZ (2018). Recent trends in potential therapeutic applications of the dietary flavonoid didymin. Molecules (Basel, Switzerland) 23(10):2547. https://doi.org/10.3390/molecules23102547

Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, … Wang J (2006). WEGO: a web tool for plotting GO annotations. Nucleic Acids Research 34:W293-W297.

Yuan Y, Zhang J, Liu X, Meng M, Wang J, Lin J (2020). Tissue-specific transcriptome for Dendrobium officinale reveals genes involved in flavonoid biosynthesis. Genomics 112(2):1781-1794.

Zhang HN, Wei YZ, Shen JY, Lai B, Huang XM, Ding F, … Chen HB (2014). Transcriptomic analysis of floral initiation in litchi (Litchi chinensis Sonn.) based on de novo RNA sequencing. Plant Cell Reports 33(10):1723-1735.

How to Cite
ZHENG, W., ZHANG, Z., YU, X., DONG, X., & ZHANG, Q. (2020). Flavonoid accumulation and identification of flavonoid biosynthesis genes in Dimocarpus longan lour. by transcriptome sequencing. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 48(2), 636-655. https://doi.org/10.15835/nbha48211879
Research Articles