Global transcriptome analysis profiles metabolic pathways in traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao

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• 作者：Jing Chen ; Xue-Ting Wu ; Yi-Qin Xu ; Yang Zhong ; Yi-Xue Li ; Jia-Kuan Chen…
• 关键词：Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao ; Transcriptome ; Herb ; Metabolites ; Isoflavonoids ; Triterpene saponins
• 刊名：BMC Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：7-supp
• 全文大小：4,324 KB
• 参考文献：1.XY Z: Pharmacopoeia of the People's Republic of China 2005. 2005, People's Medical Publishing House, 1:
  2.Ma X, Tu P, Chen Y, Zhang T, Wei Y, Ito Y: Preparative isolation and purification of two isoflavones from Astragalus membranaceus Bge. var. mongholicus (Bge.) Hsiao by high-speed counter-current chromatography. Journal of Chromatography A. 2003, 992 (1): 193-197.CrossRef PubMed
  3.Wu T, Annie Bligh S, Gu Lh, Wang Zt, Liu Hp, Cheng Xm, Branford-White CJ, Hu Zb: Simultaneous determination of six isoflavonoids in commercial Radix Astragali by HPLC-UV. Fitoterapia. 2005, 76 (2): 157-165. 10.1016/j.fitote.2004.11.006.CrossRef PubMed
  4.Zhang Q, Gao W, Man S: Chemical composition and pharmacological activities of astragali radix. China journal of Chinese materia medica. 2012, 37 (21): 3203-3207.PubMed
  5.Pan H, Wang Y, Zhang Y, Zhou T, Fang C, Nan P, Wang X, Li X, Wei Y, Chen J: Phenylalanine ammonia lyase functions as a switch directly controlling the accumulation of calycosin and calycosin-7-O-β-D-glucoside in Astragalus membranaceus var. mongholicus plants. Journal of experimental botany. 2008, 59 (11): 3027-3037. 10.1093/jxb/ern152.CrossRef PubMed
  6.Fan Y, Wu DZ, Gong YQ, Zhou JY, Hu ZB: Effects of calycosin on the impairment of barrier function induced by hypoxia in human umbilical vein endothelial cells. European journal of pharmacology. 2003, 481 (1): 33-40. 10.1016/j.ejphar.2003.09.007.CrossRef PubMed
  7.Lee YM, Lee , Yun-Mi , Choi SI, Choi , Soo-Im , Lee JW, Lee , Jae-Won , Jung SM, Jung , Sun-Mi , Park SM, Park , Sang-Min , Heo TR, Heo , Tae-Ryeon : Isolation of hyaluronidase inhibitory component from the roots of Astraglus membranaceus Bunge (Astragali Radix). Food Science and Biotechnology. 2005, 14 (2): 263-267.
  8.CHOI S, PARK SR, HEO TR: Inhibitory effect of astragali radix on matrix degradation in human articular cartilage. Journal of microbiology and biotechnology. 2005, 15 (6): 1258-1266.
  9.Pan H, Fang C, Zhou T, Wang Q, Chen J: Accumulation of calycosin and its 7-O-β-d-glucoside and related gene expression in seedlings of Astragalus membranaceus Bge. var. mongholicus (Bge.) Hsiao induced by low temperature stress. Plant cell reports. 2007, 26 (7): 1111-1120. 10.1007/s00299-006-0301-8.CrossRef PubMed
  10.Liu CJ, Huhman D, Sumner LW, Dixon RA: Regiospecific hydroxylation of isoflavones by cytochrome p450 81E enzymes from Medicago truncatula. The Plant Journal. 2003, 36 (4): 471-484. 10.1046/j.1365-313X.2003.01893.x.CrossRef PubMed
  11.Liu CJ, Deavours BE, Richard SB, Ferrer JL, Blount JW, Huhman D, Dixon RA, Noel JP: Structural basis for dual functionality of isoflavonoid O-methyltransferases in the evolution of plant defense responses. The Plant Cell Online. 2006, 18 (12): 3656-3669. 10.1105/tpc.106.041376.CrossRef
  12.Du M, WX , Wang ZY, Hu ZB: Isolation and Identification of Genes Related to Astragaloside IV Differential Expressed Synthesis in Astragalus membranaceus. Pharmaceutical Biotechnology. 2005, 12 (2): 76-80.
  13.Luo H, Sun C, Sun Y, Wu Q, Li Y, Song J, Niu Y, Cheng X, Xu H, Li C: Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers. BMC genomics. 2011, 12 (Suppl 5): S5-10.1186/1471-2164-12-S5-S5.PubMedCentral CrossRef PubMed
  14.Dong H, Jiang B, Han Y, GENG Y, ZHAO Yq: Transformation of Compound K from Saponins in Leaves of Panax notoginseng by Immobilized β-Glucanase. Chin Herb Med. 2010, 2 (1): 41-47.
  15.Wu D, Austin RS, Zhou S, Brown D: The root transcriptome for North American ginseng assembled and profiled across seasonal development. BMC genomics. 2013, 14 (1): 564-10.1186/1471-2164-14-564.PubMedCentral CrossRef PubMed
  16.Wang S, Li J, Huang H, Gao W, Zhuang C, Li B, Zhou P, Kong D: Anti-hepatitis B virus activities of astragaloside IV isolated from radix Astragali. Biological & pharmaceutical bulletin. 2009, 32 (1): 132-135. 10.1248/bpb.32.132.CrossRef
  17.Augustin JM, Kuzina V, Andersen SB, Bak S: Molecular activities, biosynthesis and evolution of triterpenoid saponins. Phytochemistry. 2011, 72 (6): 435-457. 10.1016/j.phytochem.2011.01.015.CrossRef PubMed
  18.Kim O, Bang K, Jung S, Kim Y, Hyun D, Kim S, Cha S: Molecular characterization of ginseng farnesyl diphosphate synthase gene and its up-regulation by methyl jasmonate. Biologia plantarum. 2010, 54 (1): 47-53. 10.1007/s10535-010-0007-1.CrossRef
  19.Zhang WJ, Hufnagl P, Binder BR, Wojta J: Anti-inflammatory activity of astragaloside IV is mediated by inhibition of NF-qB activation and adhesion molecule expression. Thromb Haemost. 2003, 90 (5): 904-914.PubMed
  20.Mardis ER: The impact of next-generation sequencing technology on genetics. Trends in genetics. 2008, 24 (3): 133-141. 10.1016/j.tig.2007.12.007.CrossRef PubMed
  21.Ping J, Wang Y, Yu Y, Li Y, Li X, Hao P: A comparative analysis of tissue gene expression data from high-throughput studies. Chinese Science Bulletin. 2012, 57 (22): 2920-2927. 10.1007/s11434-012-5077-3.CrossRef
  22.Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH: Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular ecology. 2008, 17 (7): 1636-1647. 10.1111/j.1365-294X.2008.03666.x.CrossRef PubMed
  23.Shi CY, Yang H, Wei CL, Yu O, Zhang ZZ, Jiang CJ, Sun J, Li YY, Chen Q, Xia T: Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC genomics. 2011, 12 (1): 131-10.1186/1471-2164-12-131.PubMedCentral CrossRef PubMed
  24.Wang XC, Zhao QY, Ma CL, Zhang ZH, Cao HL, Kong YM, Yue C, Hao XY, Chen L, Ma JQ: Global transcriptome profiles of Camellia sinensis during cold acclimation. BMC genomics. 2013, 14 (1): 415-10.1186/1471-2164-14-415.PubMedCentral CrossRef PubMed
  25.Liu XB, Ma L, Zhang AH, Zhang YH, Jiang J, Ma W, Zhang LM, Ren WC, Kong XJ: High-Throughput Analysis and Characterization of Astragalus membranaceus Transcriptome Using 454 GS FLX. PloS one. 2014, 16 (5): e95831-CrossRef
  26.Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology. 2011, 29 (7): 644-652. 10.1038/nbt.1883.PubMedCentral CrossRef PubMed
  27.Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10 (3): R25-10.1186/gb-2009-10-3-r25.PubMedCentral CrossRef PubMed
  28.Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. Science. 1997, 278 (5338): 631-637. 10.1126/science.278.5338.631.CrossRef PubMed
  29.Jin J, Zhang H, Kong L, Gao G, Luo J: PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic acids research. 2014, 42 (D1): D1182-D1187. 10.1093/nar/gkt1016.PubMedCentral CrossRef PubMed
  30.Lorenzo CP, Anahit G, Irma RV, F M-GJ, R B-CJ, L RD: Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae. Plant Physiology. 2010, 3
  31.Khanna R, Huq E, Kikis EA, Al-Sady B, Lanzatella C, Quail PH: A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors. The Plant Cell Online. 2004, 16 (11): 3033-3044. 10.1105/tpc.104.025643.CrossRef
  32.Chinnusamy V, Ohta M, Kanrar S, Lee Bh, Hong X, Agarwal M, Zhu JK: ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes & development. 2003, 17 (8): 1043-1054. 10.1101/gad.1077503.CrossRef
  33.Kiribuchi K, Sugimori M, Takeda M, Otani T, Okada K, Onodera H, Ugaki M, Tanaka Y, Tomiyama-Akimoto C, Yamaguchi T: RERJ1, a jasmonic acid-responsive gene from rice, encodes a basic helix-loop-helix protein. Biochemical and biophysical research communications. 2004, 325 (3): 857-863. 10.1016/j.bbrc.2004.10.126.CrossRef PubMed
  34.Wei Z, Yujin S, Ljudmilla T, Changbin C, Ueli G, Hong M: Regulation of Arabidopsis tapetum development and function by DYSFUNCTIONAL TAPETUM1 (DYT1) encoding a putative bHLH transcription factor. Development (Cambridge). 2006, 16
  35.Nuno P, Liam D: Origin and diversification of basic-helix-loop-helix proteins in plants. Molecular Biology and Evolution. 2009, 4
  36.Qian W, Tan G, Liu H, He S, Gao Y, An C: Identification of a bHLH-type G-box binding factor and its regulation activity with G-box and Box I elements of the PsCHS1 promoter. Plant cell reports. 2007, 26 (1): 85-93.CrossRef PubMed
  37.R LS, F HL, L DS, R WS: Lc, a member of the maize R gene family responsible for tissue-specific anthocyanin production, encodes a protein similar to transcriptional activators and contains the myc-homology region. Proceedings of the National Academy of Sciences of the United States of America. 1989, 18
  38.Hu J, Anderson B, Wessler SR: Isolation and characterization of rice R genes: evidence for distinct evolutionary paths in rice and maize. Genetics. 1996, 142 (3): 1021-1031.PubMedCentral PubMed
  39.N N, I D, C J, G P, M C, L L: The TT8 gene encodes a basic helix-loop-helix domain protein required for expression of DFR and BAN genes in Arabidopsis siliques. The Plant Cell. 2000, 10
  40.Feller A, Machemer K, Braun EL, Grotewold E: Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. The Plant Journal. 2011, 66 (1): 94-116. 10.1111/j.1365-313X.2010.04459.x.CrossRef PubMed
  41.J PA, D G, U W, A PP, H S: The regulatory c1 locus of Zea mays encodes a protein with homology to myb proto-oncogene products and with structural similarities to transcriptional activators. The EMBO Journal. 1987, 12
  42.Hartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B: Differential combinatorial interactions of cis-acting elements recognized by R2R3-MYB, BZIP, and BHLH factors control light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes. Plant molecular biology. 2005, 57 (2): 155-171. 10.1007/s11103-004-6910-0.CrossRef PubMed
  43.Katiyar A, Smita S, Lenka SK, Rajwanshi R, Chinnusamy V, Bansal KC: Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC genomics. 2012, 13 (1): 544-10.1186/1471-2164-13-544.PubMedCentral CrossRef PubMed
  44.Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L: MYB transcription factors in Arabidopsis. Trends in plant science. 2010, 15 (10): 573-581. 10.1016/j.tplants.2010.06.005.CrossRef PubMed
  45.Chai G, Hu R, Zhang D, Qi G, Zuo R, Cao Y, Chen P, Kong Y, Zhou G: Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa). BMC genomics. 2012, 13 (1): 253-10.1186/1471-2164-13-253.PubMedCentral CrossRef PubMed
  46.Dong W, Yinghui G, Changai W, Guodong Y, Yingying L, Chengchao Z: Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice. BMC Genomics. 2008, 1
  47.I CS, R HT, B-H M, H CJ, H CB, R PS: Alleviation of osteoarthritis by calycosin-7-O-beta-D-glucopyranoside (CG) isolated from Astragali radix (AR) in rabbit osteoarthritis (OA) model. Osteoarthritis and Cartilage. 2007, 9
  48.M MS, K HT, K GR, K BH: Phytoestrogens and breast cancer prevention: possible mechanisms of action. Environmental Health Perspectives. 2008, 4
  49.Yu O, McGonigle B: Metabolic Engineering of Isoflavone Biosynthesis. Advances in Agronomy. 2005
  50.Werck-Reichhart D, Batard Y, Kochs G, Lesot A, Durst F: Monospecific polyclonal antibodies directed against purified cinnamate 4-hydroxylase from Helianthus tuberosus (immunopurification, immunoquantitation, and interspecies cross-reactivity). Plant physiology. 1993, 102 (4): 1291-1298. 10.1104/pp.102.4.1291.PubMedCentral CrossRef PubMed
  51.Jae-youl J, Mangai KG, Ji-young P, Won-jin K, Hyun-soon K, Bong-sik Y, Hyouk J, Jae-heung J: An overexpression of chalcone reductase of Pueraria montana var. lobata alters biosynthesis of anthocyanin and 5'-deoxyflavonoids in transgenic tobacco. Biochemical and Biophysical Research Communications. 2003, 1
  52.Xu RY, Nan P, Yang Y, Pan H, Zhou T, Chen J: Ultraviolet irradiation induces accumulation of isoflavonoids and transcription of genes of enzymes involved in the calycosin-7-O-β-d-glucoside pathway in Astragalus membranaceus Bge. var. mongholicus (Bge.) Hsiao. Physiologia plantarum. 2011, 142 (3): 265-273. 10.1111/j.1399-3054.2011.01474.x.CrossRef PubMed
  53.Gillissen B, Bürkle L, André B, Kühn C, Rentsch D, Brandl B, Frommer WB: A new family of high-affinity transporters for adenine, cytosine, and purine derivatives in Arabidopsis. The Plant Cell Online. 2000, 12 (2): 291-300. 10.1105/tpc.12.2.291.CrossRef
  54.Kim YB, Thwe AA, Li X, Tuan PA, Zhao S, Park CG, Lee JW, Park SU: Accumulation of Flavonoids and Related Gene Expressions in Different Organs of Astragalus membranaceus Bge. Applied Biochemistry and Biotechnology. 2014, 1-10.
  55.Dubey VS, Bhalla R, Luthra R: An overview of the non-mevalonate pathway for terpenoid biosynthesis in plants. Journal of biosciences. 2003, 28 (5): 637-646. 10.1007/BF02703339.CrossRef PubMed
  56.Lichtenthaler HK, Schwender J, Disch A, Rohmer M: Biosynthesis of isoprenoids in higher plant chloroplasts proceeds via a mevalonate-independent pathway. Febs Letters. 1997, 400 (3): 271-274. 10.1016/S0014-5793(96)01404-4.CrossRef PubMed
  57.Wolff M, Seemann M, Tse Sum Bui B, Frapart Y, Tritsch D, Estrabot AG, Rodríguez-Concepción M, Boronat A, Marquet A, Rohmer M: Isoprenoid biosynthesis via the methylerythritol phosphate pathway: the (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase (LytB/IspH) from Escherichia coli is a [4Fe-4S] protein. FEBS letters. 2003, 541 (1): 115-120.CrossRef PubMed
  58.Vincken JP, Heng L, de Groot A, Gruppen H: Saponins, classification and occurrence in the plant kingdom. Phytochemistry. 2007, 68 (3): 275-297. 10.1016/j.phytochem.2006.10.008.CrossRef PubMed
  59.CHIOU Wf, ZHANG Jt: Comparison of the pharmacological effects of Panax ginseng and Panax quinquefolium. Acta Pharmacologica Sinica. 2008, 29 (9): 1103-1108. 10.1111/j.1745-7254.2008.00868.x.CrossRef PubMed
  60.Han JY, Kwon YS, Yang DC, Jung YR, Choi YE: Expression and RNA interference-induced silencing of the dammarenediol synthase gene in Panax ginseng. Plant and cell physiology. 2006, 47 (12): 1653-1662. 10.1093/pcp/pcl032.CrossRef PubMed
  61.Y.H. L, Shi. S, H.Q. Z, Y.D. Z, B. X: 2D NMR study on cycloartane triterpenoids from Astragalus membranaceus var. mongholicus. Journal of China Pharmaceutical University. 2008, 39 (1): 15-19.
  62.Phillips DR, Rasbery JM, Bartel B, Matsuda S: Biosynthetic diversity in plant triterpene cyclization. Current opinion in plant biology. 2006, 16 (3): 305-314.CrossRef
  63.Corey E, Matsuda S, Bartel B: Isolation of an Arabidopsis thaliana gene encoding cycloartenol synthase by functional expression in a yeast mutant lacking lanosterol synthase by the use of a chromatographic screen. Proceedings of the National Academy of Sciences. 1993, 90 (24): 11628-11632. 10.1073/pnas.90.24.11628.CrossRef
  64.Nelson DR, Schuler MA, Paquette SM, Werck-Reichhart D, Bak S: Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot. Plant Physiology. 2004, 135 (2): 756-772. 10.1104/pp.104.039826.PubMedCentral CrossRef PubMed
  65.Masaaki S, Masaki H, Yuji K, Hiroaki H, Tetsuo K, Yutaka E: Identification of beta-amyrin and sophoradiol 24-hydroxylase by expressed sequence tag mining and functional expression assay. The FEBS Journal. 2006, 5
  66.Hikaru S, Kiyoshi O, Satoru S, Masaharu M, Toshiyuki O, Hiroshi S, Tomoyoshi A, Toshio A, Kazuki S, Toshiya M: Licorice beta-amyrin 11-oxidase, a cytochrome P450 with a key role in the biosynthesis of the triterpene sweetener glycyrrhizin. Proceedings of the National Academy of Sciences of the United States of America. 2008, 37
  67.Lahoucine A, V HD, A FM, W SL, W BJ, A DR: Genomics-based selection and functional characterization of triterpene glycosyltransferases from the model legume Medicago truncatula. The Plant Journal. 2005, 6
  68.WANG YP, LI XY, SONG CQ, HU ZB: Effect of astragaloside F on T, B lymphocyte proliferation and peritoneal macrophage function in mice1. Acta Pharmacol Sin. 2002, 23 (3): 263-266.PubMed
  69.Luo H, Dai R, Li Y: Nuclear cardiology study on effective ingredients of Astragalus membranaceus in treating heart failure. Chinese journal of integrated traditional and Western medicine. 1995, 15 (12): 707-709.PubMed
  70.Luo Y, Qin Z, Hong Z, Zhang X, Ding D, Fu JH, Zhang WD, Chen J: Astragaloside IV protects against ischemic brain injury in a murine model of transient focal ischemia. Neuroscience letters. 2004, 363 (3): 218-223. 10.1016/j.neulet.2004.03.036.CrossRef PubMed
  71.Zhou J, Fan Y, Kong J, Wu D, Hu Z: Effects of components isolated from Astragalus membranaceus Bunge on cardiac function injured by myocardial ischemia reperfusion in rats. China journal of Chinese materia medica. 2000, 25 (5): 300-302.PubMed
  72.Bak S, Beisson F, Bishop G, Hamberger B, Höfer R, Paquette S, Werck-Reichhart D: Cytochromes P450. The Arabidopsis Book/American Society of Plant Biologists. 2011, 16:
  73.Bernhardt R: Cytochromes P450 as versatile biocatalysts. Journal of biotechnology. 2006, 124 (1): 128-145. 10.1016/j.jbiotec.2006.01.026.CrossRef PubMed
  74.Nelson D, Werck-Reichhart D: A P450-centric view of plant evolution. The Plant Journal. 2011, 66 (1): 194-211. 10.1111/j.1365-313X.2011.04529.x.CrossRef PubMed
  75.K AG, Shigeru T, Oksoo H, Hitoshi I, Randeep R: Rice octadecanoid pathway. Biochemical and Biophysical Research Communications. 2004, 1
  76.K HR, Stefania DD, Angelo S: Plant cytochrome CYP74 family: biochemical features, endocellular localisation, activation mechanism in plant defence and improvements for industrial applications. ChemBioChem. 2009, 7
  77.Li T, Valeria M, Joonyul K, Maria ML, Dean D: The Arabidopsis LUT1 locus encodes a member of the cytochrome p450 family that is required for carotenoid epsilon-ring hydroxylation activity. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2004, 1
  78.M TE, Shozo F, Hideharu S, Yukihisa S, Suguru T, Shigeo Y, A DM, I TQ, M NM: CYP72B1 inactivates brassinosteroid hormones: an intersection between photomorphogenesis and plant steroid signal transduction. Plant Physiology. 2003, 4
  79.J BG, Csaba K: Brassinosteroids and plant steroid hormone signaling. The Plant Cell. 2002
  80.Franck P, Fred B: Cytochrome P450 metabolizing fatty acids in plants: characterization and physiological roles. The FEBS Journal (Online). 2010, 2
  
• 作者单位：Jing Chen (1)
  Xue-Ting Wu (2)
  Yi-Qin Xu (1)
  Yang Zhong (1) (3)
  Yi-Xue Li (4)
  Jia-Kuan Chen (1)
  Xuan Li (2)
  Peng Nan (1)
  
  1. Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
  2. Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
  3. Institute of Biodiversity Science and Geobiology, Tibet University, Lhasa, 850000, China
  4. Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
  
• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao (A. mongolicus, family Leguminosae) is one of the most important traditional Chinese herbs. Among many secondary metabolites it produces, the effective bioactive constituents include isoflavonoids and triterpene saponins. The genomic resources regarding the biosynthesis of these metabolites in A. mongolicus are limited. Although roots are the primary material harvested for medical use, the biosynthesis of the bioactive compounds and its regulation in A. mongolicus are not well understood. Therefore, a global transcriptome analysis on A. mongolicus tissues was performed to identify the genes essential for the metabolism and to profile their expression patterns in greater details.