[1] WANG C, WU Z C. Investigation on exploitation and utilization of medicinal biological resources in China[J]. Bull Chin Acad Sci(中国科学院院刊), 1996, 6:423-429.
[2] State Administration of Traditional Chinese Medicine of the People′s Republic of China. Q&a 41-50, outline of strategic planning for the development of traditional Chinese medicine (2016-2030) [EB/OL]. Peking, 2017, http://www.satcm.gov.cn/ fajiansi /zhengcewenjian/2018-03-24/2476.html.
[3] COSTA V, ANGELINI C, FEIS I D, et al. Uncovering the complexity of transcriptomes with RNA-Seq[J]. J Biomed Biotechnol, 2010:853916.
[4] WANG Z, MARK G, MICHAEL S. RNA-Seq:a revolutionary tool for transcriptmics[J]. Nat Rev Genet, 2008, 10:57-63.
[5] WANG Z, GERSTEIN M, SNYDER M, et al. RNA-Seq:a revolutionary tool for transcriptomics[J]. Nat Rev Genet, 2009, 10(1):57-63.
[6] HUANG C, WU M H, LI G Y. The present and advance in transcriptomics of nasopharyngeal carcinoma[J]. Prog Biochem Biophys(生物化学与生物物理进展), 2007, 34(11):1129-1135.
[7] LIN X H, ZHANG J, LI Y, et al. Functional genomics of a living fossil tree, Ginkgo, based on next-generation sequencing technology[J]. Physiol Plantarum, 2011, 143(3):207-218.
[8] LI S T, ZHANG P, ZHANG M, et al. Transcriptional profile of Taxus chinensis cells in response to methyl jasmonate[J]. BMC Genomics, 2012, 13:295.
[9] WU Q, SUN C, LUO H M, et al. Transcriptome analysis of Taxus cuspidata needles based on 454 pyrosequencing[J]. Planta Med, 2011, 77(4):394-400.
[10] DENG N, CHANG E M, LI M H, et al. Transcriptome characterization of Gnetum parvifolium reveals candidate genes involved in important secondary metabolic pathways of flavonoids and stilbenoids[J]. Front Plant Sci, 2016, 7:174.
[11] LIU T, LI X X, XIE S Q, et al. RNA-seq analysis of Paris polyphylla var. yunnanensis roots identified candidate genes for saponin synthesis[J]. Plant Diversity, 2016, 38(3):163-170.
[12] SINGH P, SINGH G, BHANDAWAT A, et al. Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum[J]. Sci Rep, 2017, 7:45295.
[13] GUO X, LI Y, LI C F, et al. Analysis of the Dendrobium officinale transcriptome reveals putative alkaloid biosynthetic genes and genetic markers[J]. Gene, 2013, 527 (1):131-138.
[14] ZHENG X F, PAN C, DIAO Y, et al. Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae)[J]. BMC Genomics, 2013, 14:490.
[15] WEI L, LI S H, LIU S G, et al. Transcriptome analysis of Houttuynia cordata Thunb. by illumina paired-end RNA sequencing and SSR marker discovery[J]. PLoS One, 2014, 9(1):e84105.
[16] ZENG S H, XIAO G, GUO J, et al. Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim[J]. BMC Genomics, 2010, 11:94.
[17] XIE D M, YU N J, HUANG L Q, et al. Next generation sequencing and transcriptome analysis of root bark from Paeonia suffruticosa cv. Feng Dan[J]. China J Chin Mater Med (中国中药杂志), 2017, 42 (5):2954-2961.
[18] PATHAK S, LAKHWANI D, GUPTA P, et al. Comparative transcriptome analysis using high papaverine mutant of Papaver somniferum reveals pathway and uncharacterized steps of papaverine biosynthesis[J]. PLoS One, 2013, 8(5):e65622.
[19] ZENG J G, LIU Y S, LIU W, et al. Integration of transcriptome, proteome and metabolism data reveals the alkaloids biosynthesis in Macleaya cordata and Macleaya microcarpa[J]. PLoS One, 2013, 8(1):e53409.
[20] ZHANG L B, JIA H B, YIN Y T, et al. Transcriptome analysis of leaf tissue of Raphanus sativus by RNA sequencing[J]. PLoS One, 2013, 8(11):e80350.
[21] BAKEL H V, STOUT J M, COTE A G, et al. The draft genome and transcriptome of Cannabis sativa[J]. Genome Biol, 2011, 12(10):R102.
[22] HAO D C, MA P, MU J, et al. De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum[J]. Sci China Life Sci, 2012, 55(5):452-466.
[23] LOKE K K, RAHNAMAIE-TAJADOD R, YEOH C C, et al. Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids[J]. Peer J, 2017, 5:e2938.
[24] ZHANG Z, GAO Z H, WEI J H, et al. The mechanical wound transcriptome of three-year-old Aquilaria sinensis[J]. Acta Pharm Sin(药学学报), 2012, 47(8):1106-1110.
[25] JIANG B, XIE D S, LIU W R, et al. De novo assembly and characterization of the transcriptome, and development of SSR markers in wax gourd (Benicasa hispida)[J]. PLoS One, 2013, 8(8):e71054.
[26] CHEN J, WU X T, XU Y Q, et al. Global transcriptome analysis profiles metabo-lic pathways in traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao[J]. BMC Genomics, 2015, 16(7):S15.
[27] FALARA V, FOTOPOULOS V, MARGARITIS T, et al. Transcriptome analysis approaches for the isolation of trichome-specific genes from the medicinal plant Cistus creticus subsp. creticus[J]. Plant Mol Biol, 2008, 68(6):633-651.
[28] FATIMA T, SNYDER C L, SCHROEDER W R, et al. Fatty acid composition of develo-ping sea buckthorn (Hippophae rhamnoides L.) berry and the transcriptome of the mature seed[J]. PLoS One, 2012, 7(4):e34099.
[29] SHARMA P C, JAIN A, CHAUDHARY S. Transcriptome anal-ysis in seabuckthorn (Hippophae rhamnoides L.), a medicinally important plant[C]. Bangkok(Thailand):International Conference on Environmental and Biological Sciences, 2012:21-24.
[30] GHANGAL R, CHAUDHARY S, JAIN M, et al. Optimization of de novo short read asse-mbly of seabuckthorn (Hippophae rhamnoides L.) transcriptome[J]. PLoS One, 2013, 8(8):e72516.
[31] JAIN A, CHAUDHARY S, SHARMA P C. Miningof microsatellites using next genera-tion sequencing of seabuckthorn (Hippophae rhamnoides L.) transcriptome[J]. Physiol Mol Biol Plants, 2014, 20(1):115-123.
[32] SATHYANARAYANA N, PITTALA R K, TRIPATHI P K, et al. Transcriptomic resources for the medicinal legume Mucuna pruriens:de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers[J]. BMC Genomics, 2017, 18(1):409.
[33] XU L, WANG J B, LEI M, et al. Transcriptome analysis of storage roots and fibrous roots of the traditional medicinal herb Callerya speciosa (Champ.) ScHot[J]. PLoS One, 2016, 11(8):e0160338.
[34] ZHANG F Q, GAO Q B, KHAN G, et al. Comparative transcriptome analysis of aboveground and underground tissues of Rhodiola algida, an important ethno-medicinal herb endemic to the Qinghai-Tibetan Plateau[J]. Gene, 2014, 553(2):90-97.
[35] HAN R C, TAKAHASHI H, NAKAMURA M, et al. Transcriptome analy-sis of nine tissues to discover genes involved in the biosynthesis of active ingredi-ents in Sophora flavescens[J]. Biol Pharm Bull, 2015, 38:876-883.
[36] LI Y, LUO H M, SUN C, et al. EST analysis reveals putative genes involved in glycyrrhizin biosynthesis[J]. BMC Genomics, 2010, 11:268.
[37] SUN Y Z, LUO H M, LI Y, et al. Pyrosequencing of the Camptotheca acuminata transcriptome reveals putative genes involved in camptothecin biosynthesis and transport[J]. BMC Genomics, 2011, 12:533.
[38] KRISHNAN N M, PATTNAIK S, JAIN P, et al. A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica[J]. BMC Genomics, 2012, 13:464.
[39] SUN C, LI Y, WU Q, et al. De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis[J]. BMC Genomics, 2010, 11:262.
[40] WU D, AUSTIN R S, ZHOU S J, et al. The root transcriptome for North American ginseng assembled and profiled across seasonal development[J]. BMC Genomics, 2013, 14:564.
[41] JAYAKODI M, LEE S C, PARK H S, et al. Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots[J]. J Ginseng Res, 2014, 38(4):278-288.
[42] LUO H M, SUN C, SUN Y Z, et al. Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers[J]. BMC Genomics, 2011, 12:S5.
[43] SUI C, CHEN M, XU J S, et al. Comparison of root transcriptomes and expressions of genes involved in main medicinal secondary metabolites from Bupleurum chinense and B. scorzonerifolium, the two Chinese official Radix bupleuri source species[J]. Physiol Plant, 2015, 153(2):230-242.
[44] ZHONG T, ZHANG H, DUAN X Y, et al. Anti-obesity effect of radix Angelica sinensis and candidate causative genes in transcriptome analyses of adipose tissues in high-fat diet-induced mice[J]. Gene, 2017, 599:92-98.
[45] GUPTA P, GOEL R, AGARWAL A V, et al. Comparative transcriptome analysis of different chemotypes elucidates withanolide biosynthesis pathway from medicinal plant Withania somnifera[J]. Sci Rep, 2015, 5:18611.
[46] GARZÓNMARTÍNEZ G A, ZHU Z I, LANDSMAN D, et al. The Physalis peruviana leaf transcriptome:assembly, annotation and gene model prediction[J]. BMC Genomics, 2012, 13:151.
[47] KHALDUN A B, HUANG W J, LIAO S H, et al. Identification of microRNAs and target genes in the fruit and shoot tip of lycium Chinense: a traditional Chinese medicinal plant[J]. PLoS One, 2015, 10(1):e0116334.
[48] GAHLAN P, SINGH H R, SHANKAR R, et al. De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments[J]. BMC Genomics, 2012, 13:126.
[49] SUN P, SONG S H, ZHOU L L, et al. Transcriptome analysis reveals putative genes involved in iridoid biosynthesis in Rehmannia glutinosa[J]. Int J Mol Sci, 2012, 13:13748-13763.
[50] WANG F Q, ZHI J Y, ZHANG Z Y, et al. Transcriptome analysis of salicylic acid treatment in Rehmannia glutinosa Hairy roots using RNA-seq technique for identification of genes involved in acteoside biosynthesis[J]. Front Plant Sci, 2017, 8:787.
[51] WU B, LI Y, YAN H X, et al. Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea[J]. BMC Genomics, 2012, 13:15.
[52] KOTWAL S, KAULS, SHARMA P, et al. De novo transcriptome analysis of medicinally important Plantago ovata using RNA-Seq[J]. PLoS One, 2016, 11 (3):e0150273.
[53] HUANG L L, YANG X, SUN P, et al. The first illumina-based De novo transcriptome sequencing and analysis of safflower flowers[J]. PLoS One, 2012, 7 (6):e38653.
[54] LI Y, SUN C, LUO H M, et al. Transcriptome characterization for Salvia miltiorrhizausing 454 GS FLX[J]. Acta Pharm Sin(药学学报),2010, 45 (4):524-529.
[55] HUA W P, ZHANG Y, SONG J, et al. De novo transcriptome sequencing in Salvia miltiorrhiza to identify genes involved in the biosynthesis of active ingredients[J]. Genomics, 2011, 98(4):272-279.
[56] YANG L, DING G H, LIN H Y, et al. Transcriptome analysis of medicinal plant Salvia miltiorrhiza and identification of genes related to tanshinone biosynthesis[J]. PLoS One, 2013, 6(11):e80464.
[57] GAO W, SUN H X, XIAO H B, et al. Combining metabolomics and transcriptomics to characterize tanshinone biosynthesis in Salvia miltiorrhiza[J]. BMC Genomics, 2014, 15:73.
[58] SONG Z Q, GUO L L, LIU T, et al. Comparative RNA-sequence transcriptome analysis of phenolic acid metabolism in Salvia miltiorrhiza, a traditional chinese medicine model plant[J]. Int J Genomics, 2017:9364594.
[59] CHERUKUPALLI N, DIVATE M, MITTAPELLI S R, et al. De novo assembly of leaf transcriptome in the medicinal plant Andrographis paniculata[J]. Front Plant Sci, 2016, 7:1203.
[60] HE M, WANG Y, HUA W P, et al. De novo sequencing of Hypericum perforatum transcriptome to identify potential genes involved in the biosynthesis of active metabolites[J]. PLoS One, 2012, 7(7):e42081.
[61] KWON C W, PARK K M, KANG B C, et al. Cysteine protease profiles of the medicinal plant Calotropis procera R. Br. revealed by de novo transcriptome analysis[J]. PLoS One, 2015, 10(3):e0119328.
[62] LIU Y, WANG Y, GUO F X, et al. Deep sequencing and transcriptome analyses to identify genes involved in secoiridoid biosynthesis in the tibetan medicinal plant Swertia mussotii[J]. Sci Rep, 2017, 7:43108.
[63] ZHANG X D, ALLAN A C, LI C X, et al. De novo assembly and characterization of the transcriptome of the Chinese medicinal herb, Gentiana rigescens[J]. Int J Mol Sci, 2015, 16(5):11550-11573.
[64] KAUSHIK P, KUMAR S. Data of de novo assembly of the leaf transcriptome in Aegle marmelos[J]. Data Brief, 2018,19:700-703.
[65] HOU D Y, SHI L C, YANG M M, et al. De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using illumina platform[J]. PLoS One, 2018,13(2):e0192610.
[66] HUANG H Y, DU H Y, TAN W Y, et al. Development of SSR molecular markers based on transcriptome sequencing of Eucommia ulmoides[J]. Sci Silv Sin (林业科学), 2013, 49(5):176-181.
[67] HOWYZEH M S, NOORI S A S, VAHID S J, et al. Comparative transcriptome analysis to identify putative genes involved in thymol biosynthesis pathway in medicinal plant Trachyspermum ammi L.[J]. Sci Reports, 2018, 8:13405.
[68] NI J, DONG L X, JIANG Z F, et al. Comprehensive transcriptome analysis and flavonoid profiling of Ginkgo leaves reveals flavonoid content alterations in day-night Cycles[J]. PLoS One, 2018, 13(3):e0193897.
[69] VASHITH D, KUMAR R, RASTOGI S, et al. Transcriptome changes induced by abiotic stresses in Artemisia annua[J]. Sci Reports, 2018, 8(1):3423.
[70] TAN X M, ZHOU Y Q, CHEN J, et al. Advances in research on diversity of endophytic fungi from medicinal plants[J]. Chin Pharm J (中国药学杂志), 2015, 50(18):1563-1580.
[71] MAMEDOV N. Medicinal plants studies: history, challenges and prospective[J]. Med Aromatic Plants, 2012, 1:8.
[72] MATASCI N, HUNG L H, YAN Z X, et al. Data access for the 1 000 plants (1 kP) project[J]. Giga Sci, 2014,3:17.
[73] HUANG L Q, GUO L P, HUA G D, et al. Attributes of Chinese geoherbs and its study strategy[J]. Chin J Inform Tradit Chin Med(中国中医药信息杂志), 2007, 14(2):44.
[74] HUANG L Q, CHEN M L, XIAO P G.The modern biological basis and model hypothesis for the study of Chinese medicinal materials′ pathogenicity[J]. China J Chin Mater Med (中国中药杂志), 2004, 29(6):494.