Renaissance in phytomedicines: promising implications of NGS technologies

Planta

Volumn 244, Issue 1, 2016, Pages 19-38

  Sharma, Sonal ^a,b   Shrivastava, Neeta ^a  

^a B V PATEL PHARMACEUTICAL EDUCATION AND RESEARCH DEVELOPMENT PERD CENTRE   (India)

^b NIRMA UNIVERSITY   (India)

Author keywords

Bioactive molecules; Genome; Medicinal plants; Next generation sequencing; Phytomedicines; Transcriptome

Indexed keywords

PLANT MEDICINAL PRODUCT;

BIOLOGY; BIOSYNTHESIS; CLASSIFICATION; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; MEDICINAL PLANT; METABOLISM; PHYTOTHERAPY; PROCEDURES; TRENDS;

BIOSYNTHETIC PATHWAYS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PHYTOTHERAPY; PLANT PREPARATIONS; PLANTS, MEDICINAL;

EID: 84961841617     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-016-2492-8     Document Type: Review

References (178)

1. Aggarwal BB, Sundaram C, Malani N, Ichikawa H (2007) Curcumin: the Indian solid gold. Adv Exp Med Biol 595:1–75
2. Al-Dous EK, George B, Al-Mahmoud ME et al (2011) De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol 29:521–527
3. Amira EA, Behija SE, Beligh M et al (2012) Effects of the ripening stage on phenolic profile, phytochemical composition and antioxidant activity of date palm fruit. J Agric Food Chem 60:10896–10902
4. Annadurai RS, Jayakumar V, Mugasimangalam RC et al (2012) Next generation sequencing and de novo transcriptome analysis of Costus pictus D. Don, a non-model plant with potent anti-diabetic properties. BMC Genomics 13:663. doi:10.1186/1471-2164-13-663
5. Annadurai RS, Neethiraj R, Jayakumar V et al (2013) De Novo transcriptome assembly (NGS) of Curcuma longa L. rhizome reveals novel transcripts related to anticancer and antimalarial terpenoids. PLoS One 8:e56217. doi:10.1371/journal.pone.0056217
6. Appendino G, Chianese G, Taglialatela-Scafati O (2011) Cannabinoids: occurrence and medicinal chemistry. Curr Med Chem 18:1085–1099
7. Baliga MS, Baliga BRV, Kandathil SM et al (2011) A review of the chemistry and pharmacology of the date fruits (Phoenix dactylifera L.). Food Res Int 44:1812–1822. doi:10.1016/j.foodres.2010.07.004
8. Bardou F, Ariel F, Simpson CG et al (2014) Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev Cell 30:166–176. doi:10.1016/j.devcel.2014.06.017
9. Barrero RA, Chapman B, Yang Y et al (2011) De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes. BMC Genomics. doi:10.1186/1471-2164-12-600
10. Bekheet SA, Hanafy MS (2011) Towards sex determination of date palm. In: Jain SM, Jameel MA, Johnson DV (eds) Date palm biotechnology, 1st edn. Springer, Netherlands, pp 551–566
11. Bell DC, Thomas WK, Murtagh KM et al (2012) DNA base identification by electron microscopy. Microsc Microanal 18:1049–1053
12. Biswas K, Chattopadhyay I, Banerjee RK, Bandyopadhyay U (2002) Biological activities and medicinal properties of neem (Azadirachta indica). Curr Sci 82:1336–1345
13. Bonnet E, Van de Peer Y, Rouzé P (2006) The small RNA world of plants. New Phytol 171:451–468
14. Bouvier F, Dogbo O, Camara B (2003) Biosynthesis of the food and cosmetic plant pigment bixin (annatto). Science 300:2089–2091
15. Boycheva S, Daviet L, Wolfender JL, Fitzpatrick TB (2014) The rise of operon-like gene clusters in plants. Trends Plant Sci 19:447–459
16. Brozynska M, Furtado A, Henry RJ (2014) Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding. PLoS One 9:e110387. doi:10.1371/journal.pone.0110387
17. Cao H, Nuruzzaman M, Xiu H et al (2015) Transcriptome analysis of methyl jasmonate-elicited Panax ginseng adventitious roots to discover putative ginsenoside biosynthesis and transport genes. Int J Mol Sci 16:3035–3057
18. Chagné D, Crowhurst RN, Pindo M et al (2014) The draft genome sequence of European pear (Pyrus communis L. “Bartlett”). PLoS One 9:1–12. doi:10.1371/journal.pone.0092644
19. Chen S, Sun YZ, Xu J et al (2010) Strategies of the study on herb genome program. Yao Xue Xue Bao 45:807–812
20. Chen S, Li Xiang Xu, Guo QL (2011) An introduction to the medicinal plant genome project. Front Med 5:178–184
21. Chen J, Dong X, Li Q et al (2013) Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling. BMC Genomics. doi:10.1186/1471-2164-14-857
22. Chen J, Chan PH, Lam CTW et al (2015) Fruit of Ziziphus jujuba (Jujube) at two stages of maturity: distinction by metabolic profiling and biological assessment. J Agric Food Chem 63:739–744
23. Cheng X, Su X, Chen X et al (2014) Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing: the story for Liuwei Dihuang Wan. Sci Rep 4:5147
24. Chiang Y-M, Lee K-H, Sanchez JF et al (2009) Unlocking fungal cryptic natural products. Nat Prod Commun 4:1505–1510
25. Coghlan ML, Haile J, Houston J et al (2012) Deep sequencing of plant and animal DNA contained within traditional Chinese medicines reveals legality issues and health safety concerns. PLoS Genet 8:e1002657. doi:10.1371/journal.pgen.1002657
26. http://www.qiagen.com, press release October 2014. Last accessed on 26 june 2015
27. Dai X, Zhao PX (2011) PsRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:155–159
28. Ding J, Lu Q, Ouyang Y et al (2012) A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc Natl Acad Sci 109:2654–2659
29. El-Alfy AT, Ivey K, Robinson K et al (2010) Antidepressant-like effect of delta9-tetrahydrocannabinol and other cannabinoids isolated from Cannabis sativa L. Pharmacol Biochem Behav 95:434–442
30. Fang Y, Wu H, Zhang T (2012) A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome. PLoS One. doi:10.1371/journal.pone.0037164
31. Fischbach M, Voigt CA (2010) Prokaryotic gene clusters: a rich toolbox for synthetic biology. Biotechnol J 5:1277–1296
32. Fougat R, Joshi C, Kulkarni K et al (2014) Rapid development of microsatellite markers for Plantago ovata Forsk.: using next generation sequencing and their cross-species transferability. Agriculture 4:199–216
33. Galimberti A, De Mattia F, Losa A et al (2013) DNA barcoding as a new tool for food traceability. Food Res Int 50:55–63
34. Gandhi SG, Mahajan V, Bedi YS (2015) Changing trends in biotechnology of secondary metabolism in medicinal and aromatic plants. Planta 241:303–317
35. Gantait S, Debnath S, Nasim Ali M (2014) Genomic profile of the plants with pharmaceutical value. 3 Biotech. doi:10.1007/s13205-014-0218-9
36. Gao QH, Sen WuC, Wang M (2013) The Jujube (Ziziphus Jujuba Mill.) fruit: a review of current knowledge of fruit composition and health benefits. J Agric Food Chem 61:3351–3363. doi:10.1021/jf4007032
37. Gao W, Sun H-X, Xiao H et al (2014) Combining metabolomics and transcriptomics to characterize tanshinone biosynthesis in Salvia miltiorrhiza. BMC Genomics. doi:10.1186/1471-2164-15-73
38. Ge Q, Zhang Y, Hua W-P et al (2015) Combination of transcriptomic and metabolomic analyses reveals a JAZ repressor in the jasmonate signaling pathway of Salvia miltiorrhiza. Sci Rep 5:14048–14061. doi:10.1038/srep14048
39. Graham IA, Besser K, Blumer S et al (2010) The genetic map of Artemisia annua L. identifies loci affecting yield of the antimalarial drug artemisinin. Science 327:328–331
40. Guo Q, Ma X, Wei S et al (2014) De novo transcriptome sequencing and digital gene expression analysis predict biosynthetic pathway of rhynchophylline and isorhynchophylline from Uncaria rhynchophylla, a non-model plant with potent anti-alzheimer’s properties. BMC Genomics. doi:10.1186/1471-2164-15-676
41. Gupta P, Goel R, Pathak S et al (2013) De Novo assembly, functional annotation and comparative analysis of Withania somnifera leaf and root transcriptomes to identify putative genes involved in the withanolides biosynthesis. PLoS One. doi:10.1371/journal.pone.0062714
42. Hamad I, Abdelgawad H, Al Jaouni S et al (2015) Metabolic analysis of various date palm fruit (Phoenix dactylifera L.) cultivars from Saudi Arabia to assess their nutritional quality. Molecules 20:13620–13641. doi:10.3390/molecules200813620
43. Hamilton JP, Buell CR (2012) Advances in plant genome sequencing. Plant J 70:177–190
44. Han XJ, Wang YD, Chen YC et al (2013) Transcriptome sequencing and expression analysis of terpenoid biosynthesis genes in Litsea cubeba. PLoS One. doi:10.1371/journal.pone.0076890
45. Hansen BO, Vaid N, Musialak-Lange M et al (2014) Elucidating gene function and function evolution through comparison of co-expression networks of plants. Front Plant Sci. doi:10.3389/fpls.2014.00394
46. Hao DC, Chen SL, Xiao PG, Liu M (2012) Application of high-throughput sequencing in medicinal plant transcriptome studies. Drug Dev Res 73:487–498. doi:10.1002/ddr.21041
47. He M, Wang Y, Hua W et al (2012) De novo sequencing of Hypericum perforatum transcriptome to identify potential genes involved in the biosynthesis of active metabolites. PLoS One. doi:10.1371/journal.pone.0042081
48. Hegde PK, Rao HA, Rao PN (2014) A review on insulin plant (Costus igneus Nak). Pharmacogn Rev 8:67–72
49. Heo JB, Lee Y-S, Sung S (2013) Epigenetic regulation by long noncoding RNAs in plants. Chromosome Res 21:685–693
50. Higashi Y, Saito K (2013) Network analysis for gene discovery in plant-specialized metabolism. Plant Cell Environ 36:1597–1606
51. Hirsch CN, Buell CR (2013) Tapping the promise of genomics in species with complex, nonmodel genomes. Annu Rev Plant Biol 64:89–110
52. Hollingsworth PM, Graham SW, Little DP (2011) Choosing and using a plant DNA barcode. PLoS One. doi:10.1371/journal.pone.0019254
53. https://nanoporetech.com/community/the-minion-access-programme. Last accessed on 26 june 2015
54. Hu L, Hao C, Fan R et al (2015) De novo assembly and characterization of fruit transcriptome in black pepper (Piper nigrum). PLoS One. doi:10.1371/journal.pone.0129822
55. Huang Y, Zhang JL, Yu XL et al (2013) Molecular functions of small regulatory noncoding RNA. Biochemistry 78:221–230
56. Jehan T, Lakhanpaul S (2006) Single nucleotide polymorphism (SNP)—methods and applications in plant genetics: a review. Indian J Biotechnol 5:435–459
57. Jiang J, Wang Y, Zhu B et al (2015) Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids. BMC Plant Biol. doi:10.1186/s12870-015-0417-5
58. Jin J, Kim MJ, Dhandapani S et al (2015) The floral transcriptome of ylang ylang (Cananga odorata var. fruticosa) uncovers biosynthetic pathways for volatile organic compounds and a multifunctional and novel sesquiterpene synthase. J Exp Bot 66:3959–3975
59. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53
60. Joshi K, Chavan P, Warude D, Patwardhan B (2004) Molecular markers in herbal drug technology. Curr Sci 87:159–165
61. Kalra S, Puniya BL, Kulshreshtha D (2013) De novo transcriptome sequencing reveals important molecular networks and metabolic pathways of the plant, Chlorophytum borivilianum. PLoS One. doi:10.1371/journal.pone.0083336
62. Khadke GN, Hima Bindu K, Ravishankar KV (2012) Development of SCAR marker for sex determination in dioecious betelvine (Piper betle L.). Curr Sci 103:712–716
63. Krishnan NM, Pattnaik S, Jain P et al (2012) A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica. BMC Genomics. doi:10.1186/1471-2164-13-464
64. Krokida A, Delis C, Geisler K et al (2013) A metabolic gene cluster in Lotus japonicus discloses novel enzyme functions and products in triterpene biosynthesis. New Phytol 200:675–690
65. Larkin J, Henley R, Bell DC et al (2013) Slow DNA transport through nanopores in hafnium oxide membranes. ACS Nano 7:10121–10128
66. http://www.zsgenetics.com/third-generation-sequencing/. Last accessed on 26 june 2015
67. http://medicinalplantgenomics.msu.edu. Last accessed on 26 june 2015
68. http://www.reveo.com/node/309. Last accessed on 26 june 2015
69. http://www.reveo.com/node/52. Last accessed on 26 june 2015
70. http://gnubio.com/. Last accessed on 26 june 2015
71. http://www.geniachip.com/technology/. Last accessed on 26 june 2015
72. http://www.stratosgenomics.com. Last accessed on 26 june 2015
73. http://www.base4.co.uk/. Last accessed on 26 june 2015
74. http://www.quantumbiosystems.com. Last accessed on 26 june 2015
75. http://genapsys.com. Last accessed on 26 june 2015
76. Laszlo AH, Derrington IM, Ross BC et al (2014) Decoding long nanopore sequencing reads of natural DNA. Nat Biotechnol 32:829–833
77. Li Y, Luo H-M, Sun C et al (2010) EST analysis reveals putative genes involved in glycyrrhizin biosynthesis. BMC Genomics. doi:10.1186/1471-2164-11-268
78. Li C, Zhu Y, Guo X et al (2013) Transcriptome analysis reveals ginsenosides biosynthetic genes, microRNAs and simple sequence repeats in Panax ginseng C. A. Meyer. BMC Genomics. doi:10.1186/1471-2164-14-245
79. Li L, Eichten SR, Shimizu R et al (2014a) Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol. doi:10.1186/gb-2014-15-2-r40
80. Li X, Yang Y, Henry RJ et al (2014b) Plant DNA barcoding: from gene to genome. Biol Rev. doi:10.1111/brv.12104
81. Li Y, Xu C, Lin X (2014c) De novo assembly and characterization of the fruit transcriptome of Chinese jujube (Ziziphus jujuba Mill.) using 454 pyrosequencing and the development of novel tri-nucleotide SSR markers. PLoS One. doi:10.1371/journal.pone.0106438
82. Li Y, Wang X, Chen T et al (2015) RNA-seq based De Novo transcriptome assembly and gene discovery of Cistanche deserticola fleshy stem. PLoS One 10:e0125722. doi:10.1371/journal.pone.0125722
83. Lin X, Zhang J, Li Y et al (2011) Functional genomics of a living fossil tree, Ginkgo, based on next-generation sequencing technology. Physiol Plant 143:207–218
84. Liu S, Lu B, Zhao Q et al (2013a) Boron nitride nanopores: highly sensitive DNA single-molecule detectors. Adv Mater 25:4549–4554
85. Liu Y, Huo N, Dong L et al (2013b) Complete chloroplast genome sequences of Mongolia medicine Artemisia frigida and phylogenetic relationships with other plants. PLoS One. doi:10.1371/journal.pone.0057533
86. Liu M-J, Zhao J, Cai Q-L et al (2014) The complex jujube genome provides insights into fruit tree biology. Nat Commun. doi:10.1038/ncomms6315
87. Loke K-K, Rahnamaie-Tajadod R, Yeoh C-C et al (2016) RNA-seq analysis for secondary metabolite pathway gene discovery in Polygonum minus. Genom Data 7:12–13
88. Lu Y, Rijzaani H, Karcher D et al (2013) Efficient metabolic pathway engineering in transgenic tobacco and tomato plastids with synthetic multigene operons. Proc Natl Acad Sci USA. doi:10.1073/pnas.1216898110
89. Luo H, Sun C, Sun Y et al (2011) Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers. BMC Genomics. doi:10.1186/1471-2164-12-S5-S5
90. Luo Y, Cobb RE, Zhao H (2014) Recent advances in natural product discovery. Curr Opin Biotechnol 30:230–237
91. Mahajan RTCM (2009) Phyto-Pharmacology of Ziziphus jujuba Mill—a plant review. Pharmacogn Rev 3:320–329
92. Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S (2012) SNP markers and their impact on plant breeding. Int J Plant Genom. doi:10.1155/2012/728398
93. Marques JV, Kim KW, Lee C et al (2013) Next generation sequencing in predicting gene function in podophyllotoxin biosynthesis. J Biol Chem 288:466–479
94. Matsuba Y, Nguyen TTH, Wiegert K et al (2013) Evolution of a complex locus for terpene biosynthesis in Solanum. Plant Cell 25:2022–2036
95. Maxam AM, Gilbert W (1977) A new method for sequencing DNA. Proc Natl Acad Sci 74:560–564
96. Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46
97. Michael TP, Jackson S (2013) The first 50 plant genomes. Plant Genome. doi:10.3835/plantgenome2013.030001in
98. Ming R, Vanburen R, Liu Y et al (2013) Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome. doi:10.1186/gb-2013-14-5-r41
99. Mishra P, Kumar A, Nagireddy A et al (2015) DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. Plant Biotechnol J. doi:10.1111/pbi.12419
100. Mochida K, Shinozaki K (2011) Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant Cell Physiol 52:2017–2038. doi:10.1093/pcp/pcr153
101. Morey M, Fernández-marmiesse A, Castiñeiras D et al (2013) A glimpse into past, present and future DNA sequencing. Mol Genet Metab 110:3–24
102. Mugford ST, Louveau T, Melton R et al (2013) Modularity of plant metabolic gene clusters: a trio of linked genes that are collectively required for acylation of triterpenes in oat. Plant Cell 25:1078–1092
103. Muranaka T, Saito K (2013) Phytochemical genomics on the way. Plant Cell Physiol 54:645–646
104. Mutz K-O, Heilkenbrinker A, Lönne M et al (2013) Transcriptome analysis using next-generation sequencing. Curr Opin Biotechnol 24:22–30
105. Navarro E, Alonso PJ, Alonso SJ et al (2000) Cardiovascular activity of a methanolic extract of Digitalis purpurea spp. heywoodii. J Ethnopharmacol 71:437–442
106. Ndagijimana A, Wang X, Pan G et al (2013) A review on indole alkaloids isolated from Uncaria rhynchophylla and their pharmacological studies. Fitoterapia 86:35–47
107. Nutzmann H, Osbourn A (2014) Gene clustering in plant specialized metabolism. Curr Opin Biotechnol 26:91–99
108. Pal T, Malhotra N, Chanumolu SK, Chauhan RS (2015) Next-generation sequencing (NGS) transcriptomes reveal association of multiple genes and pathways contributing to secondary metabolites accumulation in tuberous roots of Aconitum heterophyllum wall. Planta 242(1):239–258
109. Palla M, Guo W, Shi S et al (2014) DNA sequencing by synthesis using 3′-O-azidomethyl nucleotide reversible terminators and surface-enhanced Raman spectroscopic detection. RSC Adv 4:49342–49346
110. Park S, Ruhlman TA, Sabir JSM et al (2014) Complete sequences of organelle Genomicses from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids. BMC Genomics. doi:10.1186/1471-2164-15-405
111. Park H-S, Kim K-Y, Kim K (2015) The complete chloroplast genome sequence of an important medicinal plant Cynanchum wilfordii (Maxim) Hemsl. (Apocynaceae). Mitochondrial DNA. doi:10.3109/19401736.2015.1079887
112. Qian J, Song J, Gao H et al (2013) The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PLoS One. doi:10.1371/journal.pone.0057607
113. Rama Reddy NR, Mehta RH, Soni PH (2015) Next generation sequencing and transcriptome analysis predicts biosynthetic pathway of sennosides from Senna (Cassia angustifolia Vahl.), a non-model plant with potent laxative properties. PLoS One. doi:10.1371/journal.pone.0129422
114. Ramilowski JA, Sawai S, Seki H et al (2013) Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals. Plant Cell Physiol 54:697–710
115. Rastogi S, Meena S, Bhattacharya A et al (2014) De novo sequencing and comparative analysis of holy and sweet basil transcriptomes. BMC Genomics. doi:10.1186/1471-2164-15-588
116. Rastogi S, Kalra A, Gupta V et al (2015) Unravelling the genome of Holy basil: an “incomparable” “elixir of life” of traditional Indian medicine. BMC Genomics. doi:10.1186/s12864-015-1640-z
117. Ray S, Satya P (2014) Next generation sequencing technologies for next generation plant breeding. Front Plant Sci. doi:10.3389/fpls.2014.00367
118. Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145–166
119. Ruhlman T, Daniell H (2007) Plastid pathways. In: Verpoorte R, Alfermann AW, Johnson TS (eds) Applications of plant metabolic engineering. Springer, Netherlands, pp 79–108
120. Salgotra RK, Gupta BB, Stewart CN (2014) From genomics to functional markers in the era of next-generation sequencing. Biotechnol Lett 36:417–426
121. Sanger F, Nicklen SCA (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467. doi:10.1073/pnas.74.12.5463
122. Sangwan RS, Tripathi S, Singh J et al (2013) De novo sequencing and assembly of Centella asiatica leaf transcriptome for mapping of structural, functional and regulatory genes with special reference to secondary metabolism. Gene 525:58–76
123. Sarwat M, Yamdagni MM (2014) DNA barcoding, microarrays and next generation sequencing: recent tools for genetic diversity estimation and authentication of medicinal plants. Crit Rev Biotechnol. doi:10.3109/07388551.2014.947563
124. Sarwat M, Nabi G, Das S, Srivastava PS (2012) Molecular markers in medicinal plant biotechnology: past and present. Crit Rev Biotechnol 32:74–92. doi:10.3109/07388551.2011.551872
125. Schneider GF, Dekker C (2012) DNA sequencing with nanopores. Nat Biotechnol 30:326–328
126. Seesai SA, Mangul S, Caciula A, Zelikovsky A, Mandoiu I (2014) Transcriptome reconstruction and quantification from RNA sequencing Data. In: Poptsova MS (ed) Genome analysis: current procedures and applications, 1st edn. Caister Academic Press, Norfolk, pp 39–60
127. Senthil K, Jayakodi M, Thirugnanasambantham P et al (2015) Transcriptome analysis reveals in vitro cultured Withania somnifera leaf and root tissues as a promising source for targeted withanolide biosynthesis. BMC Genomics. doi:10.1186/s12864-015-1214-0
128. Shi C, Yang H, Wei C et al (2011) Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics. doi:10.1186/1471-2164-12-131
129. Sui C, Zhang J, Wei J et al (2011) Transcriptome analysis of Bupleurum chinense focusing on genes involved in the biosynthesis of saikosaponins. BMC Genomics 12:539. doi:10.1186/1471-2164-12-539
130. Sui C, Chen M, Xu J et al (2015) Comparison of root transcriptomes and expressions of genes involved in main medicinal secondary metabolites from Bupleurum chinense and Bupleurum scorzonerifolium, the two Chinese official Radix bupleuri source species. Physiol Plant 153:230–242. doi:10.1111/ppl.12254
131. Sumner LW, Lei Z, Nikolaubc BJ, Saitode K (2014) Modern plan metabolomics: advanced natural product gene discoveries, improved technologies and future prospects. Prod Rep, Nat. doi:10.1039/c4np00072b
132. Sun Y, Luo H, Li Y et al (2011a) Pyrosequencing of the Camptotheca acuminata transcriptome reveals putative genes involved in camptothecin biosynthesis and transport. BMC Genomics 12:533. doi:10.1186/1471-2164-12-533
133. Sun YF, Liang ZS, Shan CJ et al (2011b) Comprehensive evaluation of natural antioxidants and antioxidant potentials in Ziziphus jujuba Mill. var. spinosa (Bunge) Hu ex H. F. Chou fruits based on geographical origin by TOPSIS method. Food Chem 124:1612–1619. doi:10.1016/j.foodchem.2010.08.026
134. Sun X, Zhou S, Meng F, Liu S (2012) De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing. Plant Cell Rep 31:1823–1828
135. Swaminathan S, Morrone D, Wang Q et al (2009) CYP76M7 is an ent-cassadiene C11alpha-hydroxylase defining a second multifunctional diterpenoid biosynthetic gene cluster in rice. Plant Cell 21:3315–3325
136. Takahashi N, Goto T, Taimatsu A et al (2009) Bixin regulates mRNA expression involved in adipogenesis and enhances insulin sensitivity in 3T3-L1 adipocytes through PPARgamma activation. Biochem Biophys Res Commun 390:1372–1376. doi:10.1016/j.bbrc.2009.10.162
137. Tan LQ, Wang L-Y, Wei K et al (2013) Floral transcriptome sequencing for SSR marker development and linkage map construction in the tea plant (Camellia sinensis). PLoS One. doi:10.1371/journal.pone.0081611
138. Tanaka H, Hamai C, Kanno T, Kawai T (1999) High-resolution scanning tunneling microscopy imaging of DNA molecules on Cu (111) surfaces. Surf Sci 432:L611–L616
139. Tang Q, Ma X, Mo C et al (2011) An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis. BMC Genomics. doi:10.1186/1471-2164-12-343
140. Tang X, Xiao Y, Lv T et al (2014) High-throughput sequencing and De Novo assembly of the Isatis indigotica transcriptome. PLoS One. doi:10.1371/journal.pone.0102963
141. Taura F, Sirikantaramas S, Shoyama Y et al (2007) Cannabidiolic-acid synthase, the chemotype-determining enzyme in the fiber-type Cannabis sativa. FEBS Lett 581:2929–2934. doi:10.1016/j.febslet.2007.05.043
142. Thompson JF, Milos PM (2011) The properties and applications of single-molecule DNA sequencing. Genome Biol. doi:10.1186/gb-2011-12-2-217
143. Treffer R, Böhme R, Deckert-Gaudig T et al (2012) Advances in TERS (tip-enhanced Raman scattering) for biochemical applications. Biochem Soc Trans 40:609–614. doi:10.1042/BST20120033
144. Van Bakel H, Stout JM, Cote AG et al (2011) The draft genome and transcriptome of Cannabis sativa. Genome Biol. doi:10.1186/gb-2011-12-10-r102
145. Van Wolfswinkel JC, Ketting RF (2010) The role of small non-coding RNAs in genome stability and chromatin organization. J Cell Sci 123:1825–1839. doi:10.1242/jcs.061713
146. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55. doi:10.1016/j.tibtech.2004.11.005
147. Vashisht I, Mishra P, Pal T et al (2015) Mining NGS transcriptomes for miRNAs and dissecting their role in regulating growth, development, and secondary metabolites production in different organs of a medicinal herb, Picrorhiza kurroa. Planta 241:1255–1268. doi:10.1007/s00425-015-2255-y
148. Venta K, Shemer G, Puster M et al (2013) Differentiation of short, single-stranded DNA homopolymers in solid-state nanopores. ACS Nano 7:4629–4636. doi:10.1021/nn4014388
149. Wada M, Takahashi H, Altaf-Ul-Amin M et al (2012) Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes. Gene 503:56–64. doi:10.1016/j.gene.2012.04.043
150. Wang Z, Hobson N, Galindo L et al (2012) The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J 72:461–473
151. Wang Y, Pan Y, Liu Z et al (2013) De novo transcriptome sequencing of radish (Raphanus sativus L.) and analysis of major genes involved in glucosinolate metabolism. BMC Genomics. doi:10.1186/1471-2164-14-836
152. Wang Y, Yang Q, Wang Z (2015) The evolution of nanopore sequencing. Front Genet. doi:10.3389/fgene.2014.00449
153. Winzer T, Gazda V, He Z et al (2012) A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid Noscapine. Science 336:1704–1708
154. Wu Q, Sun C, Luo H et al (2011) Transcriptome analysis of Taxus cuspidata needles based on 454 pyrosequencing. Planta Med 77:394–400. doi:10.1055/s-0030-1250331
155. Wu B, Li Y, Yan H et al (2012) Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea. BMC Genomics. doi:10.1186/1471-2164-13-15
156. Wu Z, Gui S, Quan Z et al (2014a) A precise chloroplast genome of Nelumbo nucifera (Nelumbonaceae) evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots. BMC Plant Biol. doi:10.1186/s12870-014-0289-0
157. Wu Z, Li X, Liu Z et al (2014b) De novo assembly and transcriptome characterization: novel insights into catechins biosynthesis in Camellia sinensis. BMC Plant Biol. doi:10.1186/s12870-014-0277-4
158. Wu G, Zhang L, Yin Y et al (2015) Sequencing, de novo assembly and comparative analysis of Raphanus sativus transcriptome. Front Plant Sci. doi:10.3389/fpls.2015.00198
159. Xin M, Wang Y, Yao Y et al (2011) Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biol. doi:10.1186/1471-2229-11-61
160. Xu Z, Peters RJ, Weirather J et al (2015) Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis. Plant J 82:951–961. doi:10.1111/tpj.12865
161. Yamazaki M, Mochida K, Asano T et al (2013) Coupling deep transcriptome analysis with untargeted metabolic profiling in Ophiorrhiza pumila to further the understanding of the biosynthesis of the anti-cancer alkaloid camptothecin and anthraquinones. Plant Cell Physiol 54:686–696. doi:10.1093/pcp/pct040
162. Yang M, Zhang X, Liu G et al (2010) The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One. doi:10.1371/journal.pone.0012762
163. Yang B, Yang H, Chen F et al (2013a) Phytochemical analyses of Ziziphus jujuba Mill. var. spinosa seed by ultrahigh performance liquid chromatography-tandem mass spectrometry and gas chromatography-mass spectrometry. Analyst 138:6881–6888. doi:10.1039/c3an01478a
164. Yang L, Ding G, Lin H et al (2013b) Transcriptome analysis of medicinal plant Salvia miltiorrhiza and identification of genes related to tanshinone biosynthesis. PLoS One. doi:10.1371/journal.pone.0080464
165. Yang Y, Yuanye D, Qing L et al (2014) Complete chloroplast genome sequence of poisonous and medicinal plant Datura stramonium: organizations and implications for genetic engineering. PLoS One. doi:10.1371/journal.pone.0110656
166. Yonekura-sakakibara K (2009) Functional genomics of family 1 glycosyltransferases in Arabidopsis. Plant Biotechnol 26:267–274
167. Yonekura-Sakakibara K, Fukushima A, Saito K (2013) Transcriptome data modeling for targeted plant metabolic engineering. Curr Opin Biotechnol 24:285–290. doi:10.1016/j.copbio.2012.10.018
168. Yuan Y, Song L, Li M et al (2012) Genetic variation and metabolic pathway intricacy govern the active compound content and quality of the Chinese medicinal plant Lonicera japonica thunb. BMC Genomics. doi:10.1186/1471-2164-13-195
169. Yun Y, Yu J, Nam GH et al (2015) Next-generation sequencing identification and characterization of microsatellite markers in Aconitum austrokoreense Koidz., an endemic and endangered medicinal plant of Korea. Genet Mol Res 14:4812–4817
170. Zalapa JE, Cuevas H, Zhu H et al (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99:193–208. doi:10.3732/ajb.1100394
171. Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isoloation: a review. Mol Ecol 11:1–16
172. Zhang GH, Ma CH, Zhang JJ et al (2015a) Transcriptome analysis of Panax vietnamensis var. fuscidicus discovers putative ocotillol-type ginsenosides biosynthesis genes and genetic markers. BMC Genomics. doi:10.1186/s12864-015-1332-8
173. Zhang X, Luo H, Xu Z et al (2015b) Genome-wide characterisation and analysis of bHLH transcription factors related to tanshinone biosynthesis in Salvia miltiorrhiza. Sci Rep 5:11244. doi:10.1038/srep11244
174. Zhao Y, Yin J, Guo H et al (2015) The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng. Front Plant Sci. doi:10.3389/fpls.2014.00696
175. Zheng XF, Chan TF (2002) Chemical genomics: a systematic approach in biological research and drug discovery. Curr Issues Mol Biol 4:33–43
176. Zheng L, McMullen MD, Bauer E et al (2015) Prolonged expression of the BX1 signature enzyme is associated with a recombination hotspot in the benzoxazinoid gene cluster in Zea mays. J Exp Bot 66:3917–3930. doi:10.1093/jxb/erv192
177. Zhu L, Zhang Y, Guo W et al (2014) De novo assembly and characterization of Sophora japonica transcriptome using RNA-seq. Biomed Res Int. doi:10.1155/2014/750961
178. Zou Z, Ishida M, Li F (2013) QTL analysis using SNP markers developed by next-generation sequencing for identification of candidate genes controlling 4-methylthio-3-butenyl glucosinolate contents in roots of radish, Raphanus sativus L. PLoS One. doi:10.1371/journal.pone.0053541