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Online resources for gene discovery and biochemical research with aromatic and medicinal plants

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Abstract

The elucidation of pathways leading to the signature metabolites accumulated in aromatic and medicinal plants has traditionally been fairly slow in comparison to progress made with much simpler microbes, where gene clustering for natural product biosynthesis is very common. However, recent advances in next-generation sequencing and innovative new approaches to gene discovery have narrowed this gap, and the elucidation of even complex plant pathways has now become significantly faster. A wealth of sequence data has been generated with aromatic and medicinal plants, and it has become increasingly difficult for researchers to stay abreast of new developments. In this review article, I will summarize the functionality of currently available genomics databases and will comment on future needs to maximize their utility.

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References

  • Ahkami A, Johnson SR, Srividya N, Lange BM (2015) Multiple levels of regulation determine monoterpenoid essential oil compositional variation in the mint family. Mol Plant 8:188–191

    Article  CAS  PubMed  Google Scholar 

  • Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JSS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Berard A, Viot C, Boccara M, Risterucci AM, Guignon V, Sabau X, Axtell MJ, Ma ZR, Zhang YF, Brown S, Bourge M, Golser W, Song XA, Clement D, Rivallan R, Tahi M, Akaza JM, Pitollat B, Gramacho K, D’Hont A, Brunel D, Infante D, Kebe I, Costet P, Wing R, McCombie WR, Guiderdoni E, Quetier F, Panaud O, Wincker P, Bocs S, Lanaud C (2011) The genome of Theobroma cacao. Nat Genet 43:101–108

    Article  CAS  PubMed  Google Scholar 

  • Cuthbertson DJ, Johnson SR, Piljac-Zegarac J, Kappel J, Schafer S, Wust M, Ketchum RE, Croteau RB, Marques JV, Davin LB, Lewis NG, Rolf M, Kutchan TM, Soejarto DD, Lange BM (2013) Accurate mass-time tag library for LC/MS-based metabolite profiling of medicinal plants. Phytochemistry 91:187–197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dai XB, Wang GD, Yang DS, Tang YH, Broun P, Marks MD, Sumner LW, Dixon RA, Zhao PX (2010) TrichOME: a comparative omics database for plant trichomes. Plant Physiol 152:44–54

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • DeLoache WC, Russ ZN, Narcross L, Gonzales AM, Martin VJJ, Dueber JE (2015) An enzyme-coupled biosensor enables (S)-reticuline production in yeast from glucose. Nat Chem Biol 11:465–471

    Article  CAS  PubMed  Google Scholar 

  • Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng CF, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Joet T, Labadie K, Lan TY, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Munoz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono Rigoreau M, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P, Lashermes P (2014) The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345:1181–1184

    Article  CAS  PubMed  Google Scholar 

  • Dong QF, Schlueter SD, Brendel V (2004) PlantGDB, plant genome database and analysis tools. Nucleic Acids Res 32:D354–D359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V (2008) PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res 36:D959–D965

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ehrenberg R (2015) Engineered yeast paves way for home-brew heroin. Nature 521:267–268

    Article  CAS  PubMed  Google Scholar 

  • Fischedick JT, Johnson SR, Ketchum REB, Croteau RB, Lange BM (2015) NMR spectroscopic search module for Spektraris, an online resource for plant natural product identification—Taxane diterpenoids from Taxus × media cell suspension cultures as a case study. Phytochemistry 113:87–95

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fossati E, Narcross L, Ekins A, Falgueyret JP, Martin VJJ (2015) Synthesis of morphinan alkaloids in Saccharomyces cerevisiae. PLoS ONE 10:e0124459. doi:10.1371/journal.pone.0124459

    Article  PubMed  PubMed Central  Google Scholar 

  • Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, Lu F, Lyon E, Voelkerding KV, Zehnbauer BA, Agarwala R, Bennett SF, Chen B, Chin EL, Compton JG, Das S, Farkas DH, Ferber MJ, Funke BH, Furtado MR, Ganova-Raeva LM, Geigenmuller U, Gunselman SJ, Hegde MR, Johnson PL, Kasarskis A, Kulkarni S, Lenk T, Liu CS, Manion M, Manolio TA, Mardis ER, Merker JD, Rajeevan MS, Reese MG, Rehm HL, Simen BB, Yeakley JM, Zook JM, Lubin IM (2012) Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol 30:1033–1036

    Article  CAS  PubMed  Google Scholar 

  • Geu-Flores F, Sherden NH, Courdavault V, Burlat V, Glenn WS, Wu C, Nims E, Cui YH, O’Connor SE (2012) An alternative route to cyclic terpenes by reductive cyclization in iridoid biosynthesis. Nature 492:138–142

    Article  CAS  PubMed  Google Scholar 

  • Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100

    Article  CAS  PubMed  Google Scholar 

  • Gongora-Castillo E, Childs KL, Fedewa G, Hamilton JP, Liscombe DK, Magallanes-Lundback M, Mandadi KK, Nims E, Runguphan W, Vaillancourt B, Varbanova-Herde M, DellaPenna D, McKnight TD, O’Connor S, Buell CR (2012) Development of transcriptomic resources for interrogating the biosynthesis of monoterpene indole alkaloids in medicinal plant species. PLoS ONE 7:e52506. doi:10.1371/journal.pone.0052506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goodstein DM, Shu SQ, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hirakawa H, Nakamura Y, Kaneko T, Isobe S, Sakai H, Kato T, Hibino T, Sasamoto S, Watanabe A, Yamada M, Nakayama S, Fujishiro T, Kishida Y, Kohara M, Tabata S, Sato S (2011) Survey of the genetic information carried in the genome of Eucalyptus camaldulensis. Plant Biotechnol 28:471–480

    Article  CAS  Google Scholar 

  • Hur M, Campbell AA, Almeida-de-Macedo M, Li L, Ransom N, Jose A, Crispin M, Nikolau BJ, Wurtele ES (2013) A global approach to analysis and interpretation of metabolic data for plant natural product discovery. Nat Prod Rep 30:565–583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Johnson SR, Lange BM (2015) Open-Access metabolomics databases for natural product research: present capabilities and future potential. Front Bioeng Biotechnol 3:22

    Article  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kellner F, Kim J, Clavijo BJ, Hamilton JP, Childs KL, Vaillancourt B, Cepela J, Habermann M, Steuernagel B, Clissold L, McLay K, Buell CR, O’Connor SE (2015) Genome-guided investigation of plant natural product biosynthesis. Plant J 82:680–692

    Article  CAS  PubMed  Google Scholar 

  • Kim S, Park M, Yeom SI, Kim YM, Lee JM, Lee HA, Seo E, Choi J, Cheong K, Kim KT, Jung K, Lee GW, Oh SK, Bae C, Kim SB, Lee HY, Kim SY, Kim MS, Kang BC, Jo YD, Yang HB, Jeong HJ, Kang WH, Kwon JK, Shin C, Lim JY, Park JH, Huh JH, Kim JS, Kim BD, Cohen O, Paran I, Suh MC, Lee SB, Kim YK, Shin Y, Noh SJ, Park J, Seo YS, Kwon SY, Kim HA, Park JM, Kim HJ, Choi SB, Bosland PW, Reeves G, Jo SH, Lee BW, Cho HT, Choi HS, Lee MS, Yu Y, Do Choi Y, Park BS, van Deynze A, Ashrafi H, Hill T, Kim WT, Pai HS, Ahn HK, Yeam I, Giovannoni JJ, Rose JKC, Sorensen I, Lee SJ, Kim RW, Choi IY, Choi BS, Lim JS, Lee YH, Choi D (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46:270–278

    Article  CAS  PubMed  Google Scholar 

  • Lange BM, Wildung MR, Stauber EJ, Sanchez C, Pouchnik D, Croteau R (2000) Probing essential oil biosynthesis and secretion by functional evaluation of expressed sequence tags from mint glandular trichomes. Proc Natl Acad Sci USA 97:2934–2939

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Michael TP, Jackson S (2013) The First 50 Plant Genomes. Plant Genome. doi:10.3835/plantgenome2013.03.0001in

    Google Scholar 

  • Motamayor JC, Mockaitis K, Schmutz J, Haiminen N, Livingstone D, Cornejo O, Findley SD, Zheng P, Utro F, Royaert S, Saski C, Jenkins J, Podicheti R, Zhao MX, Scheffler BE, Stack JC, Feltus FA, Mustiga GM, Amores F, Phillips W, Marelli JP, May GD, Shapiro H, Ma JX, Bustamante CD, Schnell RJ, Main D, Gilbert D, Parida L, Kuhn DN (2013) The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol 14:r53

    Article  PubMed  PubMed Central  Google Scholar 

  • Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan ARK, Hussey SG, Pinard D, Van der Merwe K, Singh P, Van Jaarsveld I, Silva OB, Togawa RC, Pappas MR, Faria DA, Sansaloni CP, Petroli CD, Yang XH, Ranjan P, Tschaplinski TJ, Ye CY, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente HS, Saidi N, Cassan-Wang H, Dunand C, Hefer CA, Bornberg-Bauer E, Kersting AR, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd AE, Liston A, Spatafora JW, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Lheim CK, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel SH, Pasquali G, Byrne M, Rigault P, Tibbits J, Spokevicius A, Jones RC, Steane DA, Vaillancourt RE, Potts BM, Joubert F, Barry K, Pappas GJ, Strauss SH, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar DS, Schmutz J (2014) The genome of Eucalyptus grandis. Nature 510:356–362

    CAS  PubMed  Google Scholar 

  • Nutzmann HW, Osbourn A (2014) Gene clustering in plant specialized metabolism. Current Op Biotechnol 26:91–99

    Article  CAS  Google Scholar 

  • Paddon CJ, Westfall PJ, Pitera DJ, Benjamin K, Fisher K, McPhee D, Leavell MD, Tai A, Main A, Eng D, Polichuk DR, Teoh KH, Reed DW, Treynor T, Lenihan J, Fleck M, Bajad S, Dang G, Dengrove D, Diola D, Dorin G, Ellens KW, Fickes S, Galazzo J, Gaucher SP, Geistlinger T, Henry R, Hepp M, Horning T, Iqbal T, Jiang H, Kizer L, Lieu B, Melis D, Moss N, Regentin R, Secrest S, Tsuruta H, Vazquez R, Westblade LF, Xu L, Yu M, Zhang Y, Zhao L, Lievense J, Covello PS, Keasling JD, Reiling KK, Renninger NS, Newman JD (2013) High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 496:528–532

    Article  CAS  PubMed  Google Scholar 

  • Qin C, Yu CS, Shen YO, Fang XD, Chen L, Min JM, Cheng JW, Zhao SC, Xu M, Luo Y, Yang YL, Wu ZM, Mao LK, Wu HY, Ling-Hu CY, Zhou HK, Lin HJ, Gonzalez-Morales S, Trejo-Saavedra DL, Tian H, Tang X, Zhao MJ, Huang ZY, Zhou AW, Yao XM, Cui JJ, Li WQ, Chen Z, Feng YQ, Niu YC, Bi SM, Yang XW, Li WP, Cai HM, Luo XR, Montes-Hernandez S, Leyva-Gonzalez MA, Xiong ZQ, He XJ, Bai LJ, Tan S, Tang XQ, Liu D, Liu JW, Zhang SX, Chen MS, Zhang L, Zhang L, Zhang YC, Liao WQ, Zhang Y, Wang M, Lv XD, Wen B, Liu HJ, Luan HM, Zhang YG, Yang S, Wang XD, Xu JH, Li XQ, Li SC, Wang JY, Palloix A, Bosland PW, Li YR, Krogh A, Rivera-Bustamante RF, Herrera-Estrella L, Yin Y, Yu JP, Hu KL, Zhang ZM (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci USA 111:5135–5140

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31:224–228

    Article  CAS  PubMed  Google Scholar 

  • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  • Thodey K, Galanie S, Smolke CD (2014) A microbial biomanufacturing platform for natural and semisynthetic opioids. Nat Chem Biol 10(10):837–844

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van Bakel H, Stout JM, Cote AG, Tallon CM, Sharpe AG, Hughes TR, Page JE (2011) The draft genome and transcriptome of Cannabis sativa. Genome Biol 12:r102

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang LH, Yu JY, Li DH, Zhang XR (2015) Sinbase: an integrated database to study genomics, genetics and comparative genomics in Sesamum indicum. Plant Cell Physiol 56:e2

    Article  PubMed  Google Scholar 

  • Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, Cattonaro F, Del Fabbro C, Pinosio S, Zuccolo A, Chapman J, Grimwood J, Tadeo FR, Estornell LH, Munoz-Sanz JV, Ibanez V, Herrero-Ortega A, Aleza P, Perez-Perez J, Ramon D, Brunel D, Luro F, Chen CX, Farmerie WG, Desany B, Kodira C, Mohiuddin M, Harkins T, Fredrikson K, Burns P, Lomsadze A, Borodovsky M, Reforgiato G, Freitas-Astua J, Quetier F, Navarro L, Roose M, Wincker P, Schmutz J, Morgante M, Machado MA, Talon M, Jaillon O, Ollitrault P, Gmitter F, Rokhsar D (2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 32:656–662

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiao M, Zhang Y, Chen X, Lee EJ, Barber CJS, Chakrabarty R, Desgagne-Penix I, Haslam TM, Kim YB, Liu EW, MacNevin G, Masada-Atsumi S, Reed DW, Stout JM, Zerbe P, Zhang YS, Bohlmann J, Covello PS, De Luca V, Page JE, Ro DK, Martin VJJ, Facchini PJ, Sensen CW (2013) Transcriptome analysis based on next-generation sequencing of non-model plants producing specialized metabolites of biotechnological interest. J Biotechnol 166:122–134

    Article  CAS  PubMed  Google Scholar 

  • Xu Q, Chen LL, Ruan XA, Chen DJ, Zhu AD, Chen CL, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen JJ, Gao S, Xing F, Lan H, Chang JW, Ge XH, Lei Y, Hu Q, Miao Y, Wang L, Xiao SX, Biswas MK, Zeng WF, Guo F, Cao HB, Yang XM, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang ZH, Guo WW, Kuang HH, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan YJ (2013) The draft genome of sweet orange (Citrus sinensis). Nature Genet 45:59–66

    Article  CAS  PubMed  Google Scholar 

  • Yeo YS, Nybo SE, Chittiboyina AG, Weerasooriya AD, Wang YH, Gongora-Castillo E, Vaillancourt B, Buell CR, DellaPenna D, Celiz MD, Jones AD, Wurtele ES, Ransom N, Dudareva N, Shaaban KA, Tibrewal N, Chandra S, Smillie T, Khan IA, Coates RM, Watt DS, Chappell J (2013) Functional identification of valerena-1,10-diene synthase, a terpene synthase catalyzing a unique chemical cascade in the biosynthesis of biologically active sesquiterpenes in Valeriana officinalis. J Biol Chem 288:3163–3173

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92

    Article  CAS  PubMed  Google Scholar 

  • Zerbe P, Chiang A, Yuen M, Hamberger B, Hamberger B, Draper JA, Britton R, Bohlmann J (2012) Bifunctional cis-abienol synthase from Abies balsamea discovered by transcriptome sequencing and its implications for diterpenoid fragrance production. J Biol Chem 287:12121–12131

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zerbe P, Hamberger B, Yuen MMS, Chiang A, Sandhu HK, Madilao LL, Nguyen A, Hamberger B, Bach SS, Bohlmann J (2013) Gene discovery of modular diterpene metabolism in nonmodel systems. Plant Physiol 162:1073–1091

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Lange, B.M. Online resources for gene discovery and biochemical research with aromatic and medicinal plants. Phytochem Rev 15, 489–510 (2016). https://doi.org/10.1007/s11101-015-9450-0

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