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Zhou, F., and Pichersky, E. 2020. The complete functional characterization of the terpene synthase family in tomato. New Phytologist DOI: 10.1111/nph.16431

Zhou F., Pichersky E. 2020. More is better: The diversity of terpene metabolism in plants. Current Opinion in Plant Biology, accepted.

Moore BM, Wang P, Fan P, Lee Au, Leong B, Lou YR, Schenck C, Sugimoto K, Last R, Lehti-Shiu MD, Barry CS, Shiu SH 2020. Within and cross species predictions of plant specialized metabolism genes using transfer learning. bioRxiv DOI pending

Wang PP, Meng FR, Moore BM, Shiu SH. Read coverage as an indicator of misassembly in a short-read based genome assembly. bioRxiv DOI: 10.1101/790337

Schwarz B, Azodi CB, Shiu SH, Bauer P. 2020. Putative cis-regulatory elements predict iron deficiency responses in Arabidopsis roots. Plant Physiol (accepted)

Moore, B.M., P. Wang, P. Fan, B. Leong, C.A. Schenck, J.P. Lloyd, M. Lehti-Shiu, R.L. Last, E. Pichersky, S.-H. Shiu. 2019. Robust predictions of specialized metabolism genes through machine learning. Proc. Natl. Acad. Sci, USA 116:2344-2353. https://www.pnas.org/content/116/6/2344.short

Leong, B.J., D. Lybrand, Y.-R. Lou, P. Fan, A.L. Schilmiller, R.L. Last. 2019. Evolution of metabolic novelty: a trichome-expressed invertase creates specialized metabolic diversity in wild tomato. Sci. Advances 5 (4), eaaw3754 https://advances.sciencemag.org/content/5/4/eaaw3754

Wrenbeck E.E., Bedewitz M.A., Klesmith J.R., Noshin S., Barry C.S., Whitehead T.A. 2019. An automated data-driven pipeline for improving heterologous enzyme expression. ACS Synthetic Biology 8: 474-481. https://doi.org/10.1021/acssynbio.8b00486

Schenck, C.A. and R.L. Last. 2019. Location, location! cellular relocalization primes specialized metabolic diversification. FEBS J. https://febs.onlinelibrary.wiley.com/doi/abs/10.1111/febs.15097.

Fan, P., B.J. Leong, R.L. Last. 2019. Tip of the trichome: evolution of acylsugar metabolic diversity in Solanaceae. Curr. Opin. Plant Biol. 49:8-16. https://www.sciencedirect.com/science/article/pii/S1369526618300906?via%3Dihub

Azodi CB, Pardo J, VanBuren R, de los Campos G, Shiu SH. 2019. Transcriptome-based prediction of complex traits in maize. The Plant Cell 32:139-151

Bedewitz M.A., Jones A.D., D’Auria J.C., Barry C.S. 2018. Tropinone synthesis via an atypical polyketide synthase and P450-mediated cyclization. Nature Communications 9: article number 5281. DOI: 10.1038/s41467-018-07671-3.

Xu, H., Lybrand, D., Bennewitz, S., Tissier, A., Last, R.L. and Pichersky, E. 2018. High-level production of trans-chrysanthemic acid, the monoterpene acid moiety of natural pyrethrin insecticides, in tomato fruit. Metab. Eng. https://doi.org/10.1016/j.ymben.2018.04.004.

Fan, P., Miller, A.M., Liu, X., Jones, A.D. and Last, R.L. 2018. Evolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity. Nat. Comm. 8, Article number: 2080 DOI: 10.1038/s41467-017-02045-7

Moghe, G.D., Leong, B.J., Hurney, S., Jones, A.D. and Last, R.L. 2017. Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant defense related specialized metabolic pathway. eLife 2017;6:e28468 DOI: 10.7554/eLife.28468

Xu, H., Moghe, G.D. Wiegert-Rininger, K., Schilmiller, A.L. Barry, C.S., Last, R.L. and Pichersky, E. 2017. Identification of dehydrogenases involved in the biosynthesis of the monoterpene moiety of pyrethrin. Plant Physiol. 176: 524-537 DOI: https://doi.org/10.1104/pp.17.01330

Nadakuduti, S.S., Uebler. J.B., Liu, X., Jones, A.D. and Barry, C.S. 2017. Characterization of trichome-expressed BAHD acyltransferases in Petunia axillaris reveals distinct acylsugar assembly mechanisms within the Solanaceae. Plant Physiol. DOI:10.1104/pp.17.00538

Leong, B. and Last, R.L. 2017. Promiscuity, impersonation and accommodation: evolution of plant specialized metabolism. Curr. Opin. Struct. Biol., Volume 47, December 2017, Pages 105–112 https://doi.org/10.1016/j.sbi.2017.07.005.

Liu, X., Enright, M., Barry, C.S. and Jones, A.D. Profiling, isolation and structure elucidation of specialized acylsucrose metabolites accumulating in trichomes of Petunia species. Metabolomics 13:85 https://link.springer.com/article/10.1007/s11306-017-1224-9

Ghosh, B and Jones, A.D. 2017. Profiling, characterization, and analysis of natural and synthetic acylsugars (sugar esters). Anal. Methods. 9:892-905 http://pubs.rsc.org/-/content/articlehtml/2017/ay/c6ay02944b

Pichersky E, Raguso RA. Why do plants make so many terpenoid compounds? New Phytologist, doi: 10.1111/nph.14178 (2016).

Uyung, S., Seddon, A.E., Azodi, C.B. and Shiu, S. 2017. Predictive models of spatial transcriptional response to high salinity. Plant Physiol. 174:450-464. DOI:10.1104/pp.16.01828

Schilmiller, A.L., K. Gilagon, B. Ghosh, A.D. Jones and R.L. Last. 2016. Acylsugar acylhydrolases: carboxylesterase catalyzed hydrolysis of acylsugars in tomato trichomes. Plant Physiol. 170:1331-1344 http://www.plantphysiol.org/content/170/3/1331.long

Fan, P., Miller, A.M., Schilmiller, A.L., Liu, X., Ofner, I., Jones, A.D., Zamir, D. and Last, A.D. 2016. In vitro reconstruction and analysis of evolutionary variation of the tomato acylsucrose metabolic network. Proc. Natl. Acad. USA, 113 (2) E239-E248. doi/10.1073/pnas.1517930113.

Fan, P., Moghe, G.D. and Last, R.L. 2016. Comparative biochemistry and in vitro pathway reconstruction as powerful partners in studies of metabolic diversity. Methods in Enzymology, Volume 576, 2016, Pages 1–17. doi:10.1016/bs.mie.2016.02.023.

Smeda, J.R., Schilmiller, A.L., Last, R.L. and M. Mutschler. 2016. Introgression of acylsugar chemistry QTL modifies the composition and structure of acylsugars produced by high-accumulating tomato lines. Molec. Breeding, Mol Breeding (2016) 36: 160. doi:10.1007/s11032-016-0584-6.

Uyung, S., Cheng, P., Lehti-Shiu, M.D., Last, R.L. and Shiu, S. 2016. Utility and limitations of using gene expression data to identify functional associations. PLoS Comp. Biol. 12(12): e1005244. https://doi.org/10.1371/journal.pcbi.1005244

Ning, J., Moghe, G.D., Leong, B., Kim, J., Offner, I. Wang, Z., Adams, C., Jones, A.D. Zamir, D. and Last, R.L. 2015. A feedback insensitive isopropylmalate synthase affects acylsugar composition in cultivated and wild tomato. Plant Physiol. doi: http:/?/?dx.?doi.?org/?10.?1104/?pp.?15.?00474

Moghe, G.D. and R.L. Last. 2015. Something old, something new: Conserved enzymes and the evolution of novelty in plant specialized metabolism. Plant Physiol. DOI:10.1104/pp.15.00994

Guo, Y., Wiegert-Rininger, K.E., Vallejo, V.A., Barry, C.S., Warner, R.M. 2015. Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp. BMC Genomics 16:726, DOI: 10.1186/s12864-015-1931-4

Ghosh, B., Jones, A.D. 2015.  Dependence of negative-mode electrospray ionization response factors on mobile phase composition and molecular structure for newly-authenticated neutral acylsucrose metabolites.  Analyst 140:  6522-6531.  DOI: 10.1039/c4an02124j

Brasher MI , Surmacz L , Leong B , Pitcher J, Swiezewskab E, Pichersky E, Akhtar, TA. 2015. A two-component enzyme complex is required for dolichol biosynthesis in tomato. Plant J. 82: 903–914. DOI:10.1111/tpj.12859

Schilmiller, A.L., G.D. Moghe, P. Fan, B. Ghosh, J. Ning, A.D. Jones, R.L. Last. 2015. Functionally divergent alleles and duplicated loci encoding an acyltransferase contribute to acylsugar metabolite diversity inSolanum Trichomes. Plant Cell. 27:1002-1017. DOI:10.1105/tpc.15. 00087

Matsuba, Y, Zi, J., Jones, A.D., Peters, R. and Pichersky, E. 2015. Biosynthesis of the Diterpenoid Lycosantalonol via Nerylneryl Diphosphate in Solanum lycopersicum PLoS One vol: 10 (3) pp: e0119302 DOI:10.1371/journal.pone.0119302

Ekanayaka, EAP, Celiz, MD and Jones, A.D. 2015. Relative mass defect filtering of mass spectra: a path to discovery of plant specialized metabolites. Plant Physiol. 167: 1221-1232. DOI:10.1104/ pp.114.251165

Zi, J. Y. Matsuba, Y.J. Hong, A.J. Jackson, D.J. Tantillo, E. Pichersky and R.J. Peters 2014. Biosynthesis of lycosantalonol, a cis-prenyl derived diterpenoid. J. Am. Chem Soc. DOI:10.1021/ja508477e

Bedewitz, M.A., Gongora-Castillo, E., Uebler, J.B. Gonzales-Vigil, E., Wiegert-Rininger, K.E. et al. 2014. A root-expressed L-phenylalanine:4-hydroxyphenylpyruvate aminotransferase is required for tropane alkaloid biosynthesis in Atropa belladonna. Plant Cell 26:3745-3762. DOI:10.1105/ tpc.114.130534

Kim, J., Y. Matsuba, J. Ning, A.L. Schilmiller, D. Hammar, A.D. Jones, E. Pichersky and R.L. Last. 2014. Analysis of natural and induced variation in tomato glandular trichome flavonoids identifies a gene not present in the reference genome. Plant Cell. 26:3272-3285. DOI:10.1105/tpc.114.129460.

Wang, Z. and Jones, A.D. 2014. Profiling of stable isotope enrichment in specialized metabolites using liquid chromatography and multiplexed nonselective collision-induced dissociation. Anal. Chem. 86:10600-10607. DOI:10.1021/ac502205y

Kang, J.-H., J. McRoberts, F. Shi, J. E. Moreno, A. D. Jones, and G. A. Howe. 2014. The Flavonoid Biosynthetic Enzyme Chalcone Isomerase Modulates Terpenoid Production in Glandular Trichomes of Tomato.” Plant Physiol. 164: 1161-74. DOI:10.1104/ pp. 113.233395

Falara, V., Alba, J.M., Kant, M.R., Schuurink, R.C. and Pichersky, E. 2014. Geranyllinalool synthases in solanaceae and other angiosperms constitute an ancient branch of diterpene synthases involved in the synthesis of defensive compounds. Plant Physiol. 166:428-441. DOI:10.1104/pp.114.243246

Ekanayaka EAP, Li C, Jones AD. 2013.  Sesquiterpenoid glycosides from glandular trichomes of the wild tomato relative Solanum habrochaites. Phytochemistry 98:223-231. DOI:10.1016/j.phytochem.2013.11.011

Yu G, Pichersky E. Heterologous expression of methylketone synthases 1 and 2 leads to production of methylketones and myristic acid in transgenic plants. Plant Physiol., 164:612-622. DOI:10.1104/pp.113.228502.

Kang, J-H., E. Gonzales-Vigil, Y. Matsuba, E. Pichersky and C. Barry. 2014. Determination of reidues responsible for substrate and product specificity of Solanum habrochaites short-chain cis-prenyltransferases. Plant Physiol. 164:80-91. DOI:10.1104/pp.113.230466.

Kang, J.-H., J. McRoberts, F. Shi, J. E. Moreno, A. D. Jones, and G. A. Howe. 2014. The Flavonoid Biosynthetic Enzyme Chalcone Isomerase Modulates Terpenoid Production in Glandular Trichomes of Tomato.” Plant Physiol. 164: 1161-74. DOI:10.1104/pp.113.233395.

Li, C., Z. Wang and A.D. Jones. 2013. Chemical imaging of trichome specialized metabolites using contact printing and laser desorption/ionization mass spectrometry. Anal. and Bioanal. Chem. 406:171-182. DOI:10.1007/s00216-013-7444-6

Ghosh, B., T.C. Westbrook, T.C. and A.D. Jones. 2013. Comparative structural profiling of trichome specialized metabolites in tomato (Solanum lycopersicum) and S. habrochaites: acylsugar profiles revealed by UHPLC/MS and NMR. Metabolomics. 10:496-507. DOI:10.1007/s11306-013-0585-y

Li, C., A. Schmidt, E. Pichersky, F. Shi, and A. D. Jones. 2013. Identification of methylated flavonoid regioisomeric metabolites using enzymatic semisynthesis and liquid chromatography-tandem mass spectrometry, Metabolomics, 9: S92-S101. DOI:10.1007/s11306-012-0451-3.

Matsuba, Y, Nguyen, T.T., Wiegert, K., Falara, V., Gonzales-Vigil, E., Leong, B., Schafer, P., Kudrna, D., Wing, R.A., Bolger, A.M., Usadel, B., Tissier, A., Fernie, A.R., Barry, C.S., and Pichersky, E. 2013. Evolution of a complex locus for terpene biosynthesis in Solanum. Plant Cell 25: 2022-2036. DOI:10.1105/tpc.113.111013.

Akhtar, T.A., Matsuba, Y., Schauvinhold, I., Yu, G., Lees, H.A., Klein, S.E. and Pichersky, E. 2013. The tomato cis-prenyltransferase gene family. Plant J., 73 :640-52. DOI:10.1111/tpj.12063.

Kim, J., K. Kang, E. Gonzales-Vigil, F. Shi, C.S. Barry, A.D. Jones and R.L. Last. 2012. Mass spectrometry reveals strong diversity in glandular trichome acylsugars of the wild tomato Solanum habrochaites. Plant Physiol. 160 (4), 1854-1870. DOI:10.1104/pp.112.204735

Schilmiller, A.L., A.L. Charbonneau and R.L. Last. 2012. Identification of a BAHD acetyltransferase that produces protective acyl sugars in tomato trichomes. Proc. Natl. Acad. U.S.A. 109:16377-16382. DOI:10.1073/pnas.1207906109.

Milo, R. and R.L. Last. 2012. Achieving diversity in the face of constraints - lessons from metabolism. Science. 336:1663-1667. DOI:10.1126/science.1217665

Gonzales-Vigil, E., D.E. Hufnagel, J. Kim, R.L. Last and C.S. Barry. (2012) Evolution of TPS20-related terpene synthases influences chemical diversity in the glandular trichomes of the wild tomato relative Solanum habrochaites. Plant J. 71: 921–935. DOI: 10.1111/j.1365-313X.2012.05040.x

Schmidt, A. C. Li, A.D. Jones and E. Pichersky. Characterization of a flavonol 3-O-methyltransferase in the trichomes of the wild tomato species Solanum habrochaites. 2012. Planta. 236:839-49. DOI:10.1007/s00425-012-1676-0.

Schilmiller , A.L., E. Pichersky and R.L. Last. (2012) Taming the hydra of specialized metabolism: how systems biology and comparative approaches are revolutionizing plant biochemistry. Curr. Opin. Plant Biol. 15:338-344. DOI:10.1016/j.pbi.2011.12.005

L. W. Sumner, D. S. Yang, B. J. Bench, B. S. Watson, C. Li, and A. D. Jones.  Spatially resolved plant metabolomics. in Biology of Plant Metabolomics, Annual Plant Reviews, Volume 43, R. Hall, Ed., Chapter 11, pp. 344-366, Wiley/Blackwell, 2011. DOI:10.1002/9781444339956.ch11

Falara, V., T. Akhtar, T.H. Nguyen, E.A. Spyropoulou, P.M. Bleeker, I. Schauvinhold, Y. Matsuba, M.E. Bonini, A.L. Schilmiller, R.L. Last, R.C. Schuurink and E. Pichersky. (2011) Plant Physiol. 157 (2), 770-789. DOI:10.1104/pp.111.179648

Schmidt, A., Li, C., Shi, F., Jones, D. and Pichersky, E. (2011) Polymethlated myricetin in trichomes of the wild tomato species Solanum habrochaites and characterization of trichome specific 3'/5' and 7/4' myricetin O-methyltransferases. Plant Physiol. 155:1999-2009 DOI:10.1104/ pp.110.169961.

McDowell et al. (2011) Comparative functional genomic analysis of Solanum glandular trichome types. Plant Physiol. 155:524-539 DOI:10.1104/pp.110.167114

Kang, J.-H., Liu, G., Shi, F., Jones, A.D., Beaudry, R.M. and Howe, G.M. (2010) The tomato odorless-2mutant is defective in trichome-based production of diverse specialized metabolites and broad-spectrum resistance to insect herbivores. Plant Physiol. 154:262-272. DOI:10.1104/pp.110.160192

Schilmiller, A.L. Miner, D.P., Larson, M.,  McDowell, E., Gang, D.R., Wilkerson, C. and  Last, R.L. (2010) Studies of a Biochemical Factory: Tomato Trichome Deep EST Sequencing and Proteomics. Plant Physiol. 153:1212-1223. DOI:10.1104/pp.110.157214

Schilmiller, A.L*., F. Shi*, J. Kim, A.L. Charbonneau, D. Holmes, A.D. Jones, R.L. Last. 2010. Mass spectrometry screening reveals widespread diversity in trichome specialized metabolites of tomato chromosomal substitution lines. Plant J. 62: 391–403.  DOI:10.1111/j.1365-313X.2010.04154.x

Kang, J.-H., F. Shi, A.D. Jones, M.D. Marks and G.A. Howe. 2009. Distortion of trichome morphology by thehairless mutation of tomato affects leaf surface chemistry. J. Exp. Bot.  2010 61: 1053-1064 DOI:10.1093/jxb/erp370
Cover art: http://jxb.oxfordjournals.org/content/vol61/issue4/cover.dtl

Kang, J.-H., F. Shi, A.D. Jones, M.D. Marks and G.A. Howe. 2009. Distortion of trichome morphology by the hairless mutation of tomato affects leaf surface chemistry. J. Exp. Bot. DOI:10.1093/jxb/erp370.

Schilmiller*, A.L., I. Schauvinhold*, M. Larson, R. Xu, A.L. Charbonneau, A. Schmidt, R.L. Last and E. Pichersky 2009. Monoterpenes in the glandular trichomes of tomato are synthesized via a neryl diphosphate intermediate rather than geranayl diphosphate. Proc. Natl. Acad. Sci. U.S.A., 106:10865-10870. DOI:10.1073/pnas.0904113106

To read a commentary on this article by J. Bohlmann and J. Gershenzon click on DOI:10.1073/pnas.0905226106

Schilmiller, A.L., R.L. Last and E. Pichersky. 2008. Harnessing plant trichome biochemistry for the production of useful compounds. Plant J. 54:702-711. DOI:10.1111/j.1365-313X.2008.03432.x

DellaPenna, D and R.L. Last 2008. The expanding universe of genomics enabled plant biochemistry. Science. 320:479-481. DOI:10.1126/science.1153715

Last, R.L., A.D. Jones and Y. Shachar-Hill. 2007. Towards the Plant Metabolome and Beyond. Nature Rev. Molec. Cell. Biol. 8, 167-174. DOI:10.1038/nrm2098

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