Jim Giovannoni
Professor
Office/Lab: 429/426
jjg33@cornell.edu
Office: 607-254-1259
Lab: 607-254-1259
Professor
Office/Lab: 429/426
jjg33@cornell.edu
Office: 607-254-1259
Lab: 607-254-1259
Research Summary
Research Summary
The focus of research in the Giovannoni laboratory is molecular and genetic analysis of fruit ripening and related signal transduction systems with emphasis on the relationship of fruit ripening to nutritional quality. We are also involved in development of tools for genomics of the Solanaceae including participation in the International Tomato Sequencing Project. We employ several experimental systems but the majority of our work involves the use of tomato. The broad objectives of the lab include deciphering the underlying molecular basis of components of ripening regulation conserved through evolution and how these regulatory networks coordinate ripening events including those related to quality and nutritional content.
Experimental approaches include: 1) positional cloning of loci known via mutation to harbor genes necessary for normal fruit development and ripening, and 2) isolation of candidate ripening regulatory genes based on expression pattern or relationship to ripening-related signal transduction systems (e.g. ethylene, light), and functional analysis in transgenic plants.
Selected Publications
Cao, Y., Tang, X., Giovannoni, J., Xiao, F. and Liu, Y. 2012. Functional characterization of a tomato COBRA-like gene functioning in fruit development and ripening. Bmc Plant Biol 12: 211
Chen, Y.R., Zheng, Y., Liu, B., Zhong, S., Giovannoni, J. and Fei, Z. 2012. A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters. Plant Methods 8: 41
Goyal, R.K., Kumar, V., Shukla, V., Mattoo, R., Liu, Y.S., Chung, S.H., Giovannoni, J.J. and Mattoo, A.K. 2012. Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum). Planta 235: 453-471
Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W.J., Zhang, H., Zheng, Y., Mao, L., Ren, Y., Wang, Z., Min, J., Guo, X., Murat, F., Ham, B.K., Zhang, Z., Gao, S., Huang, M., Xu, Y., Zhong, S., Bombarely, A., Mueller, L.A., Zhao, H., He, H., Zhang, Y., Zhang, Z., Huang, S., Tan, T., Pang, E., Lin, K., Hu, Q., Kuang, H., Ni, P., Wang, B., Liu, J., Kou, Q., Hou, W., Zou, X., Jiang, J., Gong, G., Klee, K., Schoof, H., Huang, Y., Hu, X., Dong, S., Liang, D., Wang, J., Wu, K., Xia, Y., Zhao, X., Zheng, Z., Xing, M., Liang, X., Huang, B., Lv, T., Wang, J., Yin, Y., Yi, H., Li, R., Wu, M., Levi, A., Zhang, X., Giovannoni, J.J., Wang, J., Li, Y., Fei, Z. and Xu, Y. 2012. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45: 51-58
Harb, J., Gapper, N.E., Giovannoni, J.J. and Watkins, C.B. 2012. Molecular analysis of softening and ethylene synthesis and signaling pathways in a non-softening apple cultivar, 'Honeycrisp' and a rapidly softening cultivar, 'McIntosh'. Postharvest Biology and Technology 64: 94-103
Lee, J.M., Joung, J.G., McQuinn, R., Chung, M.Y., Fei, Z., Tieman, D., Klee, H. and Giovannoni, J. 2012. Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation. The Plant journal : for cell and molecular biology 70: 191-204
Liu, J.K., Li, H.J., Miao, M., Tang, X.F., Giovannoni, J., Xiao, F.M. and Liu, Y.S. 2012. The tomato UV-damaged DNA-binding protein-1 (DDB1) is implicated in pathogenesis-related (PR) gene expression and resistance to Agrobacterium tumefaciens. Molecular Plant Pathology 13: 123-134
Liu, J.K., Tang, X.F., Gao, L.Y., Gao, Y.F., Li, Y.X., Huang, S.X., Sun, X.C., Miao, M., Zeng, H., Tian, X.F., Niu, X.L., Zheng, L., Giovannoni, J., Xiao, F.M. and Liu, Y.S. 2012. A role of tomato UV-damaged DNA binding protein 1 (DDB1) in organ size control via an epigenetic manner. PLoS One 0: 7
Lopez-Casado, G., Covey, P.A., Bedinger, P.A., Mueller, L.A., Thannhauser, T.W., Zhang, S., Fei, Z.J., Giovannoni, J.J. and Rose, J.K.C. 2012. Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case. Proteomics 12: 761-774
Ma, Q., Du, W.Y., Brandizzi, F., Giovannoni, J.J. and Barry, C.S. 2012. Differential control of ethylene responses by GREEN-RIPE and GREEN-RIPE LIKE1 provides evidence for distinct ethylene signaling modules in tomato. Plant Physiology 160: 1968-1984
Osorio, S., Alba, R., Nikoloski, Z., Kochevenko, A., Fernie, A.R. and Giovannoni, J.J. 2012. Integrative comparative analyses of transcript and metabolite profiles from pepper and tomato ripening and development stages uncovers species-specific patterns of network regulatory behavior. Plant Physiology 159: 1713-1729
Powell, A.L.T., Nguyen, C.V., Hill, T., Cheng, K.L., Figueroa-Balderas, R., Aktas, H., Ashrafi, H., Pons, C., Fernandez-Munoz, R., Vicente, A., Lopez-Baltazar, J., Barry, C.S., Liu, Y.S., Chetelat, R., Granell, A., Van Deynze, A., Giovannoni, J.J. and Bennett, A.B. 2012. Uniform ripening encodes a Golden 2-like transcription factor regulating tomato fruit chloroplast development. Science 336: 1711-1715
Sato, S., Tabata, S., Hirakawa, H., Asamizu, E., Shirasawa, K., Isobe, S., Kaneko, T., Nakamura, Y., Shibata, D., Aoki, K., Egholm, M., Knight, J., Bogden, R., Li, C.B., Shuang, Y., Xu, X., Pan, S.K., Cheng, S.F., Liu, X., Ren, Y.Y., Wang, J., Albiero, A., Dal Pero, F., Todesco, S., Van Eck, J., Buels, R.M., Bombarely, A., Gosselin, J.R., Huang, M.Y., Leto, J.A., Menda, N., Strickler, S., Mao, L.Y., Gao, S., Tecle, I.Y., York, T., Zheng, Y., Vrebalov, J.T., Lee, J., Zhong, S.L., Mueller, L.A., Stiekema, W.J., Ribeca, P., Alioto, T., Yang, W.C., Huang, S.W., Du, Y.C., Zhang, Z.H., Gao, J.C., Guo, Y.M., Wang, X.X., Li, Y., He, J., Li, C.Y., Cheng, Z.K., Zuo, J.R., Ren, J.F., Zhao, J.H., Yan, L.H., Jiang, H.L., Wang, B., Li, H.S., Li, Z.J., Fu, F.Y., Chen, B.T., Han, B., Feng, Q., Fan, D.L., Wang, Y., Ling, H.Q., Xue, Y.B.A., Ware, D., McCombie, W.R., Lippman, Z.B., Chia, J.M., Jiang, K., Pasternak, S., Gelley, L., Kramer, M., Anderson, L.K., Chang, S.B., Royer, S.M., Shearer, L.A., Stack, S.M., Rose, J.K.C., Xu, Y.M., Eannetta, N., Matas, A.J., McQuinn, R., Tanksley, S.D., Camara, F., Guigo, R., Rombauts, S., Fawcett, J., Van de Peer, Y., Zamir, D., Liang, C.B., Spannagl, M., Gundlach, H., Bruggmann, R., Mayer, K., Jia, Z.Q., Zhang, J.H., Ye, Z.B.A., Bishop, G.J., Butcher, S., Lopez-Cobollo, R., Buchan, D., Filippis, I., Abbott, J., Dixit, R., Singh, M., Singh, A., Pal, J.K., Pandit, A., Singh, P.K., Mahato, A.K., Dogra, V., Gaikwad, K., Sharma, T.R., Mohapatra, T., Singh, N.K., Causse, M., Rothan, C., Schiex, T., Noirot, C., Bellec, A., Klopp, C., Delalande, C., Berges, H., Mariette, J., Frasse, P., Vautrin, S., Zouine, M., Latche, A., Rousseau, C., Regad, F., Pech, J.C., Philippot, M., Bouzayen, M., Pericard, P., Osorio, S., del Carmen, A.F., Monforte, A., Granell, A., Fernandez-Munoz, R., Conte, M., Lichtenstein, G., Carrari, F., De Bellis, G., Fuligni, F., Peano, C., Grandillo, S., Termolino, P., Pietrella, M., Fantini, E., Falcone, G., Fiore, A., Giuliano, G., Lopez, L., Facella, P., Perrotta, G., Daddiego, L., Bryan, G., Orozco, M., Pastor, X., Torrents, D., van Schriek, K.N.V.M.G.M., Feron, R.M.C., van Oeveren, J., de Heer, P., daPonte, L., Jacobs-Oomen, S., Cariaso, M., Prins, M., van Eijk, M.J.T., Janssen, A., van Haaren, M.J.J., Jo, S.H., Kim, J., Kwon, S.Y., Kim, S., Koo, D.H., Lee, S., Hur, C.G., Clouser, C., Rico, A., Hallab, A., Gebhardt, C., Klee, K., Jocker, A., Warfsmann, J., Gobel, U., Kawamura, S., Yano, K., Sherman, J.D., Fukuoka, H., Negoro, S., Bhutty, S., Chowdhury, P., Chattopadhyay, D., Datema, E., Smit, S., Schijlen, E.W.M., van de Belt, J., van Haarst, J.C., Peters, S.A., van Staveren, M.J., Henkens, M.H.C., Mooyman, P.J.W., Hesselink, T., van Ham, R.C.H.J., Jiang, G.Y., Droege, M., Choi, D., Kang, B.C., Kim, B.D., Park, M., Kim, S., Yeom, S.I., Lee, Y.H., Choi, Y.D., Li, G.C., Gao, J.W., Liu, Y.S., Huang, S.X., Fernandez-Pedrosa, V., Collado, C., Zuniga, S., Wang, G.P., Cade, R., Dietrich, R.A., Rogers, J., Knapp, S., Fei, Z.J., White, R.A., Thannhauser, T.W., Giovannoni, J.J., Botella, M.A., Gilbert, L., Gonzalez, R., Goicoechea, J.L., Yu, Y., Kudrna, D., Collura, K., Wissotski, M., Wing, R., Schoof, H., Meyers, B.C., Gurazada, A.B., Green, P.J., Mathur, S., Vyas, S., Solanke, A.U., Kumar, R., Gupta, V., Sharma, A.K., Khurana, P., Khurana, J.P., Tyagi, A.K., Dalmay, T., Mohorianu, I., Walts, B., Chamala, S., Barbazuk, W.B., Li, J.P., Guo, H., Lee, T.H., Wang, Y.P., Zhang, D., Paterson, A.H., Wang, X.Y., Tang, H.B., Barone, A., Chiusano, M.L., Ercolano, M.R., D'Agostino, N., Di Filippo, M., Traini, A., Sanseverino, W., Frusciante, L., Seymour, G.B., Elharam, M., Fu, Y., Hua, A., Kenton, S., Lewis, J., Lin, S.P., Najar, F., Lai, H.S., Qin, B.F., Qu, C.M., Shi, R.H., White, D., White, J., Xing, Y.B., Yang, K.Q., Yi, J., Yao, Z.Y., Zhou, L.P., Roe, B.A., Vezzi, A., D'Angelo, M., Zimbello, R., Schiavon, R., Caniato, E., Rigobello, C., Campagna, D., Vitulo, N., Valle, G., Nelson, D.R., De Paoli, E., Szinay, D., de Jong, H.H., Bai, Y.L., Visser, R.G.F., Lankhorst, R.M.K., Beasley, H., McLaren, K., Nicholson, C., Riddle, C., Gianese, G. and Consortium, T.G. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641
Zhou, T., Zhang, H., Lai, T.F., Qin, C., Shi, N.N., Wang, H.Z., Jin, M.F., Zhong, S.L., Fan, Z.F., Liu, Y.L., Wu, Z.R., Jackson, S., Giovannoni, J.J., Rolin, D., Gallusci, P. and Hong, Y.G. 2012. Virus-induced gene complementation reveals a transcription factor network in modulation of tomato fruit ripening. Sci Rep-Uk 2: 836
Zhou, X.J., Mcquinn, R., Fei, Z.J., Wolters, A.M.A., Van Eck, J., Brown, C., Giovannoni, J.J. and Li, L. 2011. Regulatory control of high levels of carotenoid accumulation in potato tubers. Environ 34: 1020-1030
Zhong, S., Joung, J.G., Zheng, Y., Chen, Y.R., Liu, B., Shao, Y., Xiang, J.Z., Fei , Z. and Giovannoni, J.J. 2011. High-throughput Illumina strand-specific RNA sequencing library preparation. Cold Spring Harb Protoc 2011: 940-949
Seymour, G.B., Ryder, C.D., Cevik, V., Hammond, J.P., Popovich, A., King, G.J., Vrebalov, J., Giovannoni, J.J. and Manning, K. 2011. A SEPALLATA gene is involved in the development and ripening of strawberry (FragariaXananassa Duch.) fruit, a non-climacteric tissue. J Exp Bot 62: 1179-1188
Rugkong, A., McQuinn, R., Giovannoni, J.J., Rose, J.K.C. and Watkins, C.B. 2011. Expression of ripening-related genes in cold-stored tomato fruit. Postharvest Biol Tec 61: 1-14
Rohrmann, J., Tohge, T., Alba, R., Osorio, S., Caldana, C., McQuinn, R., Arvidsson, S., van der Merwe, M.J., Riano-Pachon, D.M., Mueller-Roeber, B., Fei, Z., Nesi, A.N., Giovannoni, J.J. and Fernie, A.R. 2011. Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. Plant J 68: 999-1013
Osorio, S., Alba, R., Damasceno, C.M.B., Lopez-Casado, G., Lohse, M., Zanor, M.I., Tohge, T., Usadel, B., Rose, J.K.C., Fei, Z.J., Giovannoni, J.J. and Fernie, A.R. 2011. Systems biology of tomato fruit development: Combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions. Plant Physiol 157: 405-425
Matas, A.J., Yeats, T.H., Buda, G.J., Zheng, Y., Chatterjee, S., Tohge, T., Ponnala, L., Adato, A., Aharoni, A., Stark, R., Fernie, A.R., Fei, Z., Giovannoni, J.J. and Rose, J.K. 2011. Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. Plant Cell 23: 3893-3910
Martel, C., Vrebalov, J., Tafelmeyer , P. and Giovannoni, J.J. 2011. The tomato MADS-box transcription factor RIPENING INHIBITOR interacts with promoters involved in numerous ripening processes in a COLORLESS NONRIPENING-dependent Manner. Plant Physiol 157: 1568-1579
Klee, H.J. and Giovannoni, J.J. 2011. Genetics and control of tomato fruit ripening and quality attributes. Annu Rev Genet 45: 41-59
Fei, Z., Joung, J.G., Tang, X., Zheng, Y., Huang, M., Lee, J.M., McQuinn, R., Tieman, D.M., Alba, R., Klee, H.J. and Giovannoni, J.J. 2011. Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. Nucleic Acids Res 39: D1156-1163
Dai, N., Cohen, S., Portnoy, V., Tzuri, G., Harel-Beja, R., Pompan-Lotan, M., Carmi, N., Zhang, G.F., Diber, A., Pollock, S., Karchi, H., Yeselson, Y., Petreikov, M., Shen, S., Sahar, U., Hovav, R., Lewinsohn, E., Tadmor, Y., Granot, D., Ophir, R., Sherman, A., Fei, Z.J., Giovannoni, J., Burger, Y. , Katzir, N. and Schaffer, A.A. 2011. Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation. Plant Mol Biol 76: 1-18
Clepet, C., Joobeur, T., Zheng, Y., Jublot, D., Huang, M.Y., Truniger, V., Boualem, A., Hernandez-Gonzalez, M.E., Dolcet-Sanjuan, R., Portnoy, V., Mascarell-Creus, A., Cano-Delgado, A.I., Katzir, N., Bendahmane, A., Giovannoni, J.J., Aranda, M.A., Garcia-Mas, J. and Fei, Z.J. 2011. Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. Bmc Genomics 12: 252
Milone, D.H., Stegmayer, G.S., Kamenetzky, L., Lopez, M., Lee, J.M., Giovannoni, J.J. and Carrari, F. 2010. omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants. BMC Bioinformatics 11: 438
Kamenetzky, L., Asis, R., Bassi, S., de Godoy, F., Bermudez, L., Fernie, A.R., Van Sluys, M.A., Vrebalov, J., Giovannoni, J.J., Rossi, M. and Carrari, F. 2010. Genomic analysis of wild tomato introgressions determining metabolism- and yield-associated traits. Plant Physiology 152: 1772-1786
Harel-Beja, R., Tzuri, G., Portnoy, V., Lotan-Pompan, M., Lev, S., Cohen, S., Dai, N., Yeselson, L., Meir, A., Libhaber, S.E., Avisar, E., Melame, T., van Koert, P., Verbakel, H., Hofstede, R., Volpin, H., Oliver, M., Fougedoire, A., Stalh, C., Fauve, J., Copes, B., Fei, Z., Giovannoni, J., Ori, N., Lewinsohn, E., Sherman, A., Burger, J., Tadmor, Y., Schaffer, A.A. and Katzir, N. 2010. A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes. Theoretical and Applied Genetics 121: 511-533
Gonda, I., Bar, E., Portnoy, V., Lev, S., Burger, J., Schaffer, A.A., Tadmor, Y., Gepstein, S., Giovannoni, J.J., Katzir, N. and Lewinsohn, E. 2010. Branched-chain and aromatic amino acid catabolism into aroma volatiles in Cucumis melo L. fruit. Journal of Experimental Botany 61: 1111-1123
Giovannoni, J. 2010. Harvesting the apple genome. Nature Genetics 42: 822-823
Enfissi, E.M.A., Barneche, F., Ahmed, I., Lichtle, C., Gerrish, C., McQuinn, R.P., Giovannoni, J.J., Lopez-Juez, E., Bowler, C., Bramley, P.M. and Fraser, P.D. 2010. Integrative transcript and metabolite analysis of nutritionally enhanced DE-ETIOLATED1 downregulated tomato fruit. Plant Cell 22: 1190-1215
Elitzur, T., Vrebalov, J., Giovannoni, J.J., Goldschmidt, E.E. and Friedman, H. 2010. The regulation of MADS-box gene expression during ripening of banana and their regulatory interaction with ethylene. Journal of Experimental Botany 61: 1523-1535
Costa, F., Alba, R., Schouten, H., Soglio, V., Gianfranceschi, L., Serra, S., Musacchi, S., Sansavini, S., Costa, G., Fei, Z.J. and Giovannoni, J. 2010. Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening. BMC Plant Biology 10: 229
Chung, M.Y., Han, J.S., Giovannoni, J., Liu, Y., Kim, C.K., Lim, K.B. and Chung, J.D. 2010. Modest calcium increase in tomatoes expressing a variant of Arabidopsis cation/H+ antiporter. Plant Biotechnology Reports 4: 15-21
Chung, M.Y., Vrebalov, J., Alba, R., Lee, J., McQuinn, R., Chung, J.D., Klein , P. and Giovannoni, J. 2010. A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening. Plant Journal 64: 936-947
Pan, I.L., McQuinn, R., Giovannoni, J.J. and Irish, V.F. 2010. Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development. Journal of Experimental Botany 61: 1795-1806
Rugkong, A., Rose, J.K.C., Lee, S.J., Giovannoni, J.J., O'Neill, M.A. and Watkins, C.B. 2010. Cell wall metabolism in cold-stored tomato fruit. Postharvest Biology and Technology 57: 106-113
Waller, J.C., Akhtar, T.A., Lara-Nunez, A., Gregory, J.F., McQuinn, R.P., Giovannoni, J.J. and Hanson, A.D. 2010. Developmental and feedforward control of the expression of folate biosynthesis genes in tomato fruit. Molecular Plant 3: 66-77
Vrebalov, J., Pan, I.L., Arroyo, A.J., McQuinn, R., Chung, M., Poole, M., Rose, J., Seymour, G., Grandillo, S., Giovannoni, J. and Irish, V.F. 2009. Fleshy fruit expansion and ripening are regulated by the Tomato SHATTERPROOF gene TAGL1. Plant Cell 21: 3041-3062
Ponce-Valadez, M., Fellman, S.M., Giovannoni, J., Gan, S.S. and Watkins, C.B. 2009. Differential fruit gene expression in two strawberry cultivars in response to elevated CO2 during storage revealed by a heterologous fruit microarray approach. Postharvest Biol Tec 51: 131-140
Mueller, L.A., Lankhorst, R.K., Tanksley, S.D., Giovannoni, J.J., White, R., Vrebalov, J., Fei, Z., van Eck, J., Buels, R., Mills, A.A., Menda, N., Tecle, I.Y., Bombarely, A., Stack, S., Royer, S.M., Chang, S.-B., Shearer, L.A., Kim, B.D., Jo, S.-H., Hur, C.-G., Choi, D., Li, C.-B., Zhao, J., Jiang, H., Geng, Y., Dai, Y., Fan, H., Chen, J., Lu, F., Shi, J., Sun, S., Chen, J., Yang, X., Lu, C., Chen, M., Cheng, Z., Li, C., Ling, H., Xue, Y., Wang, Y., Seymour, G.B., Bishop, G.J., Bryan, G., Rogers, J., Sims, S., Butcher, S., Buchan, D., Abbott, J., Beasley, H., Nicholson, C., Riddle, C., Humphray, S., McLaren, K., Mathur, S., Vyas, S., Solanke, A.U., Kumar, R., Gupta, V., Sharma, A.K., Khurana, P., Khurana, J.P., Tyagi, A., Sarita, Chowdhury, P., Shridhar, S., Chattopadhyay, D., Pandit, A., Singh, P., Kumar, A., Dixit, R., Singh, A., Praveen, S., Dalal, V., Yadav, M., Ghazi, I.A., Gaikwad, K., Sharma, T.R., Mohapatra, T., Singh, N.K., Szinay, D., de Jong, H., Peters, S., van Staveren, M., Datema, E., Fiers, M.W.E.J., van Ham, R.C.H.J., Lindhout, P., Philippot, M., Frasse, P., Regad, F., Zouine, M., Bouzayen, M., Asamizu, E., Sato, S., Fukuoka, H., Tabata, S., Shibata, D., Botella, M.A., Perez-Alonso, M., Fernandez-Pedrosa, V., Osorio, S., Mico, A., Granell, A., Zhang, Z., He, J., Huang, S., Du, Y., Qu, D., Liu, L., Liu, D., Wang, J., Ye, Z., Yang, W., Wang, G., Vezzi, A., Todesco, S., Valle, G., Falcone, G., Pietrella, M., Giuliano, G., Grandillo, S., Traini, A., D'Agostino, N., Chiusano, M.L., Ercolano, M., Barone, A., Frusciante, L., Schoof, H., Jöcker, A., Bruggmann, R., Spannagl, M., Mayer, K.X.F., Guigó, R., Camara, F., Rombauts, S., Fawcett, J.A., Van de Peer, Y., Knapp, S., Zamir, D. and Stiekema, W. 2009. A snapshot of the emerging tomato genome sequence. The Plant Genome 2: 78-92
Joung, J.G., Corbett, A.M., Fellman, S.M., Tieman, D.M., Klee, H.J., Giovannoni , J.J. and Fei, Z. 2009. Plant MetGenMAP: an integrative analysis system for plant systems biology. Plant Physiol 151: 1758-1768
Matas, A.J., Gapper, N.E., Chung, M.Y., Giovannoni, J.J. and Rose, J.K.C. 2009. Biology and genetic engineering of fruit maturation for enhanced quality and shelf-life. Curr Opin Biotech 20: 197-203
Stack, S.M., Royer, S.M., Shearer, L.A., Chang, S.B., Giovannoni, J.J., Westfall, D.H., White, R.A. and Anderson, L.K. 2009. Role of fluorescence in situ hybridization in sequencing the tomato genome. Cytogenet Genome Res 124: 339-350
Wang, Y., Diehl, A., Wu, F.N., Vrebalov, J., Giovannoni, J., Siepel, A. and Tanksley, S.D. 2008. Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics 180: 391-408
Wang, S.H., Liu, J.K., Feng, Y.Y., Niu, X.L., Giovannoni, J. and Liu, Y.S. 2008. Altered plastid levels and potential for improved fruit nutrient content by downregulation of the tomato DDB1-interacting protein CUL4. Plant Journal 55: 89-103
Slocombe, S.P., Schauvinhold, I., McQuinn, R.P., Besser, K., Welsby, N.A., Harper, A., Aziz, N., Li, Y., Larson, T.R., Giovannoni, J., Dixon, R.A. and Broun, P. 2008. Transcriptomic and reverse genetic analyses of branched-chain fatty acid and acyl sugar production in Solanum pennellii and Nicotiana benthamiana. Plant Physiol 148: 1830-1846
Portnoy, V., Benyamini, Y., Bar, E., Harel-Beja, R., Gepstein, S., Giovannoni, J.J., Schaffer, A.A., Burger, J., Tadmor, Y., Lewinsohn, E. and Katzir, N. 2008. The molecular and biochemical basis for varietal variation in sesquiterpene content in melon (Cucumis melo L.) rinds. Plant Molecular Biology 66: 647-661
Datema, E., Mueller, L.A., Buels, R., Giovannoni, J.J., Visser, R.G.F., Stiekema, W.J. and van Ham, R.C.H.J. 2008. Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. Bmc Plant Biol 8: 34
Cara, B. and Giovannoni, J.J. 2008. Molecular biology of ethylene during tomato fruit development and maturation. Plant Sci 175: 106-113
Barry, C.S., McQuinn, R.P., Chung, M.Y., Besuden, A. and Giovannoni, J.J. 2008. Amino acid substitutions in homologs of the STAY-GREEN protein are responsible for the green-flesh and chlorophyll retainer mutations of tomato and pepper. Plant Physiology 147: 179-187
Akhtar, T.A., McQuinn, R.P., Naponelli, V., Gregory, J.F., Giovannoni, J.J. and Hanson, A.D. 2008. Tomato gamma-glutamyl hydrolases: Expression, characterization, and evidence for heterodimer formation. Plant Physiology 148: 775-785
Giovannoni, J., . 2007. Fruit Ripening Mutants Yield Insights Into Ripening Control. Current Opinion in Plant Biology 10: 283-289
Giovannoni, J., . 2007. A New Plant Gene in the Pathway to Vitamin C. PNAS USA 104: 9109-9110
Kelleher, C., R. Chiu, H. Shin, I. Bosdet, M. Krzywinski, C. Fjell, J. Wilkin, T. Yin, S. DiFazio, J. Ali, J. Asano, S. Chan, A. Cloutier, N. Girn, S. Leach, J. Giovannoni, J. Grimwood, G. Tuskan, C. Douglas. 2007. A Physical Map of the Highly Heterozygous Populus Genome: Integration With the Genome Sequence and Genetic Map and Analysis of Haplotype Variation. The Plant Journal 50: 1063-1078
Barry, C., J. Giovannoni. 2007. Ethylene and Fruit Ripening. J. of Plant Growth Regulation 26: 143-159
Fei, Z., X. Tang, R. Alba, J. Giovannoni. 2006. Tomato Expression Database (TED): A Suite of Data Presentation and Analysis Tools. Nucleic Acids Research 34: D766
Barry, C. S., J. J. Giovannoni. 2006. Ripening in the Tomato Green-ripe Mutant is Inhibited by Ectopic Expression of a Protein that Disrupts Ethylene Signaling. Proc Natl Acad USA 103: 7923-7928
Mueller, L. A., S. D. Tanksley, J. J. Giovannoni, J. Van Eck, S. Stack, D. Choi, B. D. Kim, M. Chen, Z. Cheng, C. Li, H. Ling, Y. Xue, G. Seymour, G. Bishop, G. Bryan, R. Sharma, J. Khurana, A. Tyagi, D. Chattopadhyay, N. K. Singh, W. Stiekema, P. Lindhout, T. Jesse, R. K. Lankhorst, M. Bouzayen, D. Shibata, S. Tabata, A. Granell, M. A. Botella, G. Giuliano, L. Frusciante, M. Causse, D. Zamir. 2005. The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (SOL). Comparative and Functional Genomics 6: 153-158
Moore, S., P. Payton, M. Wright, S. Tanksley, J. Giovannoni. 2005. Utilization of Tomato Microarrays for Comparative Gene Expression Analysis in the Solanaceae. Journal of Experimental Botany 56: 2885-2895
Li, C., A. L. Schilmiller, G. Liu, G. I. Lee, S. Jayanty, C. Sageman, J. Vrebalov, J. J. Giovannoni, K. Yagi, Y. Kobayashi, G. A. Howe. 2005. Role of Beta-Oxidation in Jasmonate Biosynthesis and Systemic Wound Signaling in Tomato. Plant Cell 17: 971-986
Giovannoni, J. J., S. El-Rakshy. 2005. Genetic Regulation of Tomato Fruit Ripening and Development and Implementation of Associated Genomics Tools. Acta Horticulturae 682: 63-72
Barry, C., R. P. McQuinn, A. J. Thompson, G. B. Seymour, D. Grierson, J. J. Giovannoni. 2005. Ethylene Insensitivity Conferred by the Green-ripe (Gr) and Never-ripe 2 (Nr-2) Ripening Mutants of Tomato. Plant Physiology 138: 267-275
Liu, Y., S. Roof, Z. Ye, C. Barry, A. van Tuinen, J. Vrebalov, C. Bowler, J. Giovannoni. 2004. Manipulation of Light Signal Transduction as a Means of Modifying Fruit Nutritional Quality in Tomato. Proceedings of the National Academy of Sciences, USA 101: 9897-9902
Giovannoni, J., . 2004. Genetic Regulation of Fruit Development and Ripening. The Plant Cell 16: S170 -180
Basset, G. J. C., E. P. Quinlivan, S. Ravanel, F. Rébeillé, B. P. Nichols, K. Shinozaki, M. Seki, L. C. Adams-Phillips, J. J. Giovannoni, J. F. Gregory III, A. D. Hanson. 2004. Folate synthesis in plants: The p-aminobenzoate branch is initiated by a bifunctional PabA-PabB protein that is targeted to plastids. Proceedings of the National Academy of Sciences, USA 101: 1496-1501
Adams-Phillips, L., C. Barry, P. Kannan, J. Leclercq, M. Bouzayen, J. Giovannoni. 2004. Evidence that CTR1-mediated Ethylene Signal Transduction in Tomato is Encoded by a Multigene Family Whose Members Display Distinct Regulatory Features. Plant Molecular Biology 54: 387-404
Adams-Phillips, L., C. Barry, J. Giovannoni. 2004. Signal transduction systems regulating fruit ripening. Trends in Plant Science 9: 331-338
Vrebalov, J., D. Ruezinsky, V. Padmanabhan, R. White, D. Medrano, R. Drake, W. Schuch, J. Giovannoni. 2002. A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296: 343-346
Wilkinson, J., M. Lanahan, H. Yen, J. Giovannoni, H. Klee. 1995. An Ethylene-inducible Component of Signal Transduction Encoded by Never-ripe. Science 270: 1807-1809
Selected Publication
Barry, C.S., Aldridge, G.M., Herzog, G., Ma, Q., McQuinn, R.P., Hirschberg, J. and Giovannoni, J.J. 2012. Altered chloroplast development and delayed fruit ripening caused by mutations in a zinc metalloprotease at the lutescent2 locus of tomato. Plant Physiology 159: 1086-1098Cao, Y., Tang, X., Giovannoni, J., Xiao, F. and Liu, Y. 2012. Functional characterization of a tomato COBRA-like gene functioning in fruit development and ripening. Bmc Plant Biol 12: 211
Chen, Y.R., Zheng, Y., Liu, B., Zhong, S., Giovannoni, J. and Fei, Z. 2012. A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters. Plant Methods 8: 41
Goyal, R.K., Kumar, V., Shukla, V., Mattoo, R., Liu, Y.S., Chung, S.H., Giovannoni, J.J. and Mattoo, A.K. 2012. Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum). Planta 235: 453-471
Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W.J., Zhang, H., Zheng, Y., Mao, L., Ren, Y., Wang, Z., Min, J., Guo, X., Murat, F., Ham, B.K., Zhang, Z., Gao, S., Huang, M., Xu, Y., Zhong, S., Bombarely, A., Mueller, L.A., Zhao, H., He, H., Zhang, Y., Zhang, Z., Huang, S., Tan, T., Pang, E., Lin, K., Hu, Q., Kuang, H., Ni, P., Wang, B., Liu, J., Kou, Q., Hou, W., Zou, X., Jiang, J., Gong, G., Klee, K., Schoof, H., Huang, Y., Hu, X., Dong, S., Liang, D., Wang, J., Wu, K., Xia, Y., Zhao, X., Zheng, Z., Xing, M., Liang, X., Huang, B., Lv, T., Wang, J., Yin, Y., Yi, H., Li, R., Wu, M., Levi, A., Zhang, X., Giovannoni, J.J., Wang, J., Li, Y., Fei, Z. and Xu, Y. 2012. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45: 51-58
Harb, J., Gapper, N.E., Giovannoni, J.J. and Watkins, C.B. 2012. Molecular analysis of softening and ethylene synthesis and signaling pathways in a non-softening apple cultivar, 'Honeycrisp' and a rapidly softening cultivar, 'McIntosh'. Postharvest Biology and Technology 64: 94-103
Lee, J.M., Joung, J.G., McQuinn, R., Chung, M.Y., Fei, Z., Tieman, D., Klee, H. and Giovannoni, J. 2012. Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation. The Plant journal : for cell and molecular biology 70: 191-204
Liu, J.K., Li, H.J., Miao, M., Tang, X.F., Giovannoni, J., Xiao, F.M. and Liu, Y.S. 2012. The tomato UV-damaged DNA-binding protein-1 (DDB1) is implicated in pathogenesis-related (PR) gene expression and resistance to Agrobacterium tumefaciens. Molecular Plant Pathology 13: 123-134
Liu, J.K., Tang, X.F., Gao, L.Y., Gao, Y.F., Li, Y.X., Huang, S.X., Sun, X.C., Miao, M., Zeng, H., Tian, X.F., Niu, X.L., Zheng, L., Giovannoni, J., Xiao, F.M. and Liu, Y.S. 2012. A role of tomato UV-damaged DNA binding protein 1 (DDB1) in organ size control via an epigenetic manner. PLoS One 0: 7
Lopez-Casado, G., Covey, P.A., Bedinger, P.A., Mueller, L.A., Thannhauser, T.W., Zhang, S., Fei, Z.J., Giovannoni, J.J. and Rose, J.K.C. 2012. Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case. Proteomics 12: 761-774
Ma, Q., Du, W.Y., Brandizzi, F., Giovannoni, J.J. and Barry, C.S. 2012. Differential control of ethylene responses by GREEN-RIPE and GREEN-RIPE LIKE1 provides evidence for distinct ethylene signaling modules in tomato. Plant Physiology 160: 1968-1984
Osorio, S., Alba, R., Nikoloski, Z., Kochevenko, A., Fernie, A.R. and Giovannoni, J.J. 2012. Integrative comparative analyses of transcript and metabolite profiles from pepper and tomato ripening and development stages uncovers species-specific patterns of network regulatory behavior. Plant Physiology 159: 1713-1729
Powell, A.L.T., Nguyen, C.V., Hill, T., Cheng, K.L., Figueroa-Balderas, R., Aktas, H., Ashrafi, H., Pons, C., Fernandez-Munoz, R., Vicente, A., Lopez-Baltazar, J., Barry, C.S., Liu, Y.S., Chetelat, R., Granell, A., Van Deynze, A., Giovannoni, J.J. and Bennett, A.B. 2012. Uniform ripening encodes a Golden 2-like transcription factor regulating tomato fruit chloroplast development. Science 336: 1711-1715
Sato, S., Tabata, S., Hirakawa, H., Asamizu, E., Shirasawa, K., Isobe, S., Kaneko, T., Nakamura, Y., Shibata, D., Aoki, K., Egholm, M., Knight, J., Bogden, R., Li, C.B., Shuang, Y., Xu, X., Pan, S.K., Cheng, S.F., Liu, X., Ren, Y.Y., Wang, J., Albiero, A., Dal Pero, F., Todesco, S., Van Eck, J., Buels, R.M., Bombarely, A., Gosselin, J.R., Huang, M.Y., Leto, J.A., Menda, N., Strickler, S., Mao, L.Y., Gao, S., Tecle, I.Y., York, T., Zheng, Y., Vrebalov, J.T., Lee, J., Zhong, S.L., Mueller, L.A., Stiekema, W.J., Ribeca, P., Alioto, T., Yang, W.C., Huang, S.W., Du, Y.C., Zhang, Z.H., Gao, J.C., Guo, Y.M., Wang, X.X., Li, Y., He, J., Li, C.Y., Cheng, Z.K., Zuo, J.R., Ren, J.F., Zhao, J.H., Yan, L.H., Jiang, H.L., Wang, B., Li, H.S., Li, Z.J., Fu, F.Y., Chen, B.T., Han, B., Feng, Q., Fan, D.L., Wang, Y., Ling, H.Q., Xue, Y.B.A., Ware, D., McCombie, W.R., Lippman, Z.B., Chia, J.M., Jiang, K., Pasternak, S., Gelley, L., Kramer, M., Anderson, L.K., Chang, S.B., Royer, S.M., Shearer, L.A., Stack, S.M., Rose, J.K.C., Xu, Y.M., Eannetta, N., Matas, A.J., McQuinn, R., Tanksley, S.D., Camara, F., Guigo, R., Rombauts, S., Fawcett, J., Van de Peer, Y., Zamir, D., Liang, C.B., Spannagl, M., Gundlach, H., Bruggmann, R., Mayer, K., Jia, Z.Q., Zhang, J.H., Ye, Z.B.A., Bishop, G.J., Butcher, S., Lopez-Cobollo, R., Buchan, D., Filippis, I., Abbott, J., Dixit, R., Singh, M., Singh, A., Pal, J.K., Pandit, A., Singh, P.K., Mahato, A.K., Dogra, V., Gaikwad, K., Sharma, T.R., Mohapatra, T., Singh, N.K., Causse, M., Rothan, C., Schiex, T., Noirot, C., Bellec, A., Klopp, C., Delalande, C., Berges, H., Mariette, J., Frasse, P., Vautrin, S., Zouine, M., Latche, A., Rousseau, C., Regad, F., Pech, J.C., Philippot, M., Bouzayen, M., Pericard, P., Osorio, S., del Carmen, A.F., Monforte, A., Granell, A., Fernandez-Munoz, R., Conte, M., Lichtenstein, G., Carrari, F., De Bellis, G., Fuligni, F., Peano, C., Grandillo, S., Termolino, P., Pietrella, M., Fantini, E., Falcone, G., Fiore, A., Giuliano, G., Lopez, L., Facella, P., Perrotta, G., Daddiego, L., Bryan, G., Orozco, M., Pastor, X., Torrents, D., van Schriek, K.N.V.M.G.M., Feron, R.M.C., van Oeveren, J., de Heer, P., daPonte, L., Jacobs-Oomen, S., Cariaso, M., Prins, M., van Eijk, M.J.T., Janssen, A., van Haaren, M.J.J., Jo, S.H., Kim, J., Kwon, S.Y., Kim, S., Koo, D.H., Lee, S., Hur, C.G., Clouser, C., Rico, A., Hallab, A., Gebhardt, C., Klee, K., Jocker, A., Warfsmann, J., Gobel, U., Kawamura, S., Yano, K., Sherman, J.D., Fukuoka, H., Negoro, S., Bhutty, S., Chowdhury, P., Chattopadhyay, D., Datema, E., Smit, S., Schijlen, E.W.M., van de Belt, J., van Haarst, J.C., Peters, S.A., van Staveren, M.J., Henkens, M.H.C., Mooyman, P.J.W., Hesselink, T., van Ham, R.C.H.J., Jiang, G.Y., Droege, M., Choi, D., Kang, B.C., Kim, B.D., Park, M., Kim, S., Yeom, S.I., Lee, Y.H., Choi, Y.D., Li, G.C., Gao, J.W., Liu, Y.S., Huang, S.X., Fernandez-Pedrosa, V., Collado, C., Zuniga, S., Wang, G.P., Cade, R., Dietrich, R.A., Rogers, J., Knapp, S., Fei, Z.J., White, R.A., Thannhauser, T.W., Giovannoni, J.J., Botella, M.A., Gilbert, L., Gonzalez, R., Goicoechea, J.L., Yu, Y., Kudrna, D., Collura, K., Wissotski, M., Wing, R., Schoof, H., Meyers, B.C., Gurazada, A.B., Green, P.J., Mathur, S., Vyas, S., Solanke, A.U., Kumar, R., Gupta, V., Sharma, A.K., Khurana, P., Khurana, J.P., Tyagi, A.K., Dalmay, T., Mohorianu, I., Walts, B., Chamala, S., Barbazuk, W.B., Li, J.P., Guo, H., Lee, T.H., Wang, Y.P., Zhang, D., Paterson, A.H., Wang, X.Y., Tang, H.B., Barone, A., Chiusano, M.L., Ercolano, M.R., D'Agostino, N., Di Filippo, M., Traini, A., Sanseverino, W., Frusciante, L., Seymour, G.B., Elharam, M., Fu, Y., Hua, A., Kenton, S., Lewis, J., Lin, S.P., Najar, F., Lai, H.S., Qin, B.F., Qu, C.M., Shi, R.H., White, D., White, J., Xing, Y.B., Yang, K.Q., Yi, J., Yao, Z.Y., Zhou, L.P., Roe, B.A., Vezzi, A., D'Angelo, M., Zimbello, R., Schiavon, R., Caniato, E., Rigobello, C., Campagna, D., Vitulo, N., Valle, G., Nelson, D.R., De Paoli, E., Szinay, D., de Jong, H.H., Bai, Y.L., Visser, R.G.F., Lankhorst, R.M.K., Beasley, H., McLaren, K., Nicholson, C., Riddle, C., Gianese, G. and Consortium, T.G. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641
Zhou, T., Zhang, H., Lai, T.F., Qin, C., Shi, N.N., Wang, H.Z., Jin, M.F., Zhong, S.L., Fan, Z.F., Liu, Y.L., Wu, Z.R., Jackson, S., Giovannoni, J.J., Rolin, D., Gallusci, P. and Hong, Y.G. 2012. Virus-induced gene complementation reveals a transcription factor network in modulation of tomato fruit ripening. Sci Rep-Uk 2: 836
Zhou, X.J., Mcquinn, R., Fei, Z.J., Wolters, A.M.A., Van Eck, J., Brown, C., Giovannoni, J.J. and Li, L. 2011. Regulatory control of high levels of carotenoid accumulation in potato tubers. Environ 34: 1020-1030
Zhong, S., Joung, J.G., Zheng, Y., Chen, Y.R., Liu, B., Shao, Y., Xiang, J.Z., Fei , Z. and Giovannoni, J.J. 2011. High-throughput Illumina strand-specific RNA sequencing library preparation. Cold Spring Harb Protoc 2011: 940-949
Seymour, G.B., Ryder, C.D., Cevik, V., Hammond, J.P., Popovich, A., King, G.J., Vrebalov, J., Giovannoni, J.J. and Manning, K. 2011. A SEPALLATA gene is involved in the development and ripening of strawberry (FragariaXananassa Duch.) fruit, a non-climacteric tissue. J Exp Bot 62: 1179-1188
Rugkong, A., McQuinn, R., Giovannoni, J.J., Rose, J.K.C. and Watkins, C.B. 2011. Expression of ripening-related genes in cold-stored tomato fruit. Postharvest Biol Tec 61: 1-14
Rohrmann, J., Tohge, T., Alba, R., Osorio, S., Caldana, C., McQuinn, R., Arvidsson, S., van der Merwe, M.J., Riano-Pachon, D.M., Mueller-Roeber, B., Fei, Z., Nesi, A.N., Giovannoni, J.J. and Fernie, A.R. 2011. Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. Plant J 68: 999-1013
Osorio, S., Alba, R., Damasceno, C.M.B., Lopez-Casado, G., Lohse, M., Zanor, M.I., Tohge, T., Usadel, B., Rose, J.K.C., Fei, Z.J., Giovannoni, J.J. and Fernie, A.R. 2011. Systems biology of tomato fruit development: Combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions. Plant Physiol 157: 405-425
Matas, A.J., Yeats, T.H., Buda, G.J., Zheng, Y., Chatterjee, S., Tohge, T., Ponnala, L., Adato, A., Aharoni, A., Stark, R., Fernie, A.R., Fei, Z., Giovannoni, J.J. and Rose, J.K. 2011. Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. Plant Cell 23: 3893-3910
Martel, C., Vrebalov, J., Tafelmeyer , P. and Giovannoni, J.J. 2011. The tomato MADS-box transcription factor RIPENING INHIBITOR interacts with promoters involved in numerous ripening processes in a COLORLESS NONRIPENING-dependent Manner. Plant Physiol 157: 1568-1579
Klee, H.J. and Giovannoni, J.J. 2011. Genetics and control of tomato fruit ripening and quality attributes. Annu Rev Genet 45: 41-59
Fei, Z., Joung, J.G., Tang, X., Zheng, Y., Huang, M., Lee, J.M., McQuinn, R., Tieman, D.M., Alba, R., Klee, H.J. and Giovannoni, J.J. 2011. Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. Nucleic Acids Res 39: D1156-1163
Dai, N., Cohen, S., Portnoy, V., Tzuri, G., Harel-Beja, R., Pompan-Lotan, M., Carmi, N., Zhang, G.F., Diber, A., Pollock, S., Karchi, H., Yeselson, Y., Petreikov, M., Shen, S., Sahar, U., Hovav, R., Lewinsohn, E., Tadmor, Y., Granot, D., Ophir, R., Sherman, A., Fei, Z.J., Giovannoni, J., Burger, Y. , Katzir, N. and Schaffer, A.A. 2011. Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation. Plant Mol Biol 76: 1-18
Clepet, C., Joobeur, T., Zheng, Y., Jublot, D., Huang, M.Y., Truniger, V., Boualem, A., Hernandez-Gonzalez, M.E., Dolcet-Sanjuan, R., Portnoy, V., Mascarell-Creus, A., Cano-Delgado, A.I., Katzir, N., Bendahmane, A., Giovannoni, J.J., Aranda, M.A., Garcia-Mas, J. and Fei, Z.J. 2011. Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. Bmc Genomics 12: 252
Milone, D.H., Stegmayer, G.S., Kamenetzky, L., Lopez, M., Lee, J.M., Giovannoni, J.J. and Carrari, F. 2010. omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants. BMC Bioinformatics 11: 438
Kamenetzky, L., Asis, R., Bassi, S., de Godoy, F., Bermudez, L., Fernie, A.R., Van Sluys, M.A., Vrebalov, J., Giovannoni, J.J., Rossi, M. and Carrari, F. 2010. Genomic analysis of wild tomato introgressions determining metabolism- and yield-associated traits. Plant Physiology 152: 1772-1786
Harel-Beja, R., Tzuri, G., Portnoy, V., Lotan-Pompan, M., Lev, S., Cohen, S., Dai, N., Yeselson, L., Meir, A., Libhaber, S.E., Avisar, E., Melame, T., van Koert, P., Verbakel, H., Hofstede, R., Volpin, H., Oliver, M., Fougedoire, A., Stalh, C., Fauve, J., Copes, B., Fei, Z., Giovannoni, J., Ori, N., Lewinsohn, E., Sherman, A., Burger, J., Tadmor, Y., Schaffer, A.A. and Katzir, N. 2010. A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes. Theoretical and Applied Genetics 121: 511-533
Gonda, I., Bar, E., Portnoy, V., Lev, S., Burger, J., Schaffer, A.A., Tadmor, Y., Gepstein, S., Giovannoni, J.J., Katzir, N. and Lewinsohn, E. 2010. Branched-chain and aromatic amino acid catabolism into aroma volatiles in Cucumis melo L. fruit. Journal of Experimental Botany 61: 1111-1123
Giovannoni, J. 2010. Harvesting the apple genome. Nature Genetics 42: 822-823
Enfissi, E.M.A., Barneche, F., Ahmed, I., Lichtle, C., Gerrish, C., McQuinn, R.P., Giovannoni, J.J., Lopez-Juez, E., Bowler, C., Bramley, P.M. and Fraser, P.D. 2010. Integrative transcript and metabolite analysis of nutritionally enhanced DE-ETIOLATED1 downregulated tomato fruit. Plant Cell 22: 1190-1215
Elitzur, T., Vrebalov, J., Giovannoni, J.J., Goldschmidt, E.E. and Friedman, H. 2010. The regulation of MADS-box gene expression during ripening of banana and their regulatory interaction with ethylene. Journal of Experimental Botany 61: 1523-1535
Costa, F., Alba, R., Schouten, H., Soglio, V., Gianfranceschi, L., Serra, S., Musacchi, S., Sansavini, S., Costa, G., Fei, Z.J. and Giovannoni, J. 2010. Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening. BMC Plant Biology 10: 229
Chung, M.Y., Han, J.S., Giovannoni, J., Liu, Y., Kim, C.K., Lim, K.B. and Chung, J.D. 2010. Modest calcium increase in tomatoes expressing a variant of Arabidopsis cation/H+ antiporter. Plant Biotechnology Reports 4: 15-21
Chung, M.Y., Vrebalov, J., Alba, R., Lee, J., McQuinn, R., Chung, J.D., Klein , P. and Giovannoni, J. 2010. A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening. Plant Journal 64: 936-947
Pan, I.L., McQuinn, R., Giovannoni, J.J. and Irish, V.F. 2010. Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development. Journal of Experimental Botany 61: 1795-1806
Rugkong, A., Rose, J.K.C., Lee, S.J., Giovannoni, J.J., O'Neill, M.A. and Watkins, C.B. 2010. Cell wall metabolism in cold-stored tomato fruit. Postharvest Biology and Technology 57: 106-113
Waller, J.C., Akhtar, T.A., Lara-Nunez, A., Gregory, J.F., McQuinn, R.P., Giovannoni, J.J. and Hanson, A.D. 2010. Developmental and feedforward control of the expression of folate biosynthesis genes in tomato fruit. Molecular Plant 3: 66-77
Vrebalov, J., Pan, I.L., Arroyo, A.J., McQuinn, R., Chung, M., Poole, M., Rose, J., Seymour, G., Grandillo, S., Giovannoni, J. and Irish, V.F. 2009. Fleshy fruit expansion and ripening are regulated by the Tomato SHATTERPROOF gene TAGL1. Plant Cell 21: 3041-3062
Ponce-Valadez, M., Fellman, S.M., Giovannoni, J., Gan, S.S. and Watkins, C.B. 2009. Differential fruit gene expression in two strawberry cultivars in response to elevated CO2 during storage revealed by a heterologous fruit microarray approach. Postharvest Biol Tec 51: 131-140
Mueller, L.A., Lankhorst, R.K., Tanksley, S.D., Giovannoni, J.J., White, R., Vrebalov, J., Fei, Z., van Eck, J., Buels, R., Mills, A.A., Menda, N., Tecle, I.Y., Bombarely, A., Stack, S., Royer, S.M., Chang, S.-B., Shearer, L.A., Kim, B.D., Jo, S.-H., Hur, C.-G., Choi, D., Li, C.-B., Zhao, J., Jiang, H., Geng, Y., Dai, Y., Fan, H., Chen, J., Lu, F., Shi, J., Sun, S., Chen, J., Yang, X., Lu, C., Chen, M., Cheng, Z., Li, C., Ling, H., Xue, Y., Wang, Y., Seymour, G.B., Bishop, G.J., Bryan, G., Rogers, J., Sims, S., Butcher, S., Buchan, D., Abbott, J., Beasley, H., Nicholson, C., Riddle, C., Humphray, S., McLaren, K., Mathur, S., Vyas, S., Solanke, A.U., Kumar, R., Gupta, V., Sharma, A.K., Khurana, P., Khurana, J.P., Tyagi, A., Sarita, Chowdhury, P., Shridhar, S., Chattopadhyay, D., Pandit, A., Singh, P., Kumar, A., Dixit, R., Singh, A., Praveen, S., Dalal, V., Yadav, M., Ghazi, I.A., Gaikwad, K., Sharma, T.R., Mohapatra, T., Singh, N.K., Szinay, D., de Jong, H., Peters, S., van Staveren, M., Datema, E., Fiers, M.W.E.J., van Ham, R.C.H.J., Lindhout, P., Philippot, M., Frasse, P., Regad, F., Zouine, M., Bouzayen, M., Asamizu, E., Sato, S., Fukuoka, H., Tabata, S., Shibata, D., Botella, M.A., Perez-Alonso, M., Fernandez-Pedrosa, V., Osorio, S., Mico, A., Granell, A., Zhang, Z., He, J., Huang, S., Du, Y., Qu, D., Liu, L., Liu, D., Wang, J., Ye, Z., Yang, W., Wang, G., Vezzi, A., Todesco, S., Valle, G., Falcone, G., Pietrella, M., Giuliano, G., Grandillo, S., Traini, A., D'Agostino, N., Chiusano, M.L., Ercolano, M., Barone, A., Frusciante, L., Schoof, H., Jöcker, A., Bruggmann, R., Spannagl, M., Mayer, K.X.F., Guigó, R., Camara, F., Rombauts, S., Fawcett, J.A., Van de Peer, Y., Knapp, S., Zamir, D. and Stiekema, W. 2009. A snapshot of the emerging tomato genome sequence. The Plant Genome 2: 78-92
Joung, J.G., Corbett, A.M., Fellman, S.M., Tieman, D.M., Klee, H.J., Giovannoni , J.J. and Fei, Z. 2009. Plant MetGenMAP: an integrative analysis system for plant systems biology. Plant Physiol 151: 1758-1768
Matas, A.J., Gapper, N.E., Chung, M.Y., Giovannoni, J.J. and Rose, J.K.C. 2009. Biology and genetic engineering of fruit maturation for enhanced quality and shelf-life. Curr Opin Biotech 20: 197-203
Stack, S.M., Royer, S.M., Shearer, L.A., Chang, S.B., Giovannoni, J.J., Westfall, D.H., White, R.A. and Anderson, L.K. 2009. Role of fluorescence in situ hybridization in sequencing the tomato genome. Cytogenet Genome Res 124: 339-350
Wang, Y., Diehl, A., Wu, F.N., Vrebalov, J., Giovannoni, J., Siepel, A. and Tanksley, S.D. 2008. Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics 180: 391-408
Wang, S.H., Liu, J.K., Feng, Y.Y., Niu, X.L., Giovannoni, J. and Liu, Y.S. 2008. Altered plastid levels and potential for improved fruit nutrient content by downregulation of the tomato DDB1-interacting protein CUL4. Plant Journal 55: 89-103
Slocombe, S.P., Schauvinhold, I., McQuinn, R.P., Besser, K., Welsby, N.A., Harper, A., Aziz, N., Li, Y., Larson, T.R., Giovannoni, J., Dixon, R.A. and Broun, P. 2008. Transcriptomic and reverse genetic analyses of branched-chain fatty acid and acyl sugar production in Solanum pennellii and Nicotiana benthamiana. Plant Physiol 148: 1830-1846
Portnoy, V., Benyamini, Y., Bar, E., Harel-Beja, R., Gepstein, S., Giovannoni, J.J., Schaffer, A.A., Burger, J., Tadmor, Y., Lewinsohn, E. and Katzir, N. 2008. The molecular and biochemical basis for varietal variation in sesquiterpene content in melon (Cucumis melo L.) rinds. Plant Molecular Biology 66: 647-661
Datema, E., Mueller, L.A., Buels, R., Giovannoni, J.J., Visser, R.G.F., Stiekema, W.J. and van Ham, R.C.H.J. 2008. Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. Bmc Plant Biol 8: 34
Cara, B. and Giovannoni, J.J. 2008. Molecular biology of ethylene during tomato fruit development and maturation. Plant Sci 175: 106-113
Barry, C.S., McQuinn, R.P., Chung, M.Y., Besuden, A. and Giovannoni, J.J. 2008. Amino acid substitutions in homologs of the STAY-GREEN protein are responsible for the green-flesh and chlorophyll retainer mutations of tomato and pepper. Plant Physiology 147: 179-187
Akhtar, T.A., McQuinn, R.P., Naponelli, V., Gregory, J.F., Giovannoni, J.J. and Hanson, A.D. 2008. Tomato gamma-glutamyl hydrolases: Expression, characterization, and evidence for heterodimer formation. Plant Physiology 148: 775-785
Giovannoni, J., . 2007. Fruit Ripening Mutants Yield Insights Into Ripening Control. Current Opinion in Plant Biology 10: 283-289
Giovannoni, J., . 2007. A New Plant Gene in the Pathway to Vitamin C. PNAS USA 104: 9109-9110
Kelleher, C., R. Chiu, H. Shin, I. Bosdet, M. Krzywinski, C. Fjell, J. Wilkin, T. Yin, S. DiFazio, J. Ali, J. Asano, S. Chan, A. Cloutier, N. Girn, S. Leach, J. Giovannoni, J. Grimwood, G. Tuskan, C. Douglas. 2007. A Physical Map of the Highly Heterozygous Populus Genome: Integration With the Genome Sequence and Genetic Map and Analysis of Haplotype Variation. The Plant Journal 50: 1063-1078
Barry, C., J. Giovannoni. 2007. Ethylene and Fruit Ripening. J. of Plant Growth Regulation 26: 143-159
Fei, Z., X. Tang, R. Alba, J. Giovannoni. 2006. Tomato Expression Database (TED): A Suite of Data Presentation and Analysis Tools. Nucleic Acids Research 34: D766
Barry, C. S., J. J. Giovannoni. 2006. Ripening in the Tomato Green-ripe Mutant is Inhibited by Ectopic Expression of a Protein that Disrupts Ethylene Signaling. Proc Natl Acad USA 103: 7923-7928
Mueller, L. A., S. D. Tanksley, J. J. Giovannoni, J. Van Eck, S. Stack, D. Choi, B. D. Kim, M. Chen, Z. Cheng, C. Li, H. Ling, Y. Xue, G. Seymour, G. Bishop, G. Bryan, R. Sharma, J. Khurana, A. Tyagi, D. Chattopadhyay, N. K. Singh, W. Stiekema, P. Lindhout, T. Jesse, R. K. Lankhorst, M. Bouzayen, D. Shibata, S. Tabata, A. Granell, M. A. Botella, G. Giuliano, L. Frusciante, M. Causse, D. Zamir. 2005. The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (SOL). Comparative and Functional Genomics 6: 153-158
Moore, S., P. Payton, M. Wright, S. Tanksley, J. Giovannoni. 2005. Utilization of Tomato Microarrays for Comparative Gene Expression Analysis in the Solanaceae. Journal of Experimental Botany 56: 2885-2895
Li, C., A. L. Schilmiller, G. Liu, G. I. Lee, S. Jayanty, C. Sageman, J. Vrebalov, J. J. Giovannoni, K. Yagi, Y. Kobayashi, G. A. Howe. 2005. Role of Beta-Oxidation in Jasmonate Biosynthesis and Systemic Wound Signaling in Tomato. Plant Cell 17: 971-986
Giovannoni, J. J., S. El-Rakshy. 2005. Genetic Regulation of Tomato Fruit Ripening and Development and Implementation of Associated Genomics Tools. Acta Horticulturae 682: 63-72
Barry, C., R. P. McQuinn, A. J. Thompson, G. B. Seymour, D. Grierson, J. J. Giovannoni. 2005. Ethylene Insensitivity Conferred by the Green-ripe (Gr) and Never-ripe 2 (Nr-2) Ripening Mutants of Tomato. Plant Physiology 138: 267-275
Liu, Y., S. Roof, Z. Ye, C. Barry, A. van Tuinen, J. Vrebalov, C. Bowler, J. Giovannoni. 2004. Manipulation of Light Signal Transduction as a Means of Modifying Fruit Nutritional Quality in Tomato. Proceedings of the National Academy of Sciences, USA 101: 9897-9902
Giovannoni, J., . 2004. Genetic Regulation of Fruit Development and Ripening. The Plant Cell 16: S170 -180
Basset, G. J. C., E. P. Quinlivan, S. Ravanel, F. Rébeillé, B. P. Nichols, K. Shinozaki, M. Seki, L. C. Adams-Phillips, J. J. Giovannoni, J. F. Gregory III, A. D. Hanson. 2004. Folate synthesis in plants: The p-aminobenzoate branch is initiated by a bifunctional PabA-PabB protein that is targeted to plastids. Proceedings of the National Academy of Sciences, USA 101: 1496-1501
Adams-Phillips, L., C. Barry, P. Kannan, J. Leclercq, M. Bouzayen, J. Giovannoni. 2004. Evidence that CTR1-mediated Ethylene Signal Transduction in Tomato is Encoded by a Multigene Family Whose Members Display Distinct Regulatory Features. Plant Molecular Biology 54: 387-404
Adams-Phillips, L., C. Barry, J. Giovannoni. 2004. Signal transduction systems regulating fruit ripening. Trends in Plant Science 9: 331-338
Vrebalov, J., D. Ruezinsky, V. Padmanabhan, R. White, D. Medrano, R. Drake, W. Schuch, J. Giovannoni. 2002. A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296: 343-346
Wilkinson, J., M. Lanahan, H. Yen, J. Giovannoni, H. Klee. 1995. An Ethylene-inducible Component of Signal Transduction Encoded by Never-ripe. Science 270: 1807-1809
Features
Features
How do fruits ripen?
feature released -2008
Learning the genetic basis of fruit ripening could significantly impact the quality and availability of certain foods. This knowledge would be particularly useful in countries where food spoilage due to over-ripening is a cause of hunger.
Jim Giovannoni’s laboratory at BTI is working to understand the process by focusing on the genes and regulatory networks that control fruit ripening in tomato – knowledge that will have applications in other plants such as pepper, peach, pineapple, banana, strawberry and melon. Because many fruits ripen in response to the release of the hormone ethylene, understanding the mechanism that controls the plant’s sensitivity to ethylene can lead to basic knowledge about the ripening process.
In studying mutant tomato plants that produce only unripe tomatoes,Giovannoni’s team discovered an alteration in a gene called Gr, or Greenripe, that causes overproduction of a certain protein in the fruit that decreases the fruit’s sensitivity to ethylene. So, though the plants produce ethylene in normal amounts, the fruit does not respond to it and, therefore, fails to ripen. Being able to control the production of this protein,which would make the fruit under- or over-sensitive to ethylene, could lead to the ability to speed or delay the ripening process.
Giovannoni further found that overproduction of the Gr protein throughout the plant has no effect on any part of the plant except the fruit. This discovery is important because it indicates there are constituents specific to the fruit involved in its response to ethylene.
The next step in the research is to develop transgenic tomato plants in which the Gr gene has been“knocked out,” or disabled, so that the plants are no longer able to produce the Gr protein. This work will demonstrate whether or not normal Gr expression plays a significant role in ripening. Giovannoni predicts that these plants will be highly sensitive to ethylene and will, therefore, ripen early.
The ability to control the ripening process by controlling the ethylene response could lead to fruit, such as strawberry, papaya and even tomato, that have a longer shelf life. Because ripening is directly related to fruit flavor, texture and nutrient content, these discoveries could lead to higher quality food as well.
Toward a Better Tomato.
feature released -2007
Most shoppers in America have access to a wide selection of fresh fruits and vegetables year-round, but these rarely measure up to home grown varieties. “In general, things are harvested very prematurely so that they have the shelf life and the firmness to survive shipping,” Giovannoni explains. “What’s always lost in that tradeoff is taste, appearance, aroma—things that are associated with quality.”
To make store-bought fruit more palatable, agricultural scientists need a better understanding of how fruits “decide” when and how much to ripen. Giovannoni’s lab studies tomatoes and other plants to find the genes responsible for that decision. In 2004 they discovered several such genes, including two that may play a role in a broad range of species. The lab is now working to find similar genes that cooperate with these genes to regulate ripening and associated quality characteristics.
Giovannoni’s group also participates in a broader effort, with others at BTI and in nine foreign countries, to map and sequence the tomato genome. The completed genome will represent a giant step toward unlocking tomato’s inner workings, just as the Human Genome Project did for people. In a related project, the lab uses microarrays and computer analysis to learn how groups of genes switch on and off at the right time at each stage of ripening. This eagle’s eye view of the dynamics of development enables them to compare the process across different species, and to pick out genes that may control the timing of ripening.
News
2013
2012
2011
Lab Members
Lab Members
Jim Giovannoni
Professor
Office/Lab: 429/426
jjg33@cornell.edu
Office: 607-254-1259
Lab: 607-254-1259
Professor
Office/Lab: 429/426
jjg33@cornell.edu
Office: 607-254-1259
Lab: 607-254-1259
Silin Zhong
Human Frontier Science Program
Office/Lab: 421/424
sz284@cornell.edu
Office:
Lab: 607-254-1254
Human Frontier Science Program
Office/Lab: 421/424
sz284@cornell.edu
Office:
Lab: 607-254-1254
PGRP
Plant Genome Research Program
Research Project – Ripening and lycopene accumulation in tomato
Participating Interns
2012 – Interns
2011 – Interns
2010 – Interns
2009 – Interns
2008 – Interns
2007 – Interns
2006 – Interns
2005 – Interns
2004 – Interns
