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Jim Giovannoni
 &emdash;  Professor/USDA Scientist

Jim Giovannoni
Office/Lab: 429/426
  • Adjunct Professor, Section of Plant Biology
  • School of Integrative Plant Science
  • Cornell University
Graduate Fields: Horticulture; Plant Breeding; Plant Biology


  • Nonuniform gene expression pattern detected along the longitudinal axis in the matured rice leaf 2015

    Li, N., Chen, Y-R., Ding, Z., Li, P., Wu Y., Zhang, A., Yu, S., Giovannoni, J.J., Fei, Z., Zhang, W., Xiang, J.Z., Xu, C., Liu, B., and Zhong, S.
    Scientific Reports 5,  Article number: 8015
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  • Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits 2015

    Freilich, S., Lev, S., Gonda, I., Reuveni, E., Portnoy, V., Oren, E., Lohse, M., Galpaz, N., Bar, E., Tzuri, G., Wissotsky, G., Meir, A., Burger, J., Tadmor, Y., Schaffer, A., Fei, Z., Giovannoni, J., Lewinsohn, E., and Katzir, N.
    BMC Plant Biology 15,  71
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  • Selection of low-variance expressed Malus x domestica (apple) genes for use as quantitative PCR reference genes (housekeepers). Tree Genetics & Genomes, 10, 751-759 2014

    Bowen, J., Ireland, H.S., Crowhurst, R., Luo, Z.W., Watson, A.E., Foster, T., Gapper, N., Giovanonni, J.J., Mattheis, J.P., Watkins, C., Rudell, D., Johnston, J.W., and Schaffer, R.J.
    Tree Genetics & Genomes 10,  751-759
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  • The PH gene determines fruit acidity and contributes to the evolution of sweet melons 2014

    Cohen, S., Itkin, M., Yeselson, Y., Tzuri, G., Portnoy, V., Harel-Baja, R., Lev, S., Sa'ar, U., Davidovitz-Rikanati, R., Baranes, N., Bar, E., Wolf, D., Petreikov, M., Shen, S., Ben-Dor, S., Rogachev, I., Aharoni, A., Ast, T., Schuldiner, M., Belausov, E., Eshed, R., Ophir, R., Sherman, A., Frei, B., Neuhaus, H.E., Xu, Y., Fei, Z., Giovannoni, J., Lewinsohn, E., Tadmor, Y., Paris, H.S., Katzir, N., Burger, Y., and Schaffer, A.A.
    Nature Communications 5,  4026
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  • The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics, 46, 1034-1038 2014

    Bolger, A., Scossa, F., Bolger, M.E., Lanz, C., Maumus, F., Tohge, T., Quesneville, H., Alseekh, S., Sorensen, I., Lichtenstein, G., Fich, E.A., Conte, M., Keller, H., Schneeberger, K., Schwacke, R., Ofner, I., Vrebalov, J., Xu, Y., Osorio, S., Aflitos, S.A., Schijlen, E., Jimenez-Gomez, J.M., Ryngajllo, M., Kimura, S., Kumar, R., Koenig, D., Headland, L.R., Maloof, J.N., Sinha, N., van Ham, R.C., Lankhorst, R.K., Mao, L., Vogel, A., Arsova, B., Panstruga, R., Fei, Z., Rose, J.K., Zamir, D., Carrari, F., Giovannoni, J.J., Weigel, D., Usadel, B., and Fernie, A.R.
    Nature Genetics 46,  1034-1038
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  • Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nature Biotechnology, 31, 154-159 2013

    Zhong, S., Fei, Z., Chen, Y.R., Zheng, Y., Huang, M., Vrebalov, J., McQuinn, R., Gapper, N., Liu, B., Xiang, J., Shao, Y., and Giovannoni, J.J .
    Nature Biotechnology 31,  154-159
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  • The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions 2012

    Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W., Zhang, H., Zheng, Y., Mao, L., Ren, Y., Wang, Z., Min, J., Guo, X., Murat, F., Ham, B., Zhang, Z., Gao, S., Huang, M., Xu, Y., Zhong, S., Bombarely, A., Mueller, L., 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., Wang, J., Li, Y., Fei, Z., and Xu, Y.
    Nature Genetics 45,  51-58
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  • Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case 2012

    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.
    Proteomics 12,  761-774
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  • 2013. Catabolism of L-methionine in the formation of sulfur and other volatiles in melon (Cucumis melo L.) fruit 2013

    Gonda, I., Lev, S., Bar, E., Sikron, N., Portnoy, V., Davidovich-Rikanati, R., Burger, J., Schaffer, A.A., Tadmor, Y., Giovannonni, J.J., Huang, M.Y., Fei, Z.J., Katzir, N., Fait, A., and Lewinsohn, E .
    Plant J. 74,  458-472
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  • The Tomato Genome Consortium. A snapshot of the emerging tomato genome sequence. 2009

    The Plant Genome 2,  78-92
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  • Regulatory Networks Controlling Ripening. In The Molecular Biology and Biochemistry of Fruit Ripening 2013

    Ampopho, B., Chapman, N., Seymour, G.B., and Giovannoni, J.J.
    Seymour, G.B., Poole, M., Giovannoni, J.J. and Tucker, G. eds) John Wiley & Sons, Inc.,  pp. 189-206
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  • Comparative genomics reveals candidate carotenoid pathway regulators of ripening watermelon fruit 2013

    Grassi, S., Piro, G., Lee, J.M., Zheng, Y., Fei, Z., Dalessandro, G., Giovannoni, J.J., and Lenucci, M.S.
    BMC Genomics 14,  781
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  • Catalyzing plant science research with RNA-seq. 2013

    Martin, L.B.B., Fei, Z.J., Giovannoni, J.J., and Rose, J.K.C.
    Frontiers in Plant Science 4,  66
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  • The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (SOL) 2005

    Mueller, L. A., Tanksley, S.D., Giovannoni, J., Van Eck, J., Stack, S., Choi, D., Kim, B.D., Chen, M., Cheng, Z., Li, C., Ling, H., Xue, Y., Seymour, G., Bishop, G., Bryan, G., Sharma, R., Khurana, J., Tyagi, A., Chattopadhyay, D., Singh, N.K., Stiekema, W., Lindhout, P., Jesse, T., Lankhorst, R.K., Bouzayen, M., Shibata, D., Tabata, S., Granell, A., Botella, M.A., Giuliano, G., Frusciante, L., Causse, M., and Zamir, D.
    Comparative and Functional Genomics 6,  153-158
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  • Molecular and genetic regulation of fruit ripening 2013

    Gapper, N.E., McQuinn, R.P., and Giovannoni, J.J.
    Plant Molecular Biology 82,  575-591
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  • Biomarker development for external CO2 injury prediction in apples through exploration of both transcriptome and DNA methylation changes. AoB Plants, 5, plt021 2013

    Gapper, N.E., Rudell, D.R., Giovannoni, J.J., and Watkins, C.B.
    AoB Plants 5,  plt021
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  • Loss of Plastoglobule Kinases ABC1K1 and ABC1K3 Causes Conditional Degreening, Modified Prenyl-Lipids, and Recruitment of the Jasmonic Acid Pathway. Plant Cell, 25, 1818-1839 2013

    Lundquist, P.K., Poliakov, A., Giacomelli, L., Friso, G., Appel, M., McQuinn, R.P., Krasnoff, S.B., Rowland, E., Ponnala, L., Sun, Q., and van Wijk, K.J.
    Plant Cell 25,  1818-1839
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  • A STAY-GREEN protein SlSGR1 regulates lycopene and beta-carotene accumulation by interacting directly with SlPSY1 during ripening processes in tomato. New Phytologist, 198, 442-452 2013

    Luo, Z., Zhang, J., Li, J., Yang, C., Wang, T., Ouyang, B., Li, H., Giovannoni, J., and Ye, Z.
    New Phytologist 198,  442-452
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  • Differential Regulation of Salmonella Typhimurium Genes Involved in O-Antigen Capsule Production and Their Role in Persistence Within Tomato Fruit. Molecular Plant-Microbe Interactions, 26, 793-800 2013

    Marvasi, M., Cox, C.E., Xu, Y.M., Noel, J.T., Giovannoni, J.J., and Teplitski, M.
    Molecular Plant-Microbe Interactions 26,  793-800
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  • Altered chloroplast development and delayed fruit ripening caused by mutations in a zinc metalloprotease at the lutescent2 locus of tomato 2012

    Barry, C.S., Aldridge, G.M., Herzog, G., Ma, Q., McQuinn, R.P., Hirschberg, J., and Giovannoni, J.J.
    Plant Physiology 159,  1086-1098
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  • Functional characterization of a tomato COBRA-like gene functioning in fruit development and ripening. BMC Plant Biol., 12, 211 2012

    Cao, Y., Tang, X., Giovannoni, J., Xiao, F., and Liu, Y.
    BMC Plant Biol. 12,  211
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  • A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters 2012

    Chen, Y.R., Zheng, Y., Liu, B., Zhong, S., Giovannoni, J., and Fei, Z.
    Plant Methods 8,  41
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  • 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 2012

    Goyal, R.K., Kumar, V., Shukla, V., Mattoo, R., Liu, Y.S., Chung, S.H., Giovannoni, J.J., and Mattoo, A.K.
    Planta 235,  453-471
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  • Molecular analysis of softening and ethylene synthesis and signaling pathways in a non-softening apple cultivar, ‘Honeycrisp’ and a rapidly softening cultivar, ‘McIntosh’ 2012

    Harb, J., Gapper, N.E., Giovannoni, J.J., and Watkins, C.B.
    Postharvest Biology and Technology 64,  94-103
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  • 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 2012

    Lee, J.M., Joung, J.G., McQuinn, R., Chung, M.Y., Fei, Z., Tieman, D., Klee, H., and Giovannoni, J.
    The Plant Journal 70,  191-204
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  • The tomato UV-damaged DNA-binding protein-1 (DDB1) is implicated in pathogenesis-related (PR) gene expression and resistance to Agrobacterium tumefaciens 2012

    Liu, J.K., Li, H.J., Miao, M., Tang, X.F., Giovannoni, J., Xiao, F.M., and Liu, Y.S.
    Molecular Plant Pathology 13,  123-134
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  • A role of tomato UV-damaged DNA binding protein 1 (DDB1) in organ size control via an epigenetic manner. PLoS ONE, 7(8): e42621 2012

    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.
    PLoS ONE 7(8),  e42621
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  • Differential control of ethylene responses by GREEN-RIPE and GREEN-RIPE LIKE1 provides evidence for distinct ethylene signaling modules in tomato 2012

    Ma, Q., Du, W.Y., Brandizzi, F., Giovannoni, J.J., and Barry, C.S.
    Plant Physiology 160,  1968-1984
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  • Integrative comparative analyses of transcript and metabolite profiles from pepper and tomato ripening and development stages uncovers species-specific patterns of network regulatory behavior 2012

    Osorio, S., Alba, R., Nikoloski, Z., Kochevenko, A., Fernie, A.R., and Giovannoni, J.J.
    , 159, 1713-1729 159,  1713-1729
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  • Uniform ripening encodes a Golden 2-like transcription factor regulating tomato fruit chloroplast development 2012

    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.
    Science 336,  1711-1715
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  • Virus-induced gene complementation reveals a transcription factor network in modulation of tomato fruit ripening 2012

    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.
    Scientific Reports 2,  836
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  • Regulatory control of high levels of carotenoid accumulation in potato tubers 2011

    Zhou, X.J., Mcquinn, R., Fei, Z.J., Wolters, A.M.A., Van Eck, J., Brown, C., Giovannoni, J.J., and Li, L.
    Environ 34,  1020-1030
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  • High-throughput Illumina strand-specific RNA sequencing library preparation 2011

    Zhong, S., Joung, J.G., Zheng, Y., Chen, Y.R., Liu, B., Shao, Y., Xiang, J.Z., Fei , Z., and Giovannoni, J.J.
    Cold Spring Harb. Protoc. 2011,  940-949
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  • A SEPALLATA gene is involved in the development and ripening of strawberry (FragariaXananassa Duch.) fruit, a non-climacteric tissue 2011

    Seymour, G.B., Ryder, C.D., Cevik, V., Hammond, J.P., Popovich, A., King, G.J., Vrebalov, J., Giovannoni, J.J., and Manning, K.
    Journal of Experimental Botany 62,  1179-1188
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  • Expression of ripening-related genes in cold-stored tomato fruit 2011

    Rugkong, A., McQuinn, R., Giovannoni, J.J., Rose, J.K.C., and Watkins, C.B.
    Postharvest Biol. Tec. 61,  1-14
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  • The tomato MADS-box transcription factor RIPENING INHIBITOR interacts with promoters involved in numerous ripening processes in a COLORLESS NONRIPENING-dependent Manner 2011

    Martel, C., Vrebalov, J., Tafelmeyer , P., and Giovannoni, J.J.
    Plant Physiol. 157,  1568-1579
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  • Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development 2011

    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.
    Plant J. 68,  999-1013
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  • 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 2011

    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.
    Plant Physiol. 157,  405-425
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  • Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation 2011

    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.
    Plant Cell 23,  3893-3910
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  • Genetics and control of tomato fruit ripening and quality attributes 2011

    Klee, H.J., and Giovannoni, J.J.
    Annu. Rev. Genet. 45,  41-59
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  • Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics 2011

    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.
    Nucleic Acids Research 39,  D1156-1163
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  • Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation 2011

    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.
    Plant Mol. Biol. 76,  1-18
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  • Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon 2011

    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.
    BMC Genomics 12,  252
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  • omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants 2010

    Milone, D.H., Stegmayer, G.S., Kamenetzky, L., Lopez, M., Lee, J.M., Giovannoni, J.J., and Carrari, F.
    BMC Bioinformatics 11,  438
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  • Genomic analysis of wild tomato introgressions determining metabolism- and yield-associated traits 2010

    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.
    Physiology 152,  1772-1786
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  • A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes 2010

    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.
    Theoretical and Applied Genetics 121,  511-533
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  • Branched-chain and aromatic amino acid catabolism into aroma volatiles inCucumis melo L. fruit 2010

    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.
    Journal of Experimental Botany 61,  1111-1123
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  • Harvesting the apple genome 2010

    Giovannoni, J.
    Nature Genetics 42,  822-823
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  • Integrative transcript and metabolite analysis of nutritionally enhanced DE-ETIOLATED1 downregulated tomato fruit. Plant Cell, 22, 1190-1215 2010

    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.
    Plant Cell 22,  1190-1215
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  • The regulation of MADS-box gene expression during ripening of banana and their regulatory interaction with ethylene. Journal of Experimental Botany, 61, 1523-1535 2010

    Elitzur, T., Vrebalov, J., Giovannoni, J.J., Goldschmidt, E.E., and Friedman, H.
    Journal of Experimental Botany 61,  1523-1535
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  • Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening 2010

    Costa, F., Alba, R., Schouten, H., Soglio, V., Gianfranceschi, L., Serra, S., Musacchi, S., Sansavini, S., Costa, G., Fei, Z.J., and Giovannoni, J.
    BMC Plant Biology 10,  229
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  • A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening 2010

    Chung, M.Y., Vrebalov, J., Alba, R., Lee, J., McQuinn, R., Chung, J.D., Klein , P., and Giovannoni, J.
    Plant Journal 64,  936-947
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  • Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development 2010

    Pan, I.L., McQuinn, R., Giovannoni, J.J., and Irish, V.F.
    , 61, 1795-1806 61,  1795-1806
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  • Cell wall metabolism in cold-stored tomato fruit 2010

    Rugkong, A., Rose, J.K.C., Lee, S.J., Giovannoni, J.J., O'Neill, M.A. and Watkins, C.B.
    Postharvest Biol. Tec. 57,  106-113
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  • Developmental and feedforward control of the expression of folate biosynthesis genes in tomato fruit 2010

    Waller, J.C., Akhtar, T.A., Lara-Nunez, A., Gregory, J.F., McQuinn, R.P., Giovannoni, J.J., and Hanson, A.D.
    Molecular Plant 3,  66-77
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  • Fleshy fruit expansion and ripening are regulated by the Tomato SHATTERPROOF gene TAGL1 2009

    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.
    Plant Cell 21,  3041-3062
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  • 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 2009

    Ponce-Valadez, M., Fellman, S.M., Giovannoni, J., Gan, S.S., and Watkins, C.B.
    Postharvest Biol. Tec. 51,  131-140
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  • Plant MetGenMAP: an integrative analysis system for plant systems biology 2009

    Joung, J.G., Corbett, A.M., Fellman, S.M., Tieman, D.M., Klee, H.J., Giovannoni , J.J., and Fei, Z.
    Plant Physiol. 151,  1758-1768
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  • Biology and genetic engineering of fruit maturation for enhanced quality and shelf-life 2009

    Matas, A.J., Gapper, N.E., Chung, M.Y., Giovannoni, J.J., and Rose, J.K.C.
    Curr. Opin. Biotech. 2o,  197-203
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  • Role of fluorescence in situ hybridization in sequencing the tomato genome 2009

    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.
    Cytogenet Genome Res. 124,  339-350
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  • Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae 2008

    Wang, Y., Diehl, A., Wu, F.N., Vrebalov, J., Giovannoni, J., Siepel, A., and Tanksley, S.D.
    Genetics 180,  391-408
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  • Altered plastid levels and potential for improved fruit nutrient content by downregulation of the tomato DDB1-interacting protein CUL4 2008

    Wang, S.H., Liu, J.K., Feng, Y.Y., Niu, X.L., Giovannoni, J., and Liu, Y.S.
    Plant Journal 55,  89-103
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  • Transcriptomic and reverse genetic analyses of branched-chain fatty acid and acyl sugar production in Solanum pennellii andNicotiana benthamiana. Plant Physiol., 148, 1830-1846 2008

    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.
    Plant Physiol. 148,  1830-1846
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  • The molecular and biochemical basis for varietal variation in sesquiterpene content in melon (Cucumis melo L.) rinds 2008

    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.
    Plant Molecular Biology 66,  647-661
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  • Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato 2008

    Datema, E., Mueller, L.A., Buels, R., Giovannoni, J.J., Visser, R.G.F., Stiekema, W.J., and van Ham, R.C.H.J.
    BMC Plant Biol. 8,  34
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  • Molecular biology of ethylene during tomato fruit development and maturation 2008

    Cara, B., and Giovannoni, J.J.
    Plant Sci. 175,  106-113
    Full text...
  • Amino acid substitutions in homologs of the STAY-GREEN protein are responsible for the green-flesh and chlorophyll retainer mutations of tomato and pepper 2008

    Barry, C.S., McQuinn, R.P., Chung, M.Y., Besuden, A., and Giovannoni, J.J.
    Plant Physiology 147,  179-187
    Full text...
  • Tomato gamma-glutamyl hydrolases: Expression, characterization, and evidence for heterodimer formation 2008

    Akhtar, T.A., McQuinn, R.P., Naponelli, V., Gregory, J.F., Giovannoni, J.J., and Hanson, A.D.
    Plant Physiology 148,  775-785
    Full text...
  • Fruit Ripening Mutants Yield Insights Into Ripening Control 2007

    Giovannoni, J.
    Curr. Opin. Plant Biol. 10,  283-289
    Full text...
  • A New Plant Gene in the Pathway to Vitamin C 2007

    Giovannoni, J.
    P. Natl. Acad. Sci. USA 104,  9109-9110
    Full text...
  • A Physical Map of the Highly Heterozygous Populus Genome: Integration With the Genome Sequence and Genetic Map and Analysis of Haplotype Variation 2007

    Kelleher, C., Chiu, R., Shin, H., Bosdet, I., Krzywinski, M., Fjell, C., Wilkin, J., Yin, T., DiFazio, S., Ali, J., Asano, J., Chan, S., Cloutier, A., Girn, N., Leach, S., Giovannoni, J., Grimwood, J., Tuskan, G., and Douglas, C.
    The Plant Journal 50,  1063-1078
    Full text...
  • Ethylene and Fruit Ripening 2007

    Barry, C., and Giovannoni, J.
    Journal of Plant Growth Regulation 26,  143-159
    Full text...
  • Tomato Expression Database (TED): A Suite of Data Presentation and Analysis Tools. Nucleic Acids Research, 34, D766 2006

    Fei, Z., Tang, X., Alba, R., and Giovannoni, J.
    Nucleic Acids Research 34,  D766
    Full text...
  • Ripening in the Tomato Green-ripe Mutant is Inhibited by Ectopic Expression of a Protein that Disrupts Ethylene Signaling 2006

    Barry, C. S., and Giovannoni, J.
    P. Natl. Acad. U S A 103,  7923-7928
    Full text...
  • Utilization of Tomato Microarrays for Comparative Gene Expression Analysis in the Solanaceae 2005

    Moore, S., Payton, P., Wright, M., Tanksley, S., Giovannoni, J.
    Journal of Experimental Botany 56,  2885-2895
    Full text...
  • Role of Beta-Oxidation in Jasmonate Biosynthesis and Systemic Wound Signaling in Tomato 2005

    Li, C., Schilmiller, A.L., Liu, G., Lee, G.I., Jayanty, S., Sageman, C., Vrebalov, J., Giovannoni, J., Yagi, K., Kobayashi, Y., and Howe, G.A.
    Plant Cell 17,  971-986
    Full text...
  • Genetic Regulation of Tomato Fruit Ripening and Development and Implementation of Associated Genomics Tools 2005

    Giovannoni, J., and El-Rakshy, S.
    Acta Hortic. 682,  63-72
    Full text...
  • Ethylene Insensitivity Conferred by the Green-ripe (Gr) and Never-ripe 2 (Nr-2) Ripening Mutants of Tomato 2005

    Barry, C., McQuinn, R.P., Thompson, A.J., Seymour, G.B., Grierson, D., and Giovannoni, J.
    Plant Physiology 138,  267-275
    Full text...
  • Manipulation of Light Signal Transduction as a Means of Modifying Fruit Nutritional Quality in Tomato 2004

    Liu, Y., Roof, S., Ye, Z., Barry, C., van Tuinen, A., Vrebalov, J., Bowler, C., and Giovannoni, J.
    P. Natl. Acad. Sci. U S A 101,  9897-9902
    Full text...
  • Genetic Regulation of Fruit Development and Ripening 2004

    Giovannoni, J.
    The Plant Cell 16,  S170 -180
    Full text...
  • Folate synthesis in plants: The p-aminobenzoate branch is initiated by a bifunctional PabA-PabB protein that is targeted to plastids 2004

    Basset, G. J. C., Quinlivan, E.P., Ravanel, S., Rébeillé, F., Nichols, B.P., Shinozaki, K., Seki, M., Adams-Phillips, L.C., Giovannoni, J., Gregory III, J.F., and Hanson, A.D.
    P. Natl. Acad. Sci. U S A 101,  1496-1501
    Full text...
  • Evidence that CTR1-mediated Ethylene Signal Transduction in Tomato is Encoded by a Multigene Family Whose Members Display Distinct Regulatory Features 2004

    Adams-Phillips, L., Barry, C., Kannan, P., Leclercq, J., Bouzayen, M., and Giovannoni, J.
    Plant Molecular Biology 54,  387-404
    Full text...
  • Signal transduction systems regulating fruit ripening 2004

    Adams-Phillips, L., Barry, C., and Giovannoni, J.
    Trends in Plant Science 9,  331-338
    Full text...
  • A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus 2002

    Vrebalov, J., Ruezinsky, D., Padmanabhan, V., White, R., Medrano, D., Drake, R., Schuch, W., and Giovannoni, J.
    Science 296,  343-346
    Full text...
  • An Ethylene-inducible Component of Signal Transduction Encoded by Never-ripe. Science, 270, 1807-1809 1995

    Wilkinson, J., Lanahan, M., Yen, H., Giovannoni, J., and Klee, H.
    Science 270,  1807-1809
    Full text...

Intern Projects

Ripening is a process by which the texture, color, flavor, and nutritional content of fruit is enhanced. These traits contribute to the healthfulness and desirability of the fruit as a food source. Clearly, understanding the processes behind fruit ripening are important in terms of nutrition, but also for commercial applications such as transportation and shelf-life. Thus, the focus of research in the Giovannoni lab is molecular and genetic analysis of fruit ripening and related signal transduction systems, using tomato as the model system. Recently, researchers in the lab isolated two genes, RIN and NOR, that are part of the master switch to induce ripening in tomatoes. In addition to identifying important regulatory components of ripening, the lab also investigates lycopene production. Lycopene is the pigment that gives tomatoes their red coloring and which is also suggested to inhibit degenerative diseases such as cancer and heart disease. Using a genomics approach, the lab is investigating the regulatory mechanisms behind accumulation of this important compound in different tomato varieties.

For more information about the Giovannoni lab, please visit the Plant Biology website. Additionally, the Giovannoni lab, in conjunction with other labs on campus has developed a resource for tomato genomics, the Tomato EST Database. Additional resources and information resulting from tomato genomics activities on the Cornell campus can be found at the Solanaceae Genomics Network site.

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    • Technology Area: Fruit Quality
    • Title: Ripening inhibition in the tomato Green-ripe mutant results from ectopic expression of a novel protein which disrupts ethylene signal transduction
    • US Patent/Application(s): 7,947,867
    • Publication: PNAS 2006
    • Technology Area: Fruit Quality
    • Title: Endo-1,4-.beta.-glucanase genes and their use in plants
    • US Patent/Application(s): 5,585,545
    • Publication: Plant J 1998
    • Technology Area: Fruit Quality
    • Title: NOR gene for use in manipulation of fruit quality and ethylene response
    • US Patent/Application(s): 6,762,347
    • Publication: Plant Cell 2004
    • Technology Area: Fruit Quality
    • Title: Rin gene compositions and methods for use thereof
    • US Patent/Application(s): 6,787,687
    • Publication: Science 2002
    • Technology Area: Fruit Quality
    • Title: Banana MADS-Box Genes for Banana Ripening Control
    • US Patent/Application(s): Provisional
    • Publication: J Exp Bot 2010

Research Utilization

The Giovannoni lab deploys genetic, genomic, and molecular approaches to study the biology of fruit development and ripening, primarily in tomato with some activities in melon, apple and banana. Tomato is an economically important crop, as well as an experimentally tractable model system for fleshy fruit development. As such, genes identified and characterized in the course of our research are likely to find application across the Solanaceae (e.g. tomato, pepper eggplant) and in additional fruit crops.

The lab currently has two major focus areas: transcriptome/epigenome dynamics during fruit development and ripening, and functional characterization of genes involved in ripening and nutrient quality. The lab works with numerous international collaborators to address these questions and to translate research findings from tomato to other fruit crops.

The Giovannoni lab has been a major contributor to the international tomato sequencing project and together with collaborators at BTI and around the world has generated a high quality whole-genome sequence. The lab will continue to lead efforts to close remaining gaps so that the Solanum lycopersicum genome can serve as a robust reference genome for comparison with wild relatives and breeding varieties. The lab is currently embarking on research projects that utilize the genome sequence for genome scale analyses focused on fruit biology.

In recent years the lab has discovered a number of genes that are important in overall ripening control, including several that underlie important fruit quality and shelf-life traits of interest to plant breeders. Current efforts focus on identifying genes controlling overall ripening processes in addition to specific pathways affecting fruit nutrient quality. We are currently testing several candidate genes in transgenic plants. Many genes identified in the lab have potential application toward crop improvement through traditional breeding, molecular breeding or transgenic approaches.

Collaboration and Consulting Opportunities

  • Genetic control of fruit quality and ripening
  • Fruit biology and physiology (pre and post-harvest)
  • Genome and epigenome sequencing and analysis
  • Transcriptome profiling

Collaborations and Consulting

In the News

Research Overview

USDA affiliation: Plant Molecular Biologist, USDA-ARS Robert W. Holley Center james.giovannoni@ars.usda.gov

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.