Peer reviewed articles:
- WA Bovenberg, RE Koes, HJJ Nijkamp and AJ Kool: Physical mapping nucleotide sequencing and expression in E. coli minicells of the Koes, R. E., Spelt, C. E., & Mol, J. N. M. (1989). The chalcone synthase multigene family of Petunia hybrida (V30): Differential, light-regulated expression during flower development and UV light induction. Plant Mol. Biol., 12, 213–225.
- Koes, R. E., Spelt, C. E., Reif, H. J., van den Elzen, P. J., Veltkamp, E., & Mol, J. N. (1986). Floral tissue of Petunia hybrida (V30) expresses only one member of the chalcone synthase multigene family. Nucleic Acids Res, 14(13), 5229–5239.
- Koes, R. E., Spelt, C. E., Mol, J. N. M., & Gerats, A. G. M. (1987). The chalcone synthase multigene family of Petunia hybrida (V30): Sequence homology, chromosomal localization and evolutionary aspects. Plant Mol. Biol., 10, 375–385.
- van Tunen, A. J., Koes, R. E., Spelt, C. E., van der Krol, A. R., Stuitje, A. R., & Mol, J. N. M. (1988). Cloning of the two chalcone flavanone isomerase genes from Petunia hybrida: Coordinate, light-regulated and differential expression of flavonoid genes. EMBO J., 7, 1257–1263.
- Mol, J. N. M., Koes, R. E., Gerats, A. G. M., & Stuitje, A. R. (1988). Cloned genes of phenylpropanoid metabolism. Plant Mol. Biol. Rep., 6, 274–279.
- van der Krol, A. R., Lenting, P. E., Veenstra, J., van der Meer, I. M., Koes, R. E., Gerats, A. G. M., Mol, J. N. M., & Stuitje, A. R. (1988). An anti-sense chalcone synthase gene in transgenic plants inhibits flower pigmentation. Nature, 333, 866–869.
- Koes, R. E., Spelt, C. E., & Mol, J. N. M. (1989). The chalcone synthase multigene family of Petunia hybrida (V30): Differential, light-regulated expression during flower development and UV light induction. Plant Mol. Biol., 12, 213–225.
- Koes, R. E., Spelt, C. E., van den Elzen, P. J. M., & Mol, J. N. M. (1989). Cloning and molecular characterization of the chalcone synthase multigene family of Petunia hybrida. Gene., 81, 245–257.
- Quattrocchio, F., Tolk, M., Coraggio, I., Mol, J. N. M., Viotti, A., & Koes, R. E. (1990). The maize zein gene zE19 contains two distinct promoters, which are independently activated in endosperm and anthers of transgenic Petunia plants. Plant Mol. Biol., 15, 81–93.
- van Tunen, A. J., Mur, L., Brouns, G. S., Rienstra, J.-D., Koes, R. E., & Mol, J. N. M. (1990). Pollen- and anther-specific chi promoters from petunia: Tandem promoter regulation of the chiA gene. Plant Cell, 2, 393–401.
- Koes, R. E., van Blokland, R., Quattrocchio, F., van Tunen, A. J., & Mol, J. N. M. (1990). Chalcone synthase promoters in petunia are active in pigmented and unpigmented cell types. Plant Cell, 2, 379–392.
- Quattrocchio, F., Wing, J. F., Leppen, H. T. C., Mol, J. N. M., & Koes, R. E. (1993). Regulatory genes controlling anthocyanin pigmentation are functionally conserved among plant species and have distinct sets of target genes. Plant Cell, 5, 1497–1512.
- Koes, R. E., Quattrocchio, F., & Mol, J. N. M. (1994). The flavonoid biosynthetic pathway in plants: function and evolution. BioEssays, 16(2), 123–132.
- Kroon, J., Souer, E., de Graaff, A., Xue, Y., Mol, J., & Koes, R. (1994). Cloning and structural analysis of the anthocyanin pigmentation locus Rt of Petunia hybrida: characterization of insertion sequences in two mutant alleles. Plant J., 5(1), 69–80.
- Huits, H. S. M., Gerats, A. G. M., Kreike, M. M., Mol, J. N. M., & Koes, R. E. (1994). Genetic control of dihydroflavonol 4-reductase gene expression in Petunia hybrida. Plant J., 6(3), 295–310.
- Huits, H. S. M., Koes, R. E., Wijsman, H. J. W., & Gerats, A. G. M. (1994). Genetic characterization of Act1, the activator of a non-autonomous transposable element from Petunia hybrida. Theor. Appl. Genet., 91, 110–117.
- Mol, J. N. M., Holton, T. A., & Koes, R. E. (1995). Floriculture: genetic engineering of commercial traits. Tr. in Biotech., 13, 350–355.
- Koes, R., Souer, E., van Houwelingen, A., Mur, L., Spelt, C., Quattrocchio, F., Wing, J. F., Oppedijk, B., Ahmed, S., Maes, T., Gerats, T., Hoogeveen, P., Meesters, M., Kloos, D., & Mol, J. N. M. (1995). Targeted gene inactivation in petunia by PCR-based selection of transposon insertion mutants. Proc. Natl. Acad. Sci. USA, 81, 8149–8153.
- Souer, E., Quattrocchio, F., de Vetten, N., Mol, J. N. M., & Koes, R. E. (1995). A general method to isolate genes tagged by a high copy number transposable element. Plant J., 7, 677–685.
- Mol, J. N. M., Holton, T. A., & Koes, R. E. (1995). Floriculture: genetic engineering of commercial traits. Tr. in Biotech., 13, 350–355.
- Souer, E., van Houwelingen, A., Kloos, D., Mol, J. N. M., & Koes, R. (1996). The no apical meristem gene of petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries. Cell, 85, 159–170.
- de Vetten, N., Quattrocchio, F., Mol, J., & Koes, R. (1997). The an11 locus controlling flower pigmentation in petunia encodes a novel WD-repeat protein conserved in yeast, plants and animals. Genes Dev., 11, 1422–1434.
- Quattrocchio, F., Wing, J. F., Va, K., De, Woude, Mol, J. N. M., & Koes, R. (1998). Analysis of bHLH and MYB domain proteins: species-specific regulatory differences are caused by divergent evolution of target anthocyanin genes. Plant J, 13(4), 475–488.
- Souer, E., van der Krol, A. R., Kloos, D., Spelt, C., Bliek, M., Mol, J., & Koes, R. (1998). Genetic control of branching pattern and floral identity during Petunia inflorescence development. Development, 125, 733–742.
- Mol, J., Grotewold, E., & Koes, R. (1998). How genes paint flowers and seeds. Trends Plant Sci., 3(6), 212–217.
- Alfenito, M. R., Souer, E., Goodman, C. D., Buell, R., Mol, J., Koes, R., & Walbot, V. (1998). Functional complementation of anthocyanin sequestration in the vacuole by widely divergent glutathione S-transferases. Plant Cell, 10, 1135–1149.
- van Houwelingen, A., Souer, E., Spelt, C., Kloos, D., Mol, J., & Koes, R. (1998). Analysis of flower pigmentation mutants generated by random transposon mutagenesis in Petunia hybrida. Plant J., 13, 39–50.
- van Houwelingen, A., Souer, E., Mol, J. N. M., & Koes, R. E. (1999). Epigenetic interactions between three dTph1 transposons in two homologous chromosomes activates a new excision-repair mechanism in petunia. Plant Cell, 11, 1319–1336.
- de Vetten, N., ter Horst, J., van Schaik, H.-P., den Boer, B., Mol, J., & Koes, R. (1999). A cytochome b5 is required for full activity of flavonoid 3’5’-hydroxylase, a cytochrome P450 involved in the formation of blue flower colors. Proc. Natl. Acad. Sci. USA., 96, 778–783.
- de Bruin, R., Spelt, K., Mol, J., Koes, R., & Quattrocchio, F. (1999). Selection of high-affinity phage antibodies from phage display libraries. Nature Biotechnol., 17, 397–399.
- Mol, J., Cornish, E., Mason, J., & Koes, R. (1999). Novel coloured flowers. Curr Opin Biotechnol, 10(2), 198–201.
- Quattrocchio, F., Wing, J., van der Woude, K., Souer, E., de Vetten, N., Mol, J., & Koes, R. (1999). Molecular analysis of the anthocyanin2 gene of Petunia and its role in the evolution of flower color. Plant Cell, 11, 1433–1444
- Verwoert, I., Meller-Harel, Y., van der Linden, K., Verbree, B., Koes, R., & Stuitje, A. (2000). The molecular basis of the high linoleic acid content in Petunia seed oil: analysis of a seed-specific linoleic acid mutant. Biochem Soc Trans, 28(6), 631–632.
- Spelt, C., Quattrocchio, F., Mol, J., & Koes, R. (2000). anthocyanin1 of petunia encodes a basic-Helix Loop Helix protein that directly activates structural anthocyanin genes. Plant Cell, 12, 1619–1631.
- Tobeña-Santamaria, R., Bliek, M., Ljung, K., Sandberg, G., Mol, J., Souer, E., & Koes, R. (2002). FLOOZY of petunia is a flavin monooxygenase-like protein required for the specification of leaf and flower architecture. Genes Dev., 6(6), 753–763.
- Spelt, C., Quattrocchio, F., Mol, J., & Koes, R. (2002). ANTHOCYANIN1 of petunia controls pigment synthesis, vacuolar pH, and seed coat development by genetically distinct mechanisms. Plant Cell, 14(9), 2121-35.
- Vandenbussche, M., Zethof, J., Souer, E., Koes, R., Tornielli, G. B., Pezzotti, M., Ferrario, S., Angenent, G. C., & Gerats, T. (2003). Toward the analysis of the petunia MADS box gene family by reverse and forward transposon insertion mutagenesis approaches: B, C, and D floral organ identity functions require SEPALLATA-like MADS box genes in petunia. Plant Cell, 15(11), 2680–2693.
- Koes, R., Verweij, C. W., & Quattrocchio, F. (2005). Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci., 5, 236–242.
- Angenent, G. C., Stuurman, J., Snowden, K. C., & Koes, R. (2005). Use of Petunia to unravel plant meristem functioning. Trends Plant Sci, 10(5), 243–250
- Quattrocchio, F., Verweij, W., Kroon, A., Spelt, C., Mol, J., & Koes, R. (2006). PH4 of petunia is an R2R3-MYB protein that activates vacuolar acidification through interactions with Basic-Helix-Loop-Helix transcription factors of the anthocyanin pathway. Plant Cell, 18, 1274–1291.
- Baumann, K., Perez-Rodriguez, M., Bradley, D., Venail, J., Bailey, P., Jin, H., Koes, R., Roberts, K., & Martin, C. (2007). Control of cell and petal morphogenesis by R2R3 MYB transcription factors. Development, 134(9), 1691–1701.
- Koes, R. (2008). Evolution and development of virtual inflorescences. Trends Plant Sci., 13(1), 1–3.
- Verweij, W., Spelt, C., di Sansebastiano, G. Pietro, Vermeer, J., Reale, L., Ferranti, F., Koes, R., & Quattrocchio, F. (2008). An H+ P-ATPase on the tonoplast determines vacuolar pH and flower colour. Nature Cell Biology, 10(12), 1456–1462.
- Rebocho, A. B., Bliek, M., Kusters, E., Castel, R., Procissi, A., Roobeek, I., Souer, E., & Koes, R. (2008). Role of EVERGREEN in the development of the cymose petunia inflorescence. Dev Cell, 15(3), 437–447.
- Souer, E., Rebocho, A. B., Bliek, M., Kusters, E., de Bruin, R. A., & Koes, R. (2008). Patterning of inflorescences and flowers by the F-Box Protein DOUBLE TOP and the LEAFY Homolog ABERRANT LEAF AND FLOWER of Petunia. Plant Cell, 20, 2033–2048.
- Vandenbussche, M., Horstman, A., Zethof, J., Koes, R., Rijpkema, A. S., & Gerats, T. (2009). Differential recruitment of WOX transcription factors for lateral development and organ fusion in Petunia and Arabidopsis. Plant Cell, 21(8), 2269–2283
- Rijpkema, A. S., Vandenbussche, M., Koes, R., Heijmans, K., & Gerats, T. (2010). Variations on a theme: changes in the floral ABCs in angiosperms. Semin Cell Dev Biol, 21(1), 100–107.
- Moyroud, E., Kusters, E., Monniaux, M., Koes, R., & Parcy, F. (2010). LEAFY blossoms. Trends Plant Sci, 15(6), 346–352.
- Castel, R., Kusters, E., & Koes, R. (2010). Inflorescence development in petunia: through the maze of botanical terminology. J Exp Bot, 61(9), 2235–2246.
- Zenoni, S., D’Agostino, N., Tornielli, G. B., Quattrocchio, F., Chiusano, M. L., Koes, R., Zethof, J., Guzzo, F., Delledonne, M., Frusciante, L., Gerats, T., & Pezzotti, M. (2011). Revealing impaired pathways in the an11 mutant by high-throughput characterization of Petunia axillaris and Petunia inflata transcriptomes. Plant J, 68(1), 11–27.
- Faraco, M., di Sansebastiano, G. P., Spelt, K., Koes, R. E., & Quattrocchio, F. M. (2011). One protoplast is not the other! Plant Physiol, 156(2), 474–478.
- Verhoef, N., Yokota, T., Shibata, K., de Boer, G. J., Gerats, T., Vandenbussche, M., Koes, R., & Souer, E. (2013). Brassinosteroid biosynthesis and signalling in Petunia hybrida. J Exp Bot, 64(8), 2435–2448
- Quattrocchio, F. M., Spelt, C., & Koes, R. (2013). Transgenes and protein localization: myths and legends. Trends Plant Sci, 18(9), 473–476
- della Pina, S., Souer, E., & Koes, R. (2014). Arguments in the evo-devo debate: say it with flowers! J Exp Bot, 65(9), 2231–2242.
- Faraco, M., Spelt, C., Bliek, M., Verweij, W., Hoshino, A., Espen, L., Prinsi, B., Jaarsma, R., Tarhan, E., de Boer, A. H., di Sansebastiano, G. P., Koes, R., & Quattrocchio, F. M. (2014). Hyperacidification of vacuoles by the combined action of two different P-ATPases in the tonoplast determines flower color. Cell Rep, 6(1), 32–43.
- Kusters, E., della Pina, S., Castel, R., Souer, E., & Koes, R. (2015). Changes in cis-regulatory elements of a key floral regulator are associated with divergence of inflorescence architectures. Development, 142(16), 2822–2831.
- Appelhagen, I., Nordholt, N., Seidel, T., Spelt, K., Koes, R., Quattrochio, F., Sagasser, M., & Weisshaar, B. (2015). TRANSPARENT TESTA 13 is a tonoplast P3A -ATPase required for vacuolar deposition of proanthocyanidins in Arabidopsis thaliana seeds. Plant J, 82(5), 840–849.
- Kiferle, C., Fantini, E., Bassolino, L., Povero, G., Spelt, C., Buti, S., Giuliano, G., Quattrocchio, F., Koes, R., Perata, P., & Gonzali, S. (2015). Tomato R2R3-MYB Proteins SlANT1 and SlAN2: Same Protein Activity, Different Roles. PLoS One, 10(8), e0136365.
- Li, Y., Provenzano, S., Bliek, M., Spelt, C., Appelhagen, I., Machado de Faria, L., Verweij, W., Schubert, A., Sagasser, M., Seidel, T., Weisshaar, B., Koes, R., & Quattrocchio, F. (2016). Evolution of tonoplast P-ATPase transporters involved in vacuolar acidification. New Phytol, 211(3),
- Bombarely, A., Moser, M., Amrad, A., Bao, M., Bapaume, L., Barry, C. S., Bliek, M., Boersma, M. R., Borghi, L., Bruggmann, R., Bucher, M., D’Agostino, N., Davies, K., Druege, U., Dudareva, N., Egea-Cortines, M., Delledonne, M., Fernandez-Pozo, N., Franken, P., Laurie Grandont, L., Heslop-Harrison, J.S., Hintzsche,J., Johns,M., Koes,R., Lv,X., Lyons,E., Malla,D., Martinoia,E., Mattson, N.S., Morel, P., Mueller,L.A., Muhlemann, J., Nouri,E., Passeri, V., Pezzotti, M., Qi, Q., Reinhardt, D., Rich, M., Richert-Pöggeler,K.R., Robbins, T.P., Schatz, M.C., Schranz, M.E., Schuurink, R.C., Schwarzacher, T., Spelt, K., Tang, H., Urbanus S.L., Vandenbussche, M., Vijverberg, K., Villarino G.H., Warner, R.M., Weiss, J., Yue, Z., Zethof, J., Quattrocchio, F. 6 , Sims, T.L. & Kuhlemeier, C. (2016). Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature Plants, 2(6), 16074.
- Passeri, V., Koes, R., & Quattrocchio, F. M. (2016). New challenges for the design of high value plant products: Stabilization of anthocyanins in plant vacuoles. Frontiers in Plant Science, 7, doi: 10.3389/
- Verweij, W., Spelt, C. E., Bliek, M., de Vries, M., Wit, N., Faraco, M., Koes, R., & Quattrocchio, F. M. (2016). Functionally similar WRKY proteins regulate vacuolar acidification in petunia and hair development in Arabidopsis. Plant Cell, 28(3), 786–803.
- Prinsi, B., Negri, A. S., Quattrocchio, F. M., Koes, R. E., & Espen, L. (2016). Proteomics of red and white corolla limbs in petunia reveals a novel function of the anthocyanin regulator ANTHOCYANIN1 in determining flower longevity. J Proteomics, 131, 38–47.
- Li, Y., Iqbal, M., Zhang, Q., Spelt, C., Bliek, M., Hakvoort, H. W. J., Quattrocchio, F. M., Koes, R., & Schat, H. (2017). Two Silene vulgaris copper transporters residing in different cellular compartments confer copper hypertolerance by distinct mechanisms when expressed in Arabidopsis thaliana. New Phytol, 215(3), 1102–1114.
- Faraco, M., Li, Y., Li, S., Spelt, C., di Sansebastiano, G. P., Reale, L., Ferranti, F., Verweij, W., Koes, R., & Quattrocchio, F. M. (2017). A tonoplast P3B-ATPase mediates fusion of two types of vacuoles in petal cells. Cell Rep, 19(12), 2413–2422.
- Leijten, W., Koes, R., Roobeek, I., & Frugis, G. (2018). Translating Flowering Time From Arabidopsis thaliana to Brassicaceae and Asteraceae Crop Species. Plants (Basel), 7(4).
- Strazzer, P., Spelt, C. E. E., Li, S., Bliek, M., Federici, C. T. T., Roose, M. L. L., Koes, R., & Quattrocchio, F. M. M. (2019). Hyperacidification of Citrus fruits by a vacuolar proton-pumping P-ATPase complex. Nature Commun, 10(1), 744.
- Paauw, M., Koes, R., & Quattrocchio, F. M. M. (2019). Alteration of flavonoid pigmentation patterns during domestication of food crops. J Exp Bot, 70(15), 3719–3735.
- Zhang, H., Koes, R., Shang, H., Fu, Z., Wang, L., Dong, X., Zhang, J., Passeri, V., Li, Y., Jiang, H., Gao, J., Li, Y., Wang, H., & Quattrocchio, F. M. (2019). Identification and functional analysis of three new anthocyanin R2R3-MYB genes in Petunia. Plant Direct, 3(1), e00114.
- Amato, A., Cavallini, E., Walker, A. R. R., Pezzotti, M., Bliek, M., Quattrocchio, F., Koes, R., Ruperti, B., Bertini, E., Zenoni, S., & Tornielli, G. B. B. (2019). The MYB5-driven MBW complex recruits a WRKY factor to enhance the expression of targets involved in vacuolar hyper-acidification and trafficking in grapevine. Plant J, 99(6), 1220–1241.
- Li, S., Cerri, M., Strazzer, P., Li, Y., Spelt, C., Bliek, M., Vandenbussche, M., Martínez-Calvó, E., Lai, B., Reale, L., Koes, R., & Quattrocchio, F. M. (2021). An ancient RAB5 governs the formation of additional vacuoles and cell shape in petunia petals. Cell Reports, 36(13), 109749.
- Massa, S., Pagliarello, R., Cemmi, A., di Sarcina, I., Bombarely, A., Demurtas, O. C., Diretto, G., Paolini, F., Petzold, H. E., Bliek, M., Bennici, E., del Fiore, A., de Rossi, P., Spelt, C., Koes, R., Quattrocchio, F., & Benvenuto, E. (2022). Modifying anthocyanins biosynthesis in tomato hairy roots: A test bed for plant resistance to Ionizing radiation and antioxidant properties in space. Frontiers in Plant Science, 13, 65.
- Pagliarello, R., Bennici, E., Cemmi, A., di Sarcina, I., Spelt, C., Nardi, L., del Fiore, A., de Rossi, P., Paolini, F., Koes, R., Quattrocchio, F., Benvenuto, E., & Massa, S. (2023). Designing a novel tomato ideotype for future cultivation in space manned missions. Frontiers in Astronomy and Space Sciences, 9, 438.
- Strazzer, P., Verbree, B., Bliek, M., Koes, R., & Quattrocchio, F. M. (2023). The Amsterdam petunia germplasm collection: A tool in plant science. Frontiers in Plant Science, 14. https://doi.org/10.3389/fpls.2023.1129724
- Passeri, V., Li, S., Strazzer, P., Martínez I Calvó’, E., Senden, E., Guzzo, F., Commisso, M., Spelt, C., Vandenbussche, M., Bliek, M., Verweij, W., Koes, R., & Quattrocchio, F. M. (2023). Role of the metallo-reductase FADING and vacuolinos in anthocyanin degradation in flowers and fruits. BioRxiv, doi: 10.1101/2023.12.21.569356.
- Zhang, H., Fu,Z., Wang, L., Strazzer, L., Quattrocchio, F.M., Koes, R., Yanbang Li, (2026) Evolution of R2R3-MYB regulators of plant pigmentation, Plant Physiology, https://doi.org/10.1093/plphys/kiag210
Book sections
- Tornielli, G., Koes, R., & Quattrocchio, F. (2009). The genetics of flower color. In T. Gerats & J. Strommer (Eds.), Petunia: Evolutionary, Developmental and Physiological Genetics (pp. 269–300). Springer.
- J Mol, R Koes, R van Blokland, A van Tunen, A van der Krol and A Stuitje: The potential use of the glucuronidase reporter gene and antisense technologies to unravel biological functions of flavonoids 65-69. In: Lugtenberg B (ed) Signal molecules in plants and plant-microbe interactions, pp. 65-69. Springer Verlag (1989).
- Quattrocchio, F., Baudry, A., Lepiniec, L., and Grotewold, E. (2006a). The regulation of flavonoid biosynthesis. In: The Science of Flavonoids, E. Grotewold, ed (New York: Springer), pp. 97-122.
- Koes, R., Bliek, M., Castel, R., Kusters, E., Procissi, A., Rebocho, A. and Roobeek, I. (2009) Development of the petunia inflorescence. In: Petunia: Evolutionary, Developmental and Physiological Genetics (ed, T. Gerats and J. Strommer), Springer, Heidelberg. pp. 179-198
- Tornielli, G., Koes, R. and Quattrocchio, F. (2009) The genetics of flower color. In: Petunia: Evolutionary, Developmental and Physiological Genetics (ed, T. Gerats and J. Strommer), Springer, Heidelberg. pp. 269-300.
Patents and patent applications
- R. Koes, N. de Vetten and J. Mol. (2000) Cytochrome b5 from petunia. Application WO0009720A2
- F Brugliera and R. Koes (2002) Plant anthocyanindin rutinoside acyltransferases. (Patent 7173164; discontinued in 2019)
- F. Brugliera, L. Demelis, R. Koes and Y. Tanaka. (2010) Genetic sequences having methyltransferase activity and uses therefore. (Patent 7807877; discontinued in 2018)
- F. Brugliera, L. Demelis, R. Koes and Y. Tanaka. (2010) Flavonoid methyltransferase from Torrenia and uses therefore. (Patent EP1478753)
- F. Quattrocchio, R. Koes, W. Verweij, C. Spelt, F. Brugliera, M. Mizutani. (2007) Plant nucleic Acid associated with cellular pH and uses thereof" (Patent number US8629258; EP2024496)
- Verweij, C. W., Quattrocchio, F. M., Koes, R. E., & Passeri, V. (2022). Plant rich in anthocyanins concentration (Patent 11401525)