Latest Publications
(* full or shared corresponding authorship)
- Liu L, Kong J, Fan P, Wang Y, Duan W, Liang Z, Matus JT, Dai Z. Supplementing with monochromatic blue LED light during the day, rather than at night, increases anthocyanins in the berry skin of grapevine (Vitis vinifera L.). Planta. 2024 Aug 10;260(3):69. doi: 10.1007/s00425-024-04500-4. PMID: 39127837.
- Santo Domingo M, Orduña L, Navarro D, Mayobre C, Santiago A, Valverde L, Alexiou KG, Matus JT, Pujol M, Garcia-Mas J. The ethylene-responsive transcription factor ERF024 is a novel regulator of climacteric fruit ripening in melon. Plant J. 2024 Aug;119(4):1844-1858. doi: 10.1111/tpj.16889. Epub 2024 Jun 20. PMID: 38900073.
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Chiara Foresti, Luis Orduña, José Tomás Matus, Elodie Vandelle, Davide Danzi, Oscar Bellon, Giovanni Tornielli, Alessandra Amato, and Sara Zenoni.
NAC61 regulates late- and post-ripening osmotic, oxidative, and biotic stress responses in grapevine. J Exp Bot. 2024 Apr 15;75(8):2330-2350. doi: 10.1093/jxb/erad507. PMID: 38159048; PMCID: PMC11016852. - Felipe Pérez de los Cobos, Beatriz E. García-Gómez, Luis Orduña-Rubio, Ignasi Batlle, Pere Arús, José Tomás Matus, Iban Eduardo. Exploring large-scale gene coexpression networks in peach (Prunus persica L.): A new tool for predicting gene function. Hortic Res. 2024 Jan 2;11(2):uhad294. doi: 10.1093/hr/uhad294. PMID: 38487296; PMCID: PMC10939413.
- Chen Zhang, Zhanwu Dai, Thilia Ferrier, Luis Orduña, Antonio Santiago, Arnau Peris, Darren C J Wong, Christian Kappel, Stefania Savoi, Rodrigo Loyola, Alessandra Amato, Bartosz Kozak, Miaomiao Li, Akun Liang, David Carrasco, Carlos Meyer-Regueiro, Carmen Espinoza, Ghislaine Hilbert, Rosa Figueroa-Balderas, Dario Cantu, Rosa Arroyo-Garcia, Patricio Arce-Johnson, Patricia Claudel, Daniel Errandonea, Manuel Rodríguez-Concepción, Eric Duchêne, Shao-shan Carol Huang, Simone Diego Castellarin, Giovanni Battista Tornielli, Francois Barrieu, José Tomás Matus, MYB24 orchestrates terpene and flavonol metabolism as light responses to anthocyanin depletion in variegated grape berries, The Plant Cell, Volume 35, Issue 12, December 2023, Pages 4238–4265, https://doi.org/10.1093/plcell/koad228
- Luis Orduña, Antonio Santiago, David Navarro-Payá, Chen Zhang, Darren C J Wong, José Tomás Matus, Aggregated gene co-expression networks predict transcription factor regulatory landscapes in grapevine, Journal of Experimental Botany, Volume 74, Issue 21, 21 November 2023, Pages 6522–6540, https://doi.org/10.1093/jxb/erad344
- Sara Rosa-Téllez, Andrea Alcántara-Enguídanos, Federico Martínez-Seidel, Ruben Casatejada-Anchel, Sompop Saeheng, Clayton L Bailes, Alexander Erban, David Barbosa-Medeiros, Paula Alepúz, José Tomás Matus, Joachim Kopka, Jesús Muñoz-Bertomeu, Stephan Krueger, Sanja Roje, Alisdair R Fernie, Roc Ros, The serine–glycine–one-carbon metabolic network orchestrates changes in nitrogen and sulfur metabolism and shapes plant development, The Plant Cell, 2023;, koad256, https://doi.org/10.1093/plcell/koad256
- Álvarez-Urdiola R, Borràs E, Valverde F, Matus JT, Sabidó E, Riechmann JL. Peptidomics Methods Applied to the Study of Flower Development. Methods Mol Biol. 2023;2686:509-536. doi: 10.1007/978-1-0716-3299-4_24.
- Álvarez-Urdiola R, Matus JT, Riechmann JL. Multi-Omics Methods Applied to Flower Development. Methods Mol Biol. 2023;2686:495-508. doi: 10.1007/978-1-0716-3299-4_23.
- Luis Orduña, Antonio Santiago, David Navarro-Paya, Chen Zhang, Darren C.J. Wong, Jose Tomas Matus. Aggregated gene co-expression networks for predicting transcription factor regulatory landscapes in a non-model plant species bioRxiv 2023.04.24.538042; doi: https://doi.org/10.1101/2023.04.24.538042
- Xiaoya Shi, Shuo Cao, Xu Wang, Siyang Huang, Yue Wang, Zhongjie Liu, Wenwen Liu, Xiangpeng Leng, Yanling Peng, Nan Wang, Yiwen Wang, Zhiyao Ma, Xiaodong Xu, Fan Zhang, Hui Xue, Haixia Zhong, Yi Wang, Kekun Zhang, Amandine Velt, Komlan Avia, Daniela Holtgräwe, Jérôme Grimplet, José Tomás Matus, Doreen Ware, Xinyu Wu, Haibo Wang, Chonghuai Liu, Yuling Fang, Camille Rustenholz, Zongming Cheng, Hua Xiao, Yongfeng Zhou, The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding, Horticulture Research, 2023;, uhad061, https://doi.org/10.1093/hr/uhad061
- Amandine Velt, Bianca Frommer, Sophie Blanc, Daniela Holtgräwe, Éric Duchêne, Vincent Dumas, Jérôme Grimplet, Philippe Hugueney, Catherine Kim, Marie Lahaye, José Tomás Matus, David Navarro-Payá, Luis Orduña, Marcela K Tello-Ruiz, Nicola Vitulo, Doreen Ware, Camille Rustenholz, An improved reference of the grapevine genome reasserts the origin of the PN40024 highly-homozygous genotype, G3 Genes|Genomes|Genetics, 2023;, jkad067, https://doi.org/10.1093/g3journal/jkad067
- Cardona-Medina E, Santos M, Nodari R, Hornero-Méndez D, Peris A, Wong DCJ, Matus JT, Rodríguez-Concepcion Accumulation of azafrin in the root apoplast of the medicinal plant Escobedia grandiflora might play a role in parasitism. Plants People Planet. 2023;1–14. https://doi.org/10.1002/ppp3.10353
- Erica D’Incà, Chiara Foresti, Luis Orduña, Alessandra Amato, Elodie Vandelle, Antonio Santiago, Alessandro Botton, Stefano Cazzaniga, Edoardo Bertini, Mario Pezzotti, James Giovannoni, Julia Vrebalov, José Tomás Matus*, Giovanni Battista Tornielli*, Sara Zenoni*, The transcription factor VviNAC60 regulates senescence- and ripening-related processes in grapevine, Plant Physiology, 2023 , kiad050, https://doi.org/10.1093/plphys/kiad050.
- Amandine Velt, Bianca Frommer, Sophie Blanc, Daniela Holtgräwe, Éric Duchêne, Vincent Dumas, Jérôme Grimplet, Philippe Hugueney, Marie Lahaye, Catherine Kim, José Tomás Matus, David Navarro-Payá, Luis Orduña, Marcela K. Tello-Ruiz, Nicola Vitulo, Doreen Ware, Camille Rustenholz. An improved reference of the grapevine genome supports reasserting the origin of the PN40024 highly-homozygous genotype. bioRxiv 2022.12.21.521434.
- Shuai-Hui Ma, Guang-Qi He, David Navarro-Payá, Antonio Santiago, Yi-Zhe Cheng, Jia-Bing Jiao, Hui-Jie Li, Ding-Ding Zuo, Hao-Ting Sun, Mao-Song Pei, Yi-He Yu, José Tomás Matus, Da-Long Guo (2022) Global analysis of alternative splicing events based on long- and short-read RNA sequencing during grape berry development. Gene. 852. 147056.
- Savoi S, Santiago A, Orduña L and Matus JT* (2022) Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits. Front. Plant Sci. 13:937927. doi: 10.3389/fpls.2022.937927
- Edison Cardona-Medina, Marisa Santos, Rubens Nodari, Damaso Hornero-Mendez, Arnau Peris, Darren CJ Wong, J. Tomas Matus, Manuel Rodriguez-Concepcion. Biosynthesis and apoplast accumulation of the apocarotenoid pigment azafrin in parasitizing roots of Escobedia grandiflora. bioRxiv 2022.02.07.479377; doi:10.1101/2022.02.07.479377
- Orduña, L., Li, M., Navarro-Payá, D., Zhang, C., Santiago, A., Romero, P., Ramšak, Ž., Magon, G., Höll, J., Merz, P., Gruden, K., Vannozzi, A., Cantu, D., Bogs, J., Wong, D.C.J., Huang, S.-s.C. and Matus, J.T.* (2022), Direct regulation of shikimate, early phenylpropanoid and stilbenoid pathways by Subgroup 2 R2R3-MYBs in grapevine. Plant Journal. doi:10.1111/tpj.15686
- Navarro-Payá D, Santiago A, Orduña L, Zhang C, Amato A, D’Inca E, Fattorini C, Pezzotti M, Tornielli GB, Zenoni S, Rustenholz C and Matus JT* (2022) The Grape Gene Reference Catalogue as a Standard Resource for Gene Selection and Genetic Improvement. Front. Plant Sci. 12:803977. doi: 10.3389/fpls.2021.803977
- Moretto, Sonego, Pilati, Matus, Costantini, Malacarne and Engelen. A COMPASS for VESPUCCI: a FAIR way to explore the grapevine transcriptomic landscape. Frontiers in Plant Science.
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Pilati, S.; Malacarne, G.; Navarro-Payá, D.; Tomè, G.; Riscica, L.; Cavecchia, V.; Matus, J.T.; Moser, C.; Blanzieri, E. 2021. Vitis OneGenE, a causality-based approach to generate gene networks in Vitis vinifera, sheds light on the laccase and dirigent gene families. Biomolecules. 11(12), 1744.
- D’Incà E, Foresti C, Orduña L, Amato A, Vandelle E, Santiago A, Botton A, Cazzaniga S, Bertini E, Pezzotti M, Giovannoni J, Vrebalov J, Matus JT, Tornielli GB, Zenoni S. Initiation of organ maturation and fruit ripening in grapevine is controlled by the CARPO-NAC transcription factor. bioRxiv 2021.11.13.468481.
- Zhang C, Dai Z, Ferrier T, Orduña L, Santiago A, Peris A, WongD, Kappel C, Savoi S, Loyola R, Amato A, Kozak B, Li M, Carrasco D, Meyer C, Espinoza C, Hilbert G, Figueroa-Balderas R, Cantu D, Arroyo R, Arce-Johnson P, Claudel P, Duchene E, Huang S-sC, Castellarin SD, Tornielli GB, Barrieu F*, Matus JT*. The grape MYB24 mediates the coordination of light-induced terpene and flavonol accumulation in response to berry anthocyanin sunscreen depletion. bioRxiv 2021.12.16.472692.
- Kong J, Wu J, Guan L, Hilbert G, Delrot S, Fan P, Liang Z, Wu B, Matus JT, Gomès E, Dai Z. Metabolite analysis reveals distinct spatio-temporal accumulation of anthocyanins in two teinturier variants of cv. ‘Gamay’ grapevines (Vitis vinifera L.). Planta. 2021 Mar 31;253(4):84. doi: 10.1007/s00425-021-03613-4. PMID: 33788027.
- De Ollas C, González-Guzman M, Pitarch Z, Matus JT, Candela H, Rambla J, Granell, A Gómez-Cadenas A, Arbona V. 2021. Identification of ABA-mediated genetic and metabolic responses to soil flooding in tomato (Solanum lycopersicum Mill). Front. Plant Sci. doi: 10.3389/fpls.2021.613059
- Orduña L, Li M, Navarro-Payá D, Zhang C, Ramšak Ž, Gruden K, Höll J, Merz P, Vannozzi A, Cantu D, Bogs J, Wong D. C. J., Huang SC, Matus JT*. Orchestration of the stilbene synthase gene family and their regulators by subgroup 2 MYB genes. bioRxiv 2020.12.31.424746; doi: https://doi.org/10.1101/2020.12.31.424746
- Llorente B, Torres-Montilla S, Morelli L, Florez I, Matus JT, Ezquerro M, D’Andrea L, Houhou F, Majer E, Picó B, Cebolla J, Troncoso A, Fernie A, Daròs JA, Rodríguez-Concepción M. 2020. Synthetic conversion of leaf chloroplasts into carotenoid-rich plastids reveals mechanistic basis of natural chromoplast development. Proceedings of the National Academy of Sciences (PNAS). DOI: 10.1073/pnas.2004405117
- Leiva-Ampuero A, Agurto M, Matus JT, Hoppe G, Huidobro C, Inostroza-Blancheteau C, Reyes-Díaz M, Stange C, Canessa P, Vega A. Salinity impairs photosynthetic capacity and enhances carotenoid-related gene expression and biosynthesis in tomato (Solanum lycopersicum L. cv. Micro-Tom). PeerJ 8:e9742 http://doi.org/10.7717/peerj.9742.
- Romero P, Peris A, Vergara K, Matus JT*. 2020 Comprehending and Improving Cannabis Specialized Metabolism in the Systems Biology Era. Plant Science Vol 298. Special Issue: Specialized Metabolism. doi: 10.1016/j.plantsci.2020.110571
- Ferreira V, Matus JT, Pinto-Carnide O, Carrasco D , Arroyo-García R, Castro I. 2019. Genetic analysis of a white-to-red berry skin color reversion and its transcriptomic and metabolic consequences in grapevine (Vitis vinifera cv. ‘Moscatel Galego’). BMC Genomics. 20, 952 . doi:10.1186/s12864-019-6237-5
- Santibáñez C, Meyer C, Martínez L, Moyano T, Lunn J, Feil R, Dai Z, Carrasco D, Arroyo-García R, Hilbert G, Renaud C, Delrot S, Manke-Nachtigall F, Gutiérrez R, Matus JT*, EricGomès E*, Arce-Johnson P*. 2019. Differences in berry primary and secondary metabolisms identified by transcriptomic and metabolic profiling of two table grape color somatic variants. bioRxiv 861120; doi: https://doi.org/10.1101/861120
- Matus, J. T., Castellarin, S. D., Tornielli, G. B., eds. 2019. Ome-wide Studies of Grapevine Fruit Composition and Responses to Agro-environmental Factors in the Era of Systems Biology. Lausanne: Frontiers Media SA. doi: 10.3389/978-2-88963-211-4
- Matus JT*, Ruggieri V, Romero F, Moretto M and Wong DCJ. 2019. Status and Prospects of Systems Biology in Grapevine Research. In: The Grape Genome (Compendium of Plant Genomes). Cantu, Walker, eds.
- Sunitha S, Loyola R, Alcalde JA, Arce-Johnson P, Matus JT, Rock CD. 2019. The Role of UV-B light on Small RNA Activity During Grapevine Berry Development. G3 (Bethesda). Mar 7;9(3):769-787. doi: 10.1534/g3.118.200805.
- Vannozzi A, Wong DCJ, Höll J, Hmmam I, Matus JT, Bogs J, Ziegler T, Dry I, Barcaccia G, Lucchin M. Combinatorial Regulation of Stilbene Synthase Genes by WRKY and MYB Transcription Factors in Grapevine (Vitis vinifera L.). Plant Cell Physiol. 2018 May 1;59(5):1043-1059. doi: 10.1093/pcp/pcy045. PubMed PMID: 29529275.
- Sun X, Matus JT, Wong DCJ, Wang Z, Chai F, Zhang L, Fang T, Zhao L, Wang Y, Han Y, Wang Q, Li S, Liang Z, Xin H. The GARP/MYB-related grape transcription factor AQUILO improves cold tolerance and promotes the accumulation of raffinose family oligosaccharides. J Exp Bot. 2018 Mar 24;69(7):1749-1764. doi: 10.1093/jxb/ery020. PubMed PMID: 29385617.
Czemmel S, Höll J, Loyola R, Arce-Johnson P, Alcalde JA, Matus JT, Bogs J. Transcriptome-Wide Identification of Novel UV-B- and Light Modulated Flavonol Pathway Genes Controlled by VviMYBF1. Front Plant Sci. 2017 Jun 22;8:1084. doi: 10.3389/fpls.2017.01084. eCollection 2017. PubMed PMID: 28690624; PubMed Central
PMCID: PMC5479930.
Wong DCJ, Matus JT*. Constructing Integrated Networks for Identifying New Secondary Metabolic Pathway Regulators in Grapevine: Recent Applications and Future Opportunities. Front Plant Sci. 2017 Apr 12;8:505. doi: 10.3389/fpls.2017.00505. eCollection 2017. PubMed PMID: 28446914; PubMed Central PMCID: PMC5388765.
Matus JT, Cavallini E, Loyola R, Höll J, Finezzo L, Dal Santo S, Vialet S, Commisso M, Roman F, Schubert A, Alcalde JA, Bogs J, Ageorges A, Tornielli GB, Arce-Johnson P. A group of grapevine MYBA transcription factors located in chromosome 14 control anthocyanin synthesis in vegetative organs with different specificities compared with the berry color locus. Plant J. 2017 Jul;91(2):220-236. doi: 10.1111/tpj.13558. Epub 2017 May 17. PubMed PMID: 28370629.
- Matus JT*. Transcriptomic and Metabolomic Networks in the Grape Berry Illustrate That it Takes More Than Flavonoids to Fight Against Ultraviolet Radiation. Front Plant Sci. 2016 Aug 30;7:1337. doi: 10.3389/fpls.2016.01337. eCollection 2016. Review. PubMed PMID: 27625679; PubMed Central PMCID: PMC5003916.
- Loyola R, Herrera D, Mas A, Wong DC, Höll J, Cavallini E, Amato A, Azuma A, Ziegler T, Aquea F, Castellarin SD, Bogs J, Tornielli GB, Peña-Neira A, Czemmel S, Alcalde JA*, Matus JT*, Arce-Johnson P*. The photomorphogenic factors UV-B RECEPTOR 1, ELONGATED HYPOCOTYL 5, and HY5 HOMOLOGUE are part of the UV-B signalling pathway in grapevine and mediate flavonol accumulation in response to the environment. J Exp Bot. 2016 Oct;67(18):5429-5445. Epub 2016 Aug 19. PubMed PMID: 27543604; PubMed Central PMCID: PMC5049392.
- Wong DC, Schlechter R, Vannozzi A, Höll J, Hmmam I, Bogs J, Tornielli GB, Castellarin SD, Matus JT*. A systems-oriented analysis of the grapevine R2R3-MYB transcription factor family uncovers new insights into the regulation of stilbene accumulation. DNA Res. 2016 Jul 12. pii: dsw028. [Epub ahead of print] PubMed. PMID: 27407139; PubMed Central PMCID: PMC5066171.
- Cavallini E, Matus JT, Finezzo L, Zenoni S, Loyola R, Guzzo F, Schlechter R, Ageorges A, Arce-Johnson P, Tornielli GB. The phenylpropanoid pathway is controlled at different branches by a set of R2R3-MYB C2 repressors in grapevine. Plant Physiol. 2015 Apr;167(4):1448-70. doi: 10.1104/pp.114.256172. Epub 2015 Feb 6. PubMed PMID: 25659381; PubMed Central PMCID: PMC4378173.
- XIII International Symposium on Grapevine Breeding and Genetics, Landau (2022). Matus. Gene functional characterization assisted by genome-wide TF-binding site interrogation: watch presentation here
- XI International Symposium on Grapevine Physiology and Biotechnology (2021). Navarro-Payá; Orduña; Zhang; Santiago; Li; Huang; Matus. «Genome-wide exploration of transcription factor targets involved in grape specialized metabolism and visualization through DAPBrowse: a centralized genome-browser for DAP-seq data». Oral presentation.
- XI International Symposium on Grapevine Physiology and Biotechnology (2021). Pilati; Navarro-Payá; Malacarne; Tomé; Riscica; Cavecchia; Matus; Moser; Blanzieri. «Vitis OneGenE: a causality-based method for gene network analysis in grapevine. Characterization of the laccase and dirigent protein gene families». Oral presentation.
- Reunión de Biología Molecular de Plantas (Online, 26-27 November 2020). Luis Orduña, Chen Zhang, Miaomiao Li, Dario Cantu, Carol Huang, José Tomás Matus. DAP-Seq used to unveil MYB cistrome landscapes specifically associated to the regulation of secundary metabolism in grape. Oral presentation.
- Reunión de Biología Molecular de Plantas (Online, 26-27 November 2020). Chen Zhang, Luis Orduña, Miaomiao Li, Alessandra Amato, Giovanni Battista Tornielli, Dario Cantu, Shao-shan Carol Huang, José Tomás Matus. Genome-wide binding of VviMYB24 in the grapevine terpene synthase family. Poster.
- Symposium on Small Molecules in Plant Research (Valencia, Spain, 10-11 December 2019). Pablo Romero, Arnau Peris, Arnau Cerqueda, Chen Zhang, Zhanwu Dai, Miguel Simon, Victoria Barja, Erich Duchene, Carol Huang, Manuel Rodríguez Concepción, François Barrieu, José Tomás Matus. Deciphering the Interaction of Distinct Secondary Metabolic Pathways: Transcriptional Effects of Anthocyanin Depletion/Emergence on Isoprenoid Metabolism. Poster.
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Carlisle Bascom, MYB sommeliers: MYB24 drives UV response on the light side of variegated grape, The Plant Cell, Volume 35, Issue 12, December 2023, Pages 4193–4194, https://doi.org/10.1093/plcell/koad234