Plant Functional Genomics Lab
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Margarida Oliveira |
| Principal Investigator | |
| mmolive@itqb.unl.pt | |
| Plant Functional Genomics Lab
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Current members |
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| Ana Paula Santos | Post-Doc Researcher |
| Pedro Barros | Post-Doc Researcher |
| Valéria Custódio | PhD student |
| Maria Faustino | PhD student |
| Filippo Bergeretti | PhD student |
| Joana Belo | PhD student |
| Luís Gonçalves | PhD student |
| Luísa Ribeiro | MSc |
| Maria Beatriz Vieira | MSc |
| Diogo Antunes | MSc student |
| Hugo Rodrigues | MSc student |
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Collaborators |
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| Célia Miguel | Forest Genomics and Molecular Genetics (ForGen) Laboratory (Faculdade de Ciências, U.Lisboa) |
| Ana Cristina Figueiredo, Helena Trindade | Faculdade de Ciências, U.Lisboa (secção de Biologia Celular e Biotecnologia Vegetal) |
| Marcos Ramos, Liliana Marum | Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL) |
| Benvindo Maçãs, Ana Sofia Almeida, Augusta Costa, Corina Carranca | Instituto Nacional de Investigação Agrária e Veterinária (INIAV) |
| Teresa Lino-Neto | Centro De Biologia Funcional de Plantas (U.Minho) |
| Piet van der Linde | Invited scientist |
| Tom Beeckman | VIB, U.Ghent (Belgium) |
| Claudine Chaouiya | Aix-Marseille Université (France) |
| Ryouichi Tanaka | Assoc. Professor University of Hokkaido, Inst. of Low Temperature Science (Japan) |
| Dominique Van Der Straeten | University of Ghent, Dept. Biology (Belgium) |
| Martin R. Broadley | Plant Nutrition, U.Nottingham (United Kingdom) |
| Gabriel Castrillo | Plant Microbiome, U.Nottingham, (United Kingdom) |
| Regla Amorós | INIDA (Santiago island, Cabo Verde) |
| Chiara Pucciarelli | Scuola Superiore Sant’Anna, Pisa (Italy) |
| Michael Purugganan | NYU New York (USA) |
| László Szabados | Biological Research Centre, Szeged (Hungary) |
| Katalin Solymosi | Eötvös Loránd Univ., Budapest (Hungary) |
| Joaquim Albenísio Silveira | Univ. Fed. do Ceará, Fortaleza (Brazil) |
| Sônia Zingaretti | Univ. Estadual Paulista Júlio de Mesquita Filho, S. Paulo (Brazil) |
| COTArroz-CC | Centro Operativo e Tecnológico do Arroz - Centro de Competências, Salvaterra de Magos, Portugal |
| CCSC | Centro de Competências do Sobreiro e da Cortiça, Coruche, Portugal |
| InnovPlantProtect CoLAB | Collaborative Laboratory: Innovative Bio-based Solutions for Crop Protection, Elvas, Portugal |
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Current Projects |
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| 2022 – 2023 | CorkREMODEL - Unveiling genetic REgulatory MOdules acting on the crosstalk between cork Development and EnvironmentaL factors (EXPL/ASP-SIL/1190/2021). Coordinator: Pedro Barros (ITQB NOVA) | |
| 2023 – 2025 | Rice2B - Modelling vitamins B1 and B2 biosynthesis and biofortification in rice (2022.02916.PTDC). Coordinator: Margarida Oliveira (ITQB NOVA) | |
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2021-2023 | EpiCORK - Unveiling the role of DNA methylation in periderm and lenticel formation (PTDC/ASP-SIL/1717/2020). Project Coordinator: Vera Inácio (FC-UL) |
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| 2021 – 2023 | Increasing Plant data findability and reuse beyond ELIXIR. Coordinator: Cyril Pommier, French National Institute for Agriculture, Food, and Environment (INRAE). | |
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2020-2025 | PhotoBoost - Combining multiple approaches to grow enhanced crops (H2020-EU.2.1.4. Grant agreement ID: 862127). Project Coordinator: Stefan Schillberg |
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2020-2024 | "TRACE RICE” - Tracing rice and valorizing side streams along mediterranean blockchain" (H2020 - PRIMA Programme - Partnership for research and innovation in the Mediterranean Area) (Grant nº 1934). Project Coordinator: Carla Brites (INIAV) |
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FCT Research Unit GREEN-IT “Bioresources for Sustainability” (UIDB/04551/2020) (UIDP/04551/2020) |
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Past Projects |
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| 2018-2021 | “RicePIFs - How do Phytocrome Interacting Factors mediate the cross-talk between light and temperature signaling in rice” (PTDC/BIA-FBT/31070/2017). Project Coordinator: Nelson Saibo (Plant Gene Regulation, GPlantS Unit, ITQB NOVA) | |
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2017-2021 | “Biodata.pt - Infraestrutura Portuguesa de dados biológicos” (LISBOA-01-0145-FEDER-022231). Project Coordinator: Ana Portugal Melo (Instituto Gulbenkian de Ciência). |
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2018-2019 | CoLAB – “InnovPlantProtect - Biobased innovative solutions for plant protection”. Fundação para a Ciência e a Tecnologia (Lisboa). Contract. GRANT_NUMBER: FCT - CoLABs P.14 |
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2012-2015 | SuberStress - An integrated approach to identify stress-related regulatory genes in cork oak. (PTDC/AGR-GPL/118505/2010). |
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2012-2015 | 3to4 - Converting C3 to C4 photosynthesis for sustainable agriculture. FP7-KBBE.2011.3.1-01 (Brussels) (Contract) |
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2012-2015 | GenoSuber – Sequenciação do genoma do sobreiro (Cork Oak Genome Sequencing). QREN Project (INAlentejo). ALENT-07-0224-FEDER-001754 |
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Main Publications |
| 2022 |
| CUSTÓDIO V, Gonin M, Stabl G, Bakhoum N, Oliveira MM, Gutjahr C, Castrillo G (2022) Sculpting the soil microbiota. Plant Journal,109(3) 508-522. doi: 10.1111/tpj.15568 |
| DE OLIVEIRA JMPF, Santos C, Araújo M, Oliveira MM, Dias MC (2022) High-salinity activates photoprotective mechanisms in Quercus suber via accumulation of carbohydrates and involvement of non-enzymatic and enzymatic antioxidant pathways. New Forests,53(2) 285-300. doi: 10.1007/s11056-021-09856-z |
| DIAS MC, Santos C, Araújo M, Barros PM, Oliveira M, Ferreira De Oliveira JMP (2022) Quercus suber Roots Activate Antioxidant and Membrane Protective Processes in Response to High Salinity. Plants,11(4). doi: 10.3390/plants11040557 |
| LEAL AR, Barros PM, Parizot B, Sapeta H, Vangheluwe N, Andersen TG, Beeckman T, Oliveira MM (2022) Translational profile of developing phellem cells in Arabidopsis thaliana roots. Plant Journal,110(3) 899-915. doi: 10.1111/tpj.15691 |
| LEAL AR, Belo J, Beeckman T, Barros PM, Oliveira MM (2022) The Combined Effect of Heat and Osmotic Stress on Suberization of Arabidopsis Roots. Cells,11(15). doi: 10.3390/cells11152341 |
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LEAL AR, Sapeta H, Beeckman T, Barros PM, Oliveira MM (2022) Spatiotemporal development of suberized barriers in cork oak taproots. Tree Physiology,42(6) 1269-1285. doi: 10.1093/treephys/tpab176 |
| SOUSA F, Costa J, Ribeiro C, Varandas M, Pina-Martins F, Simões F, Matos J, Glushkova M, Miguel C, Veloso MM, Oliveira M, Ricardo CP, Batista, D., Paulo, O.S. (2022). Population structure in Quercus suber L. revealed by nuclear microsatellite markers. PeerJ,10. doi: 10.7717/peerj.13565 |
| STROBBE S, Verstraete J, Fitzpatrick TB, Faustino M, Lourenço TF, Oliveira MM, Stove C, Van Der Straeten D (2022) A novel panel of yeast assays for the assessment of thiamin and its biosynthetic intermediates in plant tissues. New Phytologist,234(2) 748-763. doi: 10.1111/nph.17974 |
| VIEIRA MB, Faustino MV, Lourenço TF, Oliveira M (2022) DNA-Based Tools to Certify Authenticity of Rice Varieties—An Overview. Foods,11(3):258 doi: 10.3390/foods11030258 |
| 2021 |
| LEAL AR, Sapeta H, Beeckman T, Barros PM, Oliveira MM (2021) Spatio-temporal development of suberized barriers in cork oak taproots. Tree Physiology, tpab176. DOI:10.1093/treephys/tpab176 |
| SALAS-GONZÁLEZ I, Reyt G, Flis P, Custódio V, Gopaulchan D, Bakhoum N, Dew TP, Suresh K, Franke RB, Dangl JL, Salt DE, Castrillo G (2021) Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis. Science, 371(6525). DOI:10.1126/science.abd0695 |
| CUSTÓDIO V, Gonin M, Stabl G,Bakhoum N, Oliveira MM,Gutjahr C, Castrillo G (2021) Sculpting the soil microbiota. The Plant Journal, 109: 508–522. DOI: 10.1111/tpj.15568 |
| CHRISTOU P, Dhingra A, Slamet-Loedin H, Oliveira MM, Chakraborty S, Buyel J, Stoger E, Shillberg E, Orzaez D, Quemada H (2021) Preface: Genome editing in plants. Transgenic Research 30, 317–320. https://doi.org/10.1007/s11248-021-00268-5 |
| GÓRSKA AM, Gouveia P, Borba AR, Zimmermann A, Serra TS, Carvalho P, Lourenço TF, Oliveira MM, Peterhänsel C, Saibo NJM (2021) ZmOrphan94 Transcription Factor Downregulates ZmPEPC1 Gene Expression in Maize Bundle Sheath Cells. Frontiers in Plant Science, 12, fpls.2021.559967. DOI: 10.3389/fpls.2021.559967 |
| ALVES HLS, Matiolli CC, Soares RC, Almadanim MC, Oliveira MM, Abreu IA (2021) Carbon/nitrogen metabolism and stress response networks – calcium-dependent protein kinases as the missing link? Journal of Experimental Botany, 72(12), pp. 4190–4201. doi: 10.1093/jxb/erab136. |
| MELO FV, Oliveira MM, Saibo NJM, Lourenço TF. (2021) Modulation of Abiotic Stress Responses in Rice by E3-Ubiquitin Ligases: A Promising Way to Develop Stress-Tolerant Crops. Front Plant Sci. 2021 Mar 23;12:640193. doi: 10.3389/fpls.2021.640193. |
| LEAL AR, Barros PM, Parizot B, Sapeta H, Vangheluwe N, Andersen TG, Beeckman T, Oliveira MM (2021) Phellem translational landscape throughout secondary development in Arabidopsis roots. bioRxiv 2021.02.08.429142; doi: https://doi.org/10.1101/2021.02.08.429142 |
| Other Selected Publications |
| SALAS-GONZÁLEZ I, Reyt G, Flis P, Custódio V, Gopaulchan D, Bakhoum N, Dew TP, Suresh K, Franke RB, Dangl JL, Salt DE, Castrillo G (2020) Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis. Science, Nov 19:eabd0695 DOI: 10.1126/science.abd0695. |
| GUTAKER Rafal M, Groen, Simon C, Bellis, Emily S, Choi, Jae Y, Pires, Inês S, Bocinsky, R. Kyle, Slayton, Emma R, et al. Genomic history and ecology of the geographic spread of rice. Nature Plants 6 5 (2020): 492-502. DOI: 10.1038/s41477-020-0659-6. |
| SANTOS AP, Gaudin V, Mozgová I, Pontvianne F, Schubert D, Tek AL, Dvořáčková M, Liu C, Fransz P, Rosa S, Farrona S. (2020) Tidying-up the plant nuclear space: domains, functions, and dynamics. J Exp Bot. 71(17): 5160-5178. DOI: 10.1093/jxb/eraa282. PMID: 32556244. |
| BARROS PM, Martinez-Gomez P, Kodad O, Farinha AP, Oliveira MM (2020) - 19.8 Prunus dulcis syn, Prunus amygdalus Almond. In: “Biotechnology of Fruit and Nut Crops” (Richard E. Litz, ed.) CAB International (CABI Publishing), Wallingford, UK. |
| FONINI LS, Lazzarotto F, Barros PM, Cabreira-Cagliari C, Martins MAB, Saibo NJM, Turchetto-Zolet AC, (2020) Margis-Pinheiro M. Molecular evolution and diversification of the GRF transcription factor family. Genet Mol Biol. Jul 24;43(3):20200080. DOI: 10.1590/1678-4685-GMB-2020-0080.. |
| AMARAL MN, Auler, PA, Rossatto, T, Barros, PM, Oliveira, MM, Braga, EJB (2020) Long-term somatic memory of salinity unveiled from physiological, biochemical and epigenetic responses in two contrasting rice genotypes. Physiol Plantarum, 170: 248-268. DOI: 10.1111/ppl.13149 |
| COSTA JM, Marques da Silva J, Pinheiro C, Barón M, Mylona P, Centritto M, Haworth M, Loreto F, Uzilday B, Turkan I, Oliveira MM (2019) Opportunities and Limitations of Crop Phenotyping in Southern European Countries. Frontiers in Plant Science, 10. DOI: 10.3389/fpls.2019.01125 |
| NINO-GONZÁLEZ M, Novo-Uzal E, Richardson DN, Barros PM, Duque P* (2019) More Transporters, More Substrates: The Arabidopsis Major Facilitator Superfamily Revisited. Molecular Plant 12 (9): 1182-1202. DOI: 10.1016/j.molp.2019.07.003 |
| CORREIA S, Alhinho AT, Casimiro B, Miguel CM, Oliveira M, Veríssimo P, Canhoto J* (2019) NEP-TC a rRNA methyltransferase involved on somatic embryogenesis of tamarillo (Solanum betaceum cav.). Frontiers in Plant Science, 10 (22 Mar) Article 438. DOI: 10.3389/fpls.2019.00438 |
| RAMOS PAB, Ferro AM, Oliveira MM, Gonçalves S, Freire CSR, Silvestre AJD, Duarte MF* (2019) Biosynthesis and bioactivity of Cynara cardunculus L. guaianolides and hydroxycinnamic acids: a genomic, biochemical and health-promoting perspective. Phytochemistry Reviews, 18: 495-526. DOI: 10.1007/s11101-019-09604-4 |
| GÓRSKA AM, Gouveia P, Borba AR, Zimmermann A, Serra T-S, Lourenço TF, Oliveira MM, Peterhänsel C, Saibo NJM* (2019) ZmbHLH80 and ZmbHLH90 transcription factors act antagonistically and contribute to regulate PEPC1 cell-specific gene expression in maize. Plant J, 99: 270-285. DOI: 10.1111/tpj.14323 |
| FERREIRA L, Donoghue MTA, Barros P, Saibo NJM, Santos AP*, Oliveira MM (2019) Uncovering differentially methylated regions (DMRs) in a salt-tolerant rice variety under stress: one step towards new regulatory regions for enhanced salt tolerance. Epigenomes 3, 4. DOI: 10.3390/epigenomes3010004 |
| TEIXEIRA S, Luis I, Oliveira MM, Abreu IA, Batista R* (2019) Goji berries superfood – contributions for the characterisation of proteome and IgE-binding proteins. Food and Agricultural Immunology, 30(1): 262-280. DOI: 10.1080/09540105.2019.1577364 |
| RAMOS AM, Usié A, Barbosa P, Barros PM, Capote T, Chaves I, Simões F, Abreu I, Carrasquinho I, Faro C, Guimarães JB, Mendonça D, Nóbrega F, Rodrigues L, Saibo NJM, Varela MC, Egas C, Matos J, Miguel CM, Oliveira MM, Ricardo CP, Gonçalves S (2018) Data descriptor: the draft genome sequence of cork oak. Sci Data 5, 180069. DOI: 10.1038/sdata.2018.69 |
| ALMADANIM MC, Alexandre BM, Rosa MTG, Sapeta H, Leitão AE, Ramalho JC, Lam KT, Negrão S, Abreu IAA*, Oliveira MM* (2017) Rice calcium-dependent protein kinase OsCPK17 targets plasma membrane intrinsic protein and sucrose-phosphate synthase and is required for a proper cold stress response. Plant Cell and Environment, 40: 1197-1213. DOI: 10.1111/pce.12916 |
| BATISTA R*, Fonseca C, Planchon S, Negrão S, Renaut J, Oliveira MM (2017) Environmental stress is the major cause of transcriptomic and proteomic changes in GM and non-GM plants. Scientific Reports 7, Article number: 10624. DOI:10.1038/s41598-017-09646-8 |
| INÁCIO V, BARROS PM, Costa AU, Roussado C, Gonçalves E, Costa R, Graça J, Oliveira MM*, Morais-Cecílio L* (2017) Differential DNA methylation patterns are related to phellogen origin and quality of Quercus suber cork. PLoS ONE 12(1): e0169018. DOI: 10.1371/journal.pone.0169018 |
| BARROS PM, Cherian S, Costa M, Saibo N, Sanchéz AM and Oliveira MM* (2017) The identification of almond GIGANTEA gene and its expression under cold stress, variable photoperiod and seasonal dormancy. Biologia Plantarum, 61(4): 631- 640. DOI: 10.1007/s10535-017-0711-1 |
| SANTOS AP, Ferreira, LJ, Oliveira, MM (2017) Concerted flexibility of chromatin structure, methylome, and histone modifications along with plant stress responses. Biology 6, 1: 3. DOI: 10.3390/biology6010003 |
| SAPETA H, Lourenço T, Lorenz S, Grumaz C, Kirstahle P, Barros PM, Costa JM, Sohn K, Oliveira MM (2016) Transcriptomics and physiological analyses reveal co-ordinated alteration of metabolic pathways in Jatropha curcas drought tolerance. Journal of Experimental Botany 67 3: 845-860. DOI: 10.1093/jxb/erv499 |
| FERREIRA LJ, Azevedo V, Maroco J, Oliveira MM, Santos AP (2015) Salt tolerant and sensitive rice varieties display differential methylome flexibility under salt stress. PLoS ONE 10. DOI: 10.1371/journal.pone.0124060 |
| LOURENÇO TF, Serra TS, Cordeiro AM, Swanson SJ, Gilroy S, Saibo NJ, Oliveira MM (2015) TRice e3-ubiquitin ligase high expression of osmotically responsive gene1 modulates the expression of root meander curling, a gene involved in root mechanosensing, through the interaction with two ethylene-response factor transcription factors. Plant Physiology 169 3: 2275-2287. DOI: 10.1104/pp.15.01131 |
| FONSECA C, Planchon S, Serra T, Chander S, Saibo NJM, Renaut J, Oliveira MM, Batista R (2015) In vitro culture may be the major contributing factor for transgenic versus nontransgenic proteomic plant differences. Proteomics 15 1: 124-134. DOI: 10.1002/pmic.201400018 |
| PEREIRA-LEAL JB, Abreu IA, Alabaça CS, Almeida M, Almeida P, Almeida T, Amorim M, et al. (2014) A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing. BMC Genomics 15 1: 371. DOI: 10.1186/1471-2164-15-371 |
| ABREU IA, Farinha AP, Negrão S, Gonçalves N, Fonseca C, Rodrigues M, Batista R, Saibo NJM, Oliveira MM (2013) Coping with abiotic stress: Proteome changes for crop improvement. Journal of Proteomics 93: 145-168. DOI: 10.1016/j.jprot.2013.07.014 |
| NEGRÃO S, Almadanim MC, Pires IS, Abreu IA, Maroco J, Courtois B, Gregorio GB, McNally KL, Oliveira MM (2013) New allelic variants found in key rice salt-tolerance genes: an association study. Plant Biotechnology Journal 11 1: 87-100. DOI: 10.1111/pbi.12010 |
| SAPETA H, Costa JM, Lourenço T, Maroco J, van der Linde, P, Oliveira MM (2013) Drought stress response in Jatropha curcas: Growth and physiology. Environmental and Experimental Botany 85: 76-84. DOI: 10.1016/j.envexpbot.2012.08.012 |
| PIRES IS, Negrão S, Pentony MM, Abreu IA, Oliveira MM, Purugganan MD (2013) Different evolutionary histories of two cation/proton exchanger gene families in plants. BMC Plant Biology 13 1. DOI: 10.1186/1471-2229-13-97 |
| LOURENÇO T, Sapeta H, Figueiredo DD, Rodrigues M, Cordeiro A, Abreu IA, Saibo NJM, Oliveira MM (2013) Isolation and characterization of rice (Oryza sativa L.) E3-ubiquitin ligase OsHOS1 gene in the modulation of cold stress response. Plant Molecular Biology 83 4-5: 351-363. DOI: 10.1007/s11103-013-0092-6 |
| BARROS PM, Gonçalves N, Saibo NJM, Oliveira MM (2012) Cold acclimation and floral development in almond bud break: Insights into the regulatory pathways. Journal of Experimental Botany 63 12: 4585-4596. DOI: 10.1093/jxb/ers144 |
| SANTOS AP, Ferreira L, Maroco J, Oliveira M (2011) Abiotic stresses and induced DNA hypometylation causes interphase chromatin structural changes in the rice rDNA loci. Cytogenet Genome Res, 132: 297-303. DOI.org/10.1159/000322287. |
| BATISTA R, Oliveira MM (2009) Facts and fiction of genetically engineered food. Trends in Biotechnology 27 5: 277-286. DOI: 10.1016/j.tibtech.2009.01.005 |
| BATISTA R, Saibo N, Lourenço T, Oliveira MM (2008) Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion. Proceedings of the National Academy of Sciences of the United States of America 105 9: 3640-3645. DOI: 10.1073/pnas.0707881105 |
