Publications

Latest publications

Florez-Rueda AM, Miguel CM, Figueiredo DD (2024) Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants . Plant Journal doi: 10.1111/tpj.16786

Usié A, Serra O, Barros PM, Barbosa P, Leão C, Capote T, Almeida T, Rodrigues L, Carrasquinho I, Guimarães JB, Mendonça D, Nóbrega F, Egas C, Chaves I, Abreu IA, Saibo NJM, Marum L, Varela MC, Matos J, Simões F, Miguel CM, Oliveira MM, Ricardo CP, Gonçalves S, Ramos A (2023) An improved reference genome and first organelle genomes of Quercus suber . Tree Genetics & Genomes 19, 54. doi: 10.1007/s11295-023-01624-8

Sousa F, Viegas MB, Costa J, Marques I, Pina-Martins F, Simões F, Matos J, Glushkova M, Miguel CM, Veloso MM, Oliveira MM, Ricardo CP, Batista D, Paulo OS (2023) Haplotype diversity patterns in Quercus suber (Fagaceae) inferred from cpDNA sequence data . Plant Syst Evol 309, 42. doi: 10.1007/s00606-023-01879-7

Agius DR, Kapazoglou A, Avramidou E, Baranek M, Carneros E, Caro E, Castiglione S, Cicatelli A, Radanovic A, Ebejer J-P, Gackowski D, Guarino F, Gulyás A, Hidvégi N, Hoenicka H, Inácio V, Johannes F, Karalija E, Lieberman-Lazarovich M, Martinelli F, Maury S, Mladenov V, Morais-Cecílio L, Pecinka A, Tani E, Testillano PS, Todorov D, Valledor L and Vassileva V (2023) Exploring the crop epigenome: a comparison of DNA methylation profiling techniques . Front Plant Sci 14:1181039. doi: 10.3389/fpls.2023.1181039

Modesto I, Miguel CM (2023) Regulatory Roles of Small RNAs in Forest Trees . In: Progress in Botany. Springer, Berlin, Heidelberg. doi: 10.1007/124_2023_75

Pommier C, Coppens F, Ćwiek-Kupczyńska H, Faria D, Beier S, Miguel C, Michotey C, D’Anna F, Owen S, Gruden K (2023) Plant Science Data Integration, from Building Community Standards to Defining a Consistent Data Lifecycle . In: Williamson, H.F., Leonelli, S. (eds) Towards Responsible Plant Data Linkage: Data Challenges for Agricultural Research and Development. Springer, Cham. doi: 10.1007/978-3-031-13276-6_8

Modesto I, Mendes A, Carrasquinho I, Miguel CM (2022) Molecular Defense Response of Pine Trees (Pinus spp.) to the Parasitic Nematode Bursaphelenchus xylophilus . Cells 11(20):3208. doi: 10.3390/cells11203208

Inácio V, Santos R, Prazeres R, Graça J, Miguel CM and Morais-Cecílio L (2022) Epigenetics at the crossroads of secondary growth regulation. Front. Plant Sci. 13:970342. doi: 10.3389/fpls.2022.970342

Modesto I, Inácio V, Van de Peer Y, Miguel CM (2022) MicroRNA-mediated post-transcriptional regulation of Pinus pinaster response and resistance to pinewood nematode . Sci. Rep. 12, 5169. doi: 10.1038/s41598-022-09163-3

Modesto I, Inácio V, Novikova P, Carrasquinho I, Van de Peer Y, Miguel CM (2022) SNP Detection in Pinus pinaster Transcriptome and Association with Resistance to Pinewood Nematode . Forests 13(6), 946. doi: 10.3390/f13060946

Sousa F, Costa J, Ribeiro C, Varandas M, Pina-Martins F, Simões F, Matos J, Glushkova M, Miguel C, Veloso MM, Oliveira M, Pinto Ricardo C, Batista D, Paulo OS (2022) Population structure in Quercus suber L. revealed by nuclear microsatellite markers. Peer J 10:e13565. doi: 10.7717/peerj.13565

Alves A, Confraria A, Lopes S, Costa B, Perdiguero P, Milhinhos A, Baena-González E, Correia S, Miguel CM (2022) miR160 Interacts in vivo With Pinus pinaster AUXIN RESPONSE FACTOR 18 Target Site and Negatively Regulates Its Expression During Conifer Somatic Embryo Development. Front. Plant Sci. doi: 10.3389/fpls.2022.857611

Sterck L, de María N, Cañas RA, de Miguel M, Perdiguero P, Raffin A, Budde KB, López-Hinojosa M, Cantón FR, Rodrigues AS, Morcillo M, Hurel A, Vélez MD, de la Torre FN, Modesto I, Manjarrez FL, Pascual MB, Alves A, Mendoza-Poudereux I, Díaz MC, Pizarro A, El-Azaz J, Hernández-Escribano L, Guevara MA, Majada J, Salse J, Grivet D, Bouffier L, Raposo R, De La Torre AR, Zas R, Cabezas JA, Ávila C, Trontin JF, Sánchez L, Alía R, Arrillaga I, González-Martínez SC, Miguel CM, Cánovas FM, Plomion C, Díaz-Sala C, Cervera MT (2022) Maritime Pine Genomics in Focus. In: De La Torre A.R. (eds) The Pine Genomes. Compendium of Plant Genomes. Springer, Cham. doi: 10.1007/978-3-030-93390-6_5

Modesto I, Sterck L, Arbona V, Gómez-Cadenas A, Carrasquinho I, Van de Peer Y and Miguel CM (2021) Insights Into the Mechanisms Implicated in Pinus pinaster Resistance to Pinewood Nematode. Front. Plant Sci. 12:690857. doi: 10.3389/fpls.2021.690857

Costa A, Barbosa I, Miguel C, Graça J (2021) Variation of cork porosity along the stem in harvested cork oak (Quercus suber L.) trees. Annals of Forest Science 78, 52. doi: 10.1007/s13595-021-01068-x

Harrow J, Hancock, Blomberg N, Brunak S, Capella-Gutierrez, Durinx C, Evelo CT, Goble C, Gut I, Ison J, Keane T, Leskošek B, Matyska L, McEntyre J, Miguel C et al. (2021) ELIXIR‐EXCELERATE: establishing Europe’s data infrastructure for the life science research of the future. EMBO J e107409. https://doi.org/10.15252/embj.2020107409

Alves A, Cordeiro D, Correia S, Miguel C (2021) Small Non-Coding RNAs at the Crossroads of Regulatory Pathways Controlling Somatic Embryogenesis in Seed Plants.  Plants 10(3):504. doi: 10.3390/plants10030504

Perdiguero P, Rodrigues AS, Chaves I, Costa B, Alves A, de María N, Vélez MD, Díaz-Sala C, Cervera MT, Miguel CM (2021) Comprehensive analysis of the isomiRome in the vegetative organs of the conifer Pinus pinaster under contrasting water availability. Plant Cell & Environment 44(3):706-728. doi: 10.1111/pce.13976

Arias-Baldrich C, Silva MC, Bergeretti F, Chaves I, Miguel CM, Saibo N, Sobral D, Faria D, Barros PM (2020) CorkOakDB – The Cork Oak Genome Database Portal. Database volume 2020, baaa114. doi: 10.1093/database/baaa114

Milhinhos A, Bollhöner B, Blazquez MA, Novák O, Miguel CM and Tuominen H (2020) ACAULIS5 Is Required for Cytokinin Accumulation and Function During Secondary Growth of Populus Trees. Front. Plant Sci. 11:601858. doi: 10.3389/fpls.2020.601858

de María N, Guevara MA, Perdiguero P, Vélez MD, Cabezas JA, López-Hinojosa M, Li Z, Díaz LM, Pizarro A, Mancha JA; Sterck L, Sánchez-Gómez D, Miguel CM, Collada C, Díaz-Sala C, Cervera MT (2020) Molecular Study of Drought Response in the Mediterranean Conifer Pinus pinaster Ait.: Differential Transcriptomic Profiling Reveals Constitutive Water-Deficit-Independent Drought Tolerance Mechanisms. Ecology and Evolution. https://doi.org/10.1002/ece3.6613

Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN, Chaves I, Coppens F, Cornut G, Costa BV, Cwiek-Kupczynska H, Droesbeke B, Finkers R, Gruden K, Junker A, King GJ, Krajewski P, Lange M, Laporte MA, Michotey C, Oppermann M, Ostler R, Poorter H, Ramirez-Gonzalez R, Ramak Z, Reif JC, Rocca-Serra P, Sansone SA, Scholz U, Tardieu F, Uauy C, Usadel B, Visser RGF, Weise S, Kersey PJ, Miguel CM, Adam-Blondon AF, Pommier C (2020) Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytologist 227:260-273. DOI: 10.1111/nph.16544

Costa A, Barbosa I, Pestana M, Miguel CM (2020) Modelling bark thickness variation in stems of cork oak in south-western Portugal. Eur J Forest Res 139:611-625. DOI: 10.1007/s10342-020-01273-9 

Milhinhos A, Lopes S, Miguel CM (2020) microRNA-Mediated Regulation of Plant Vascular Development and Secondary Growth. In: Miguel C, Dalmay T, Chaves I (eds) Plant microRNAs. Concepts and Strategies in Plant Sciences. Springer, Cham, pp 143-168. DOI: 10.1007/978-3-030-35772-6_8

Alves A, Rodrigues AS, Miguel CM (2020) microRNAs in Plant Embryogenesis. In: Miguel CM, Dalmay T, Chaves I (eds) Plant microRNAs. Concepts and Strategies in Plant Sciences. Springer, Cham, pp 99-120. DOI: 10.1007/978-3-030-35772-6

Lopes ST, Sobral D, Costa B, Perdiguero P, Chaves I, Costa A, Miguel CM (2020) Phellem versus xylem: genome-wide transcriptomic analysis reveals novel regulators of cork formation in cork oak. Tree Physiology 20;40(2):129-141. DOI: 10.1093/treephys/tpz118

 

2019-2016

Rodrigues AM, Miguel C, Chaves I, António C (2019) Mass spectrometry‐based forest tree metabolomics. Mass Spectrometry Reviews https://doi.org/10.1002/mas.21603

Rodrigues AR, Chaves I, Costa BV, Lin Y-C, Lopes S, Milhinhos A, Van de Peer Y, Miguel CM (2019) Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos. Scientific Reports DOI: 10.1038/s41598-019-47789-y

Correia S, Alhinho AT, Casimiro B, Miguel CM, Oliveira M, Veríssimo P and Canhoto J (2019) NEP-TC a rRNA Methyltransferase Involved on Somatic Embryogenesis of Tamarillo (Solanum betaceum Cav.). Front. Plant Sci. 10:438. DOI: 10.3389/fpls.2019.00438

Ramos AM, Usié A, Barbosa P, Barros PM, Capote T, Chaves I, Simões F, Abreu I, Carrasquinho I, Faro C, Guimarães J, Mendonça D, Nóbrega F, Rodrigues L, Saibo N, Varela MC, Egas C, Matos J, Miguel CM, Oliveira MM,   Ricardo CP, Gonçalves S (2018) The draft genome sequence of cork oak. Sci. Data 5:180069. DOI: 10.1038/sdata.2018.69

Rodrigues AS, de Vega JJ, Miguel CM (2018) Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos. BMC Plant Biology, DOI: 10.1186/s12870-018-1564-2

Chaves I, Costa B, Rodrigues AS, Bohn A, Miguel CM (2017) miRPursuit – a pipeline for automated analyses of small RNAs in model and non-model plants. FEBS Letters DOI: 10.1002/1873-3468.12746

Rodrigues AS, Miguel CM (2017) The pivotal role of small non-coding RNAs in the regulation of seed development. Plant Cell Reports 36: 653-667. DOI 10.1007/s00299-017-2120-5

Miguel A, Milhinhos A, Novák O, Jones B, Miguel CM (2016) The SHORT-ROOT-like gene PtSHR2B is involved in Populus phellogen activity. Journal of Experimental Botany 67: 1545-55. DOI:10.1093/jxb/erv547.

Miguel CM, Rupps A, Raschke J, Rodrigues AS, Trontin J-F (2016) Impact of molecular studies on somatic embryogenesis development for implementation in conifer multi-varietal forestry. In: Park YS, Bonga JM, Moon HK (eds) Vegetative Propagation of Forest trees. National Institute of Forest Science. Seoul, Korea, pp 373-421. http://www.iufro20902.org/Publications/documents/16%20%28Miguel%20et%20al%29.pdf

Lelu-Walter M-A, Klimaszewska K, Miguel C, Aronen T, Hargreaves C, Teyssier C, Trontin J-F (2016) Somatic embryogenesis for more effective breeding and deployment of improved varieties in Pinus spp.: bottlenecks and recent advances. In: Somatic Embryogenesis – Fundamental Aspects and Applications. Loyola-Vargas VM, Ochoa-Alejo N (eds), Springer Verlag. Chap 19, pp 319-365, ISBN 978-3-319-33704-3

 

2015-2012

Miguel A, de Vega-Bartol J, Marum L, Chaves I, Santo T, Leitão J, Varela MC, Miguel CM (2015) Characterization of the cork oak transcriptome dynamics during acorn development. BMC Plant Biology 15: 158. DOI 10.1186/s12870-015-0534-1

Gomes A, Pimpão RC, Fortalezas S, Figueira I, Miguel CM, Aguiar C, Salgueiro L, Cavaleiro C, Gonçalves MJ, Clemente A, Costa C, Martins-Loução MA, Ferreira RB, Santos CN (2015) Chemical characterization and bioactivity of phytochemicals from Iberian endemic Santolina semidentata and strategies for ex situ propagation. Industrial Crops and Products 74: 505-513. DOI 10.1016/j.indcrop.2015.04.037

Modesto I, Miguel C, Pina-Martins F, Glushkova M, Veloso M, S. Paulo O, Batista D (2014) Identifying signatures of natural selection in cork oak (Quercus suber L.) genes through SNP analysis.Tree Genetics & Genomes, DOI 10.1007/s11295-014-0786-1

Chaves I, Lin Y-C, Pinto-Ricardo C, Van de Peer Y, Miguel CM (2014) miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns. Tree Genetics & Genomes 10:721–737, DOI: 10.1007/s11295-014-0717-1

Pereira-Leal JB, Abreu IA, Alabaça CS, Almeida MH, Almeida P, Almeida T, Amorim MI, Araújo S, Azevedo H, Badia A, Batista D, Bohn A, Capote T, Carrasquinho I, Chaves I, Coelho AC, R.Costa MM, Costa R, Cravador A, Egas C, Faro C, Fortes AM, Fortunato AS, Gaspar MJ, Gonçalves S, Graça J, Horta M, Inácio V, Leitão JM, Lino-Neto T, Marum L, Matos J, Mendonça D, Miguel A, Miguel CM et al. (2014) A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing. BMC Genomics 15:371 DOI:10.1186/1471-2164-15-371

Canales J, Bautista R, Label P, Gomez-Maldonado J, Lesur I, Fernández-Pozo N, Rueda-López M, Guerrero-Fernández D, Castro-Rodriguez V, Benzekri H, Canas R, Guevara M-A, Rodrigues A, Seoane P, Teyssier C, Ehrenmann F, Morel A, Le Provost G, Lalanne C, Noirot C, Klopp C, Raymond I, Garcia-Gutierrez A, Trontin J-F, Lelu-Walter M-A, Miguel CM, Cervera MT, Canton F, Plomion C, Harvengt L, Avila C, Claros MG, Canovas F (2014) De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology. Plant Biotechnology Journal 12: 286-299. DOI: 10.1111/pbi.12136.

Milhinhos A, Prestele J, Bollhöner B, Matos A, Vera-Sirera F, Rambla JL, Ljung K, Carbonell J, Blázquez MA, Tuominen H, Miguel CM (2013) Thermospermine levels are controlled by an auxin-dependent feedback-loop mechanism in Populus xylem. Plant Journal 75: 685-698. DOI: 10.1111/tpj.12231

de Vega-Bartol J*, Simões M*, Lorenz W, Rodrigues AS, Alba R, Dean JFD, Miguel CM (2013) Transcriptomic analysis highlights epigenetic and transcriptional regulation during zygotic embryo development of Pinus pinaster. BMC Plant Biology 13:123. *equal contributors; highly accessed

Milhinhos A, Miguel C (2013) Hormone interactions in xylem development: a matter of signals. Plant Cell Reports 32 (6): 867-883. DOI: 10.1007/s00299-013-1420-7

Gomes A, Fortalezas S, Pimpão R, Figueira I, Maroco J, Aguiar C, Ferreira RB, Miguel C, Santos CN (2013) Valuing the Endangered Species Antirrhinum lopesianum: Neuroprotective Activities and Strategies for in vitro Plant Propagation. Antioxidants 2(4):273-292. DOI:: http/10.3390/antiox2040273)

Vega-Bartol J, Santos RR, Simões M, Miguel C (2013) Normalizing gene expression by quantitative PCR during somatic embryogenesis in two representative conifer species: Pinus pinaster and Picea abies. Plant Cell Reports 32 (5): 715-729. DOI: 10.1007/s00299-013-1407-

Costa PM, Milhinhos A, Simões M, Marum L, Oliveira AM, Costa MH, Miguel CM (2012) Determining DNA strand breakage from embryogenic cell cultures of a conifer species using the single-cell gel electrophoresis assay. Tree Genetics & Genomes, DOI: 10.1007/s11295-011-0434-y

Marum L*, Miguel A*, Ricardo CP, Miguel CM (2012) Reference Gene Selection for Quantitative Real-time PCR Normalization in Quercus suber. PLoS ONE, DOI: 10.1371/journal.pone.0035113. *equal contributors

 

2011 and previous

Miguel C, Marum L (2011) An epigenetic view of plant cells cultured in vitro: somaclonal variation and beyond. Journal of Experimental Botany, DOI: 10.1093/jxb/err155

Lorenz, W. W., Alba, R., Yu, Y. S., Bordeaux, J. M., Simoes, M., and Dean, J. F. D. (2011) Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine ( P. taeda L.), BMC Genomics 12 http://dx.doi.org/10.1186/1471-2164-12-264

Marum L, Loureiro J, Rodriguez E, Santos C, Oliveira MM, Miguel CM (2009) Flow cytometric and morphological analysis of Pinus pinaster somatic embryognesis. Journal of Biotechnology 143(4): 288-295.

Santos, AM, Oliver MJ, Sánchez AM, Payton PR, Gomes JP, Miguel CM, Oliveira MM (2009) An integrated strategy to identify key genes in almond adventitious shoot regeneration. Journal of Experimental Botany 60(14): 4159-4173.

Marum L, Rocheta M, Maroco J, Oliveira MM, Miguel CM (2009) Analysis of genetic stability at SSR loci during somatic embryogenesis in maritime pine (Pinus pinaster). Plant Cell Reports 28: 673-682.

Miguel CM, Simões M, Oliveira MM, Rocheta M. (2008) Envelope-like retrotransposons in the plant kingdom: evidence of their presence in gymnosperms (Pinus pinaster). Journal of Molecular Evolution 67:517–525.

Tereso S, Miguel CM, Mascarenhas M, Roque A, Trindade H, Maroco J, Oliveira MM. (2008) Improved in vitro rooting of almond (Prunus dulcis Mill.) cultivars ‘Boa Casta’ and ‘Peneda’. Biologia Plantarum 52(3): 437-444.

Oliveira MM, Miguel CM, Costa M (2008) Almond. In: “A Compendium of Transgenic Crop Plants”, vol.4 – Temperate Fruits & Nuts (Chittaranjan Kole, Timothy C Hall, Eds). Blackwell Publishing, Oxford, UK (in press).

Gonçalves S., Cairney J., Pérez Rodríguez M., Cánovas F., Oliveira M.M., Miguel C.M. (2007) PpRab1, a Rab GTPase from maritime pine is differentially expressed during embryogenesis. Molecular Genetics and Genomics 278: 273–282.

Rocheta M., Cordeiro J., Oliveira M.M., Miguel C.M. (2007) PpRT1 (Pinus pinaster retrotransposon 1): the first gypsy-like retrotransposon isolated in Pinus pinaster. Planta 225: 551-562.

Tereso S., Miguel C.M., Zoglauer K., Milhinhos A., Oliveira M.M. (2007) Zygotic and somatic embryo morphogenesis in Pinus pinaster: histological and histochemical comparative study. Tree Physiology 27: 661-669.

Tereso S., Miguel C.M., Maroco J., Oliveira M.M. (2006) Susceptability of embryogenic and organogenic tissues of maritime pine (Pinus pinaster) to antibiotics used in Agrobacterium-mediated transformation. Plant Cell Tissue & Organ Culture 87:33–40.

Tereso S., Miguel C.M., Zoglauer K., Valle-Piquera C., Oliveira M.M. (2006) Stable Agrobacterium-mediated transformation of embryogenic tissues from Pinus pinaster Portuguese genotypes. Plant Growth Regulation 50(1): 57-68.

Costa M., Miguel C.M., Oliveira M.M. (2006) An improved selection strategy and the use of acetosyringone in shoot induction medium increase almond transformation efficiency by 100-fold. Plant Cell Tissue & Organ Culture 85: 205-209.

Tereso S., Gonçalves S., Marum L., Oliveira M M, Maroco J., Miguel C.M. (2006) Improved axillary and adventitious bud regeneration from Portuguese genotypes of Pinus pinaster. Propagation of Ornamental Plants, 6(1): 24-33.

Gonçalves S., Cairney J., Maroco J., Oliveira M.M., Miguel C.M. (2005) Evaluation of control transcripts in real-time RT-PCR expression analysis during maritime pine embryogenesis. Planta 222: 556-563.

Gonçalves S., Cairney J., Maroco J., Oliveira M.M., Miguel C.M. (2005) Identification of Genes Differentially Expressed During Embryogenesis in Maritime Pine (Pinus pinaster). Silva Lusitana 13(2): 203-216.

Marum L., Estêvão C., Oliveira M.M.,Amâncio S., Rodrigues L., Miguel C.M. (2004) Recovery of cryopreserved embryogenic cultures of maritime pine – effect of cryoprotectant and suspension density. Cryoletters 25: 363-374.

Miguel C.M., Gonçalves S., Tereso S., Marum L., Maroco J., Oliveira M.M. (2004) Somatic embryogenesis from 20 open-pollinated families of Portuguese plus trees of maritime pine. Plant Cell Tissue & Organ Culture 76 (2): 121-130.