{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T03:26:45Z","timestamp":1760239605024,"version":"build-2065373602"},"reference-count":102,"publisher":"MDPI AG","issue":"23","license":[{"start":{"date-parts":[[2020,12,3]],"date-time":"2020-12-03T00:00:00Z","timestamp":1606953600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"BreedCAFS","award":["727934"],"award-info":[{"award-number":["727934"]}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["PTDC\/ASP-AGR\/31257\/2017"],"award-info":[{"award-number":["PTDC\/ASP-AGR\/31257\/2017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Research unit CEF","award":["UIDB\/00239\/2020"],"award-info":[{"award-number":["UIDB\/00239\/2020"]}]},{"name":"Research unit GeoBioTec","award":["UIDP\/04035\/2020"],"award-info":[{"award-number":["UIDP\/04035\/2020"]}]},{"name":"Research unit LEAF","award":["UID\/AGR\/04129\/2020"],"award-info":[{"award-number":["UID\/AGR\/04129\/2020"]}]},{"name":"Research Unit Green-IT","award":["UIDB\/04551\/2020"],"award-info":[{"award-number":["UIDB\/04551\/2020"]}]},{"name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico, Brazil (CNPq), and the Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Minas Gerais, Brazil","award":["CRA-RED-00053-16"],"award-info":[{"award-number":["CRA-RED-00053-16"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>As atmospheric [CO2] continues to rise to unprecedented levels, understanding its impact on plants is imperative to improve crop performance and sustainability under future climate conditions. In this context, transcriptional changes promoted by elevated CO2 (eCO2) were studied in genotypes from the two major traded coffee species: the allopolyploid Coffea arabica (Icatu) and its diploid parent, C. canephora (CL153). While Icatu expressed more genes than CL153, a higher number of differentially expressed genes were found in CL153 as a response to eCO2. Although many genes were found to be commonly expressed by the two genotypes under eCO2, unique genes and pathways differed between them, with CL153 showing more enriched GO terms and metabolic pathways than Icatu. Divergent functional categories and significantly enriched pathways were found in these genotypes, which altogether supports contrasting responses to eCO2. A considerable number of genes linked to coffee physiological and biochemical responses were found to be affected by eCO2 with the significant upregulation of photosynthetic, antioxidant, and lipidic genes. This supports the absence of photosynthesis down-regulation and, therefore, the maintenance of increased photosynthetic potential promoted by eCO2 in these coffee genotypes.<\/jats:p>","DOI":"10.3390\/ijms21239211","type":"journal-article","created":{"date-parts":[[2020,12,3]],"date-time":"2020-12-03T11:15:43Z","timestamp":1606994143000},"page":"9211","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [CO2]"],"prefix":"10.3390","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9788-4831","authenticated-orcid":false,"given":"Isabel","family":"Marques","sequence":"first","affiliation":[{"name":"Plant-Environment Interactions and Biodiversity Lab (PlantStress &amp; Biodiversity), Forest Research Centre (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 2784-505 Oeiras and Tapada da Ajuda, 1349-017 Lisboa, Portugal"},{"name":"Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1485-5942","authenticated-orcid":false,"given":"Isabel","family":"Fernandes","sequence":"additional","affiliation":[{"name":"Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4102-5012","authenticated-orcid":false,"given":"Pedro H.C.","family":"David","sequence":"additional","affiliation":[{"name":"Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5408-5212","authenticated-orcid":false,"given":"Oct\u00e1vio S.","family":"Paulo","sequence":"additional","affiliation":[{"name":"Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4613-8588","authenticated-orcid":false,"given":"Luis F.","family":"Goulao","sequence":"additional","affiliation":[{"name":"Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal"}]},{"given":"Ana S.","family":"Fortunato","sequence":"additional","affiliation":[{"name":"GREEN-IT\u2014Bioresources for Sustainability, Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier (ITQB), Universidade NOVA de Lisboa (UNL), Av. da Rep\u00fablica, 2780-157 Oeiras, Portugal"}]},{"given":"Fernando C.","family":"Lidon","sequence":"additional","affiliation":[{"name":"GeoBioSciences, GeoTechnologies and GeoEngineering (GeoBioTec), Faculdade de Ci\u00eancias e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Monte de Caparica, Portugal"}]},{"given":"F\u00e1bio M.","family":"DaMatta","sequence":"additional","affiliation":[{"name":"Departamento de Biologia Vegetal, Universidade Federal Vi\u00e7osa (UFV), Vi\u00e7osa 36570-900 (MG), Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7639-7214","authenticated-orcid":false,"given":"Jos\u00e9 C.","family":"Ramalho","sequence":"additional","affiliation":[{"name":"Plant-Environment Interactions and Biodiversity Lab (PlantStress &amp; Biodiversity), Forest Research Centre (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 2784-505 Oeiras and Tapada da Ajuda, 1349-017 Lisboa, Portugal"},{"name":"GeoBioSciences, GeoTechnologies and GeoEngineering (GeoBioTec), Faculdade de Ci\u00eancias e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Monte de Caparica, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6071-6460","authenticated-orcid":false,"given":"Ana I.","family":"Ribeiro-Barros","sequence":"additional","affiliation":[{"name":"Plant-Environment Interactions and Biodiversity Lab (PlantStress &amp; Biodiversity), Forest Research Centre (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 2784-505 Oeiras and Tapada da Ajuda, 1349-017 Lisboa, Portugal"},{"name":"GeoBioSciences, GeoTechnologies and GeoEngineering (GeoBioTec), Faculdade de Ci\u00eancias e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Monte de Caparica, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2020,12,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5264","DOI":"10.1021\/acs.jafc.7b04537","article-title":"Physiological and agronomic performance of the coffee crop in the context of climate change and global warming: A review","volume":"66","author":"DaMatta","year":"2018","journal-title":"J. Agric. Food Chem."},{"key":"ref_2","unstructured":"Osorio, N. (2002). The Global Coffee Crisis: A Threat to Sustainable Development, International Coffee Organization."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Alves, F., Leal, W., and Azeiteiro, U. (2018). Coffee Responses to Drought, Warming and High [CO2] in a Context of Future Climate Change Scenarios. Theory and Practice of Climate Adaptation, Springer.","DOI":"10.1007\/978-3-319-72874-2"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1007\/s004380050965","article-title":"Molecular characterisation and origin of the Coffea arabica L. Genome","volume":"261","author":"Lashermes","year":"1999","journal-title":"Mol. Gen. Genet."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1112","DOI":"10.1139\/G07-088","article-title":"Characterization of Coffea chloroplast microsatellites and evidence for the recent divergence of C. arabica and C. eugenioides chloroplast genomes","volume":"50","author":"Tesfaye","year":"2007","journal-title":"Genome"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/s11103-011-9852-3","article-title":"Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments","volume":"78","author":"Cenci","year":"2012","journal-title":"Plant Mol. Biol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1111\/nph.12371","article-title":"Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures","volume":"200","author":"Combes","year":"2013","journal-title":"New Phytol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"4642","DOI":"10.1038\/s41598-020-61216-7","article-title":"A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm","volume":"10","author":"Scalabrin","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_9","unstructured":"Stocker, T.F., Qin, D., Plattner, G.-K., Tignor, M.M.B., Allen, S.K., Boschung, J., Nauels, A., Xia, Y., Bex, V., and Midgley, P.M. (2013). Climate Change 2013. Physical Science Basis, IPCC. Summary for Policymakers, Technical Summary and Frequent Asked Questions. Part of the Working Group I Contribution to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change."},{"key":"ref_10","unstructured":"Edenhofer, O., Pichs-Madruga, R., Sokona, Y., Farahani, E., Kadner, S., Seyboth, K., Adler, A., Baum, I., Brunner, S., and Eickemeier, P. (2014). Climate Change 2014. Mitigation of Climate Change. Contribution of Working Group III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, Cambridge University Press."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"19686","DOI":"10.1073\/pnas.0701728104","article-title":"Crop and pasture response to climate change","volume":"104","author":"Tubiello","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_12","unstructured":"Pandey, S., Byerlee, D., Dawe, D., Dobermann, A., Mohanty, S., Rozelle, S., and Hardy, B. (2010). Rice and global climate change. Rice in the Global Economy: Strategic Research and Policy Issues for Food Security, International Rice Research Institute."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1007\/s10584-015-1422-2","article-title":"Coffee growth, pest and yield responses to free air CO2 enrichment","volume":"132","author":"Ghini","year":"2015","journal-title":"Clim. Chang."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Magrach, A., and Ghazoul, J. (2015). Climate and pest-driven geographic shifts in global coffee production: Implications for forest cover, biodiversity and carbon storage. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0133071"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"131","DOI":"10.2135\/cropsci2002.1310","article-title":"Implications of atmospheric and climate change for crop yield","volume":"42","author":"Polley","year":"2002","journal-title":"Crop Sci."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1146\/annurev.arplant.55.031903.141610","article-title":"Rising atmospheric carbon dioxide: Plants FACE the future","volume":"55","author":"Long","year":"2004","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1104\/pp.110.166819","article-title":"Does enhanced photosynthesis enhance growth? Lessons learned from CO2 enrichment studies","volume":"155","author":"Kirschbaum","year":"2011","journal-title":"Plant Physiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1111\/gcb.13088","article-title":"Long-term elevated air [CO2] strengthens photosynthetic functioning and mitigates the impact of supra-optimal temperatures in tropical Coffea arabica and C. canephora species","volume":"22","author":"Rodrigues","year":"2016","journal-title":"Glob. Chang. Biol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1016\/j.plaphy.2018.10.016","article-title":"Elevated CO2 reduces the adverse effects of drought stress on a high-yielding soybean (Glycine max (L.) Merr.) cultivar by increasing water use efficiency","volume":"132","author":"Wang","year":"2018","journal-title":"Plant Physiol. Biochem."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"e82712","DOI":"10.1371\/journal.pone.0082712","article-title":"Sustained photosynthetic performance of Coffea spp. under long-term enhanced [CO2]","volume":"8","author":"Ramalho","year":"2013","journal-title":"PLoS ONE"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1093\/aob\/mcy011","article-title":"Structural and functional changes in coffee trees after 4 years under free air CO2 enrichment","volume":"121","author":"Rakocevic","year":"2018","journal-title":"Ann. Bot."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"104148","DOI":"10.1016\/j.envexpbot.2020.104148","article-title":"Coffee plants respond to drought and elevated [CO2] through changes in stomatal function, plant hydraulic conductance, and aquaporin expression","volume":"177","author":"Avila","year":"2020","journal-title":"Environ. Exp. Bot."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"947","DOI":"10.3389\/fpls.2016.00947","article-title":"Protective response mechanisms to heat stress in interaction with high [CO2] conditions in Coffea spp","volume":"7","author":"Martins","year":"2016","journal-title":"Front. Plant Sci."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"287","DOI":"10.3389\/fpls.2018.00287","article-title":"Can elevated air [CO2] conditions mitigate the predicted warming impact on the quality of coffee bean?","volume":"9","author":"Ramalho","year":"2018","journal-title":"Front. Plant Sci."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1007\/s10584-014-1306-x","article-title":"Bitter cup: Climate change profile of global production of Arabica and Robusta coffee","volume":"129","author":"Bunn","year":"2015","journal-title":"Clim. Chang."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1111\/j.1469-8137.2010.03184.x","article-title":"The transcriptome of Populus in elevated CO2 reveals increased anthocyanin biosynthesis during delayed autumnal senescence","volume":"186","author":"Tallis","year":"2010","journal-title":"New Phytol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1111\/j.1469-8137.2005.01450.x","article-title":"The transcriptome of Populus in elevated CO2","volume":"167","author":"Taylor","year":"2005","journal-title":"New Phytol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1111\/j.1365-3040.2008.01822.x","article-title":"Elevated CO2 increases photosynthesis, biomass and productivity, and modifies gene expression in sugarcane","volume":"31","author":"Gasper","year":"2008","journal-title":"Plant Cell Environ."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2859","DOI":"10.1093\/jxb\/erp096","article-title":"Elevated CO2 effects on plant carbon, nitrogen, and water relations: Six important lessons from FACE","volume":"60","author":"Leakey","year":"2009","journal-title":"J. Exp. Bot."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1111\/ele.12274","article-title":"Contemporary evolution of an invasion grass in response to elevated atmospheric CO2 at a Mojave desert FACE site","volume":"17","author":"Grossman","year":"2014","journal-title":"Ecol. Lett."},{"key":"ref_31","first-page":"1","article-title":"Limits to future adaptation in the invasive plant Polygonum cespitosum: Expression of functional and fitness traits at elevated CO2","volume":"107","author":"Matesanz","year":"2016","journal-title":"J. Hered."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3760","DOI":"10.1111\/gcb.13322","article-title":"Plant adaptation or acclimation to rising CO2? Insight from first multigenerational RNA?Seq transcriptome","volume":"22","author":"Lin","year":"2016","journal-title":"Glob. Chang. Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1126\/science.1255274","article-title":"The coffee genome provides insight into the convergent evolution of caffeine biosynthesis","volume":"345","author":"Denoeud","year":"2014","journal-title":"Science"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.1093\/pcp\/pct116","article-title":"Long-term growth under elevated CO2 suppresses biotic stress genes in non-acclimated, but not cold-acclimated winter wheat","volume":"54","author":"Kane","year":"2013","journal-title":"Plant Cell Physiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"701","DOI":"10.3389\/fpls.2015.00701","article-title":"Response and adaptation of photosynthesis, respiration, and antioxidant systems to elevated CO2 with environmental stress in plants","volume":"6","author":"Xu","year":"2015","journal-title":"Front. Plant Sci."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1016\/j.envexpbot.2017.12.004","article-title":"Transcriptional memory contributes to drought tolerance in coffee (Coffea canephora) plants","volume":"147","author":"Guedes","year":"2018","journal-title":"Environ. Exp. Bot."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Ivamoto, S.T., Reis, O., J\u00fanior Domingues, D.S., dos Santos, T.B., de Oliveira, F.F., Pot, D., Leroy, T., Esteves Vieira, L.G., Carazzolle, M.F., and Pereira, G.A.G. (2017). Transcriptome analysis of leaves, flowers and fruits perisperm of Coffea arabica L. reveals the differential expression of genes involved in raffinose Biosynthesis. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0169595"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"108854","DOI":"10.1016\/j.scienta.2019.108854","article-title":"The \u201cpolyploid effect\u201d in the breeding of aromatic and medicinal species","volume":"260","author":"Iannicelli","year":"2020","journal-title":"Sci. Hortic."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"4649","DOI":"10.1073\/pnas.0630618100","article-title":"Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing","volume":"100","author":"Adams","year":"2003","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1146\/annurev.arplant.57.032905.105429","article-title":"Glycosyltransferases of lipophilic small molecules","volume":"57","author":"Bowles","year":"2006","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1111\/nph.13609","article-title":"The carotenoid cleavage dioxygenase CCD2 catalyzing the synthesis of crocetin in spring crocuses and saffron is a plastidial enzyme","volume":"209","author":"Ahrazem","year":"2015","journal-title":"New Phytol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1789","DOI":"10.3389\/fpls.2017.01789","article-title":"The FAD2 Gene in plants: Occurrence, regulation, and role","volume":"8","author":"Dar","year":"2017","journal-title":"Front Plant Sci."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"103856","DOI":"10.1016\/j.envexpbot.2019.103856","article-title":"Lipid profile adjustments may contribute to warming acclimation and to heat impact mitigation by elevated [CO2] in Coffea spp","volume":"167","author":"Pais","year":"2019","journal-title":"Environ. Exp. Bot."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1093\/jxb\/erq033","article-title":"cpSecA, a thylakoid protein translocase subunit, is essential for photosynthetic development in Arabidopsis","volume":"61","author":"Liu","year":"2010","journal-title":"J. Exp. Bot."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1093\/pcp\/pcr189","article-title":"Variegated tobacco leaves generated by chloroplast FtsH suppression: Implication of FtsH function in the maintenance of thylakoid membranes","volume":"53","author":"Kato","year":"2012","journal-title":"Plant Cell Physiol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1592","DOI":"10.1016\/j.bbagen.2013.09.037","article-title":"Aquaporins and membrane diffusion of CO2 in living organisms","volume":"1840","author":"Kaldenhoff","year":"2014","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1","DOI":"10.4061\/2011\/207691","article-title":"Small changes huge impact: The role of protein posttranslational modifications in cellular homeostasis and disease","volume":"2011","author":"Karve","year":"2011","journal-title":"J. Amino Acids"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1093\/jxb\/err310","article-title":"Abiotic stress tolerance mediated by protein ubiquitination","volume":"63","author":"Lyzenga","year":"2012","journal-title":"J. Exp. Bot."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1111\/j.1399-3054.2007.00889.x","article-title":"Effect of elevated CO2, temperature and limited water supply on antioxidant status during regrowth of nodulated alfalfa","volume":"130","author":"Erice","year":"2007","journal-title":"Physiol. Plant."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.plantsci.2014.11.001","article-title":"Elevated CO2 mitigates drought and temperature-induced oxidative stress differently in grasses and legumes","volume":"231","author":"AbdElgawad","year":"2015","journal-title":"Plant Sci."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1093\/pcp\/pct185","article-title":"Effects of elevated CO2 on levels of primary metabolites and transcripts of genes encoding respiratory enzymes and their diurnal patterns in Arabidopsis thaliana: Possible relationships with respiratory rates","volume":"55","author":"Watanabe","year":"2014","journal-title":"Plant Cell Physiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"5875","DOI":"10.1038\/s41598-020-62818-x","article-title":"Early growth phase and caffeine content response to recent and projected increases in atmospheric carbon dioxide in coffee (Coffea arabica and C. canephora)","volume":"10","author":"Vega","year":"2020","journal-title":"Sci Rep."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1104\/pp.126.3.993","article-title":"Ozone quenching properties of isoprene and its antioxidant role in leaves","volume":"126","author":"Loreto","year":"2001","journal-title":"Plant Physiol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1254","DOI":"10.1093\/pcp\/pcm104","article-title":"Plants utilize isoprene emission as a thermo-tolerance mechanism","volume":"48","author":"Sasaki","year":"2007","journal-title":"Plant Cell Physiol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1016\/j.jplph.2012.10.003","article-title":"Induction of trans-resveratrol and extracellular pathogenesis-related proteins in elicited suspension cultured cells of Vitis vinifera cv Monastrell","volume":"170","author":"Almagro","year":"2013","journal-title":"J. Plant Physiol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"2061","DOI":"10.1093\/jxb\/ery028","article-title":"A transcription factor network responsive to high CO2\/hypoxia is in-volved in deastringency in persimmon fruit","volume":"69","author":"Zhu","year":"2018","journal-title":"J. Exp. Bot."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1111\/j.1365-2486.2008.01803.x","article-title":"Leaf isoprene emission rate as a function of atmospheric CO2 concentration","volume":"15","author":"Wilkinson","year":"2009","journal-title":"Glob. Chang. Biol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1007\/s00299-015-1772-2","article-title":"Advances in the understanding of cuticular waxes in Arabidopsis thaliana and crop species","volume":"34","author":"Lee","year":"2015","journal-title":"Plant Cell Rep."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1038\/35047071","article-title":"The HIC signalling pathway links CO2 perception to stomatal development","volume":"408","author":"Gray","year":"2000","journal-title":"Nature"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"2515","DOI":"10.1021\/cs400637t","article-title":"Aldehyde Decarbonylases: Enigmatic enzymes of hydrocarbon biosynthesis","volume":"3","author":"Marsh","year":"2013","journal-title":"ACS Catal."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1111\/nph.12291","article-title":"APETALA2\/Ethylene responsive factor (AP2\/ERF) transcription factors: Mediators of stress responses and developmental programs","volume":"199","author":"Licausi","year":"2013","journal-title":"New Phytol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1104\/pp.15.00677","article-title":"Ethylene response factors: A key regulatory hub in hormone and stress signalling","volume":"169","year":"2015","journal-title":"Plant Physiol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"112","DOI":"10.3390\/plants4010112","article-title":"Cell wall metabolism in response to abiotic stress","volume":"4","author":"Philippe","year":"2015","journal-title":"Plants"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/S0168-9452(02)00159-0","article-title":"Effects of hydrogen peroxide and nitric oxide on both salt and heat stress tolerance in rice","volume":"163","author":"Uchida","year":"2002","journal-title":"Plant Sci."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1562","DOI":"10.1016\/j.jplph.2011.02.003","article-title":"Hydrogen peroxide spraying alleviates drought stress in soybean plants","volume":"168","author":"Ishibashi","year":"2011","journal-title":"J. Plant Physiol."},{"key":"ref_66","first-page":"109","article-title":"Hydrogen peroxide priming stimulates drought tolerance in mustard (Brassica juncea L.) seedlings","volume":"4","author":"Hossain","year":"2013","journal-title":"Plant Gene Trait"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.molp.2017.10.004","article-title":"Carbon supply and the regulation of cell wall synthesis","volume":"11","author":"Verbancic","year":"2018","journal-title":"Mol. Plant"},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Ezquer, I., Salameh, I., Colombo, L., and Kalaitzis, P. (2020). Plant cell walls tackling climate change: Biotechnological strategies to improve crop adaptations and photosynthesis in response to global warming. Plants, 9.","DOI":"10.3390\/plants9020212"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1111\/j.1469-8137.2004.01224.x","article-title":"What have we learned from 15 years of free air-CO2 enrichment (FACE)? A meta-analytic review of the responses of photosynthesis, canopy properties and plant production to rising CO2","volume":"165","author":"Ainsworth","year":"2005","journal-title":"New Phytol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"15036","DOI":"10.1038\/hortres.2015.36","article-title":"Carotenoid metabolism and regulation in horticultural crops","volume":"2","author":"Yuan","year":"2015","journal-title":"Hortic. Res."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Mondego, J.M.C., Vidal, R.O., and Carazzolle, M.F. (2011). An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora. BMC Plant Biol., 11.","DOI":"10.1186\/1471-2229-11-30"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1007\/s00438-015-1111-x","article-title":"Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits","volume":"291","author":"Yuyama","year":"2016","journal-title":"Mol. Genet. Genomics"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1590\/S1677-04202006000100006","article-title":"Impacts of drought and temperature stress on coffee physiology and production: A review","volume":"18","author":"DaMatta","year":"2006","journal-title":"Braz. J. Plant Physiol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s40626-014-0001-7","article-title":"Cold impact and acclimation response of Coffea spp. plants","volume":"26","author":"Ramalho","year":"2014","journal-title":"Theor. Exp. Plant Physiol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1242\/jeb.089938","article-title":"The role of gibberellin signalling in plant responses to abiotic stress","volume":"217","author":"Colebrook","year":"2014","journal-title":"J. Exp. Biol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"3017","DOI":"10.1093\/jxb\/erx166","article-title":"Differential fine-tuning of gene expression regulation in coffee leaves by CcDREB1D promoter haplotypes under water deficit","volume":"68","author":"Alves","year":"2017","journal-title":"J. Exp. Bot."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1007\/s12042-019-09223-5","article-title":"Expression of DREB-Like genes in Coffea canephora and C. arabica subjected to various types of abiotic stress","volume":"12","author":"Torres","year":"2019","journal-title":"Trop. Plant Biol."},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Sakr, S., Wang, M., D\u00e9dald\u00e9champ, F., Perez-Garcia, M.D., Og\u00e9, L., Hamama, L., and Atanassova, R. (2018). The sugar-signaling hub: Overview of regulators and interaction with the hormonal and metabolic network. Int. J. Mol. Sci., 19.","DOI":"10.3390\/ijms19092506"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.fcr.2010.11.018","article-title":"Gene expression profiling of rice grown in free air CO2 enrichment (FACE) and elevated soil temperature","volume":"121","author":"Fukayama","year":"2011","journal-title":"Field Crop. Res."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"7907","DOI":"10.3390\/molecules15117907","article-title":"Elevated carbon dioxide increases contents of flavonoids and phenolic compounds, and antioxidant activities in Malaysian young ginger (Zingiber officinale Roscoe.) varieties","volume":"15","author":"Ghasemzadeh","year":"2010","journal-title":"Molecules"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1007\/s00425-013-1987-9","article-title":"Effects of elevated CO2, warming and precipitation change on plant growth, photosynthesis and peroxidation in dominant species from North China grassland","volume":"239","author":"Xu","year":"2014","journal-title":"Planta"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"3670","DOI":"10.1111\/gcb.12626","article-title":"Physiological, biochemical, and genome-wide transcriptional analysis reveals that elevated CO2 mitigates the impact of combined heat wave and drought stress in Arabidopsis thaliana at multiple organizational levels","volume":"20","author":"Zinta","year":"2014","journal-title":"Glob. Chang. Biol."},{"key":"ref_83","first-page":"1061","article-title":"The influence of elevated CO2 on the activities of antioxidative enzymes in two soybean genotypes","volume":"27","author":"Pritchard","year":"2000","journal-title":"Aust. J. Plant Physiol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/S0168-9452(98)00073-9","article-title":"Nitrogen dependent changes in antioxidant systems and in fatty acid composition of chloroplast membranes from Coffea arabica L. plants submitted to high irradiance","volume":"135","author":"Ramalho","year":"1998","journal-title":"Plant Sci."},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Semedo, J.N., Rodrigues, A.P., Lidon, F.C., Pais, I.P., Marques, I., Gouveia, D., Armengaud, J., Martins, S., Semedo, M.C., and Silva, M.J. (2020). Intrinsic non-stomatal resilience to drought of the photosynthetic apparatus in Coffea spp. can be strengthened by elevated Air CO2. Tree Physiol., tpaa158.","DOI":"10.1093\/treephys\/tpaa158"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"119","DOI":"10.3389\/fgene.2015.00119","article-title":"Annotation and curation of uncharacterized proteins-challenges","volume":"6","author":"Ijaq","year":"2015","journal-title":"Front. Genet."},{"key":"ref_87","first-page":"73","article-title":"Annotation and curation of hypothetical proteins: Prioritizing targets for experimental study","volume":"5","author":"Naveed","year":"2018","journal-title":"Adv. Life Sci."},{"key":"ref_88","unstructured":"Andrews, S. (2019, November 12). FastQC: A Quality Control Tool for High Throughput Sequence Data. Available online: http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"1338","DOI":"10.12688\/f1000research.15931.1","article-title":"FastQ Screen: A tool for multi-genome mapping and quality control","volume":"7","author":"Wingett","year":"2018","journal-title":"F1000 Res."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: Ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq-a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"1000 genome project data processing subgroup. The sequence alignment\/map (SAM) format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_94","unstructured":"Pertea, G. (2019, November 24). Gffread: GFF\/GTF Utility Providing Format Conversions, Region Filtering, FASTA Sequence Extraction and More. Available online: https:\/\/github.com\/gpertea\/gffread."},{"key":"ref_95","unstructured":"R Core Team (2018). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing. Available online: https:\/\/www.R-project.org."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"60","DOI":"10.2307\/1165312","article-title":"On the adaptive control of the false discovery rate in multiple testing with independent statistics","volume":"25","author":"Benjamini","year":"2000","journal-title":"J. Educ. Behav. Sci."},{"key":"ref_99","doi-asserted-by":"crossref","unstructured":"Chen, H., and Boutros, P.C. (2011). VennDiagram: A package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-35"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"3420","DOI":"10.1093\/nar\/gkn176","article-title":"High-throughput functional annotation and data mining with the Blast2GO suite","volume":"36","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"ref_101","doi-asserted-by":"crossref","unstructured":"Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis, Springer. Available online: https:\/\/ggplot2.tidyverse.org.","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"3045","DOI":"10.1093\/bioinformatics\/btp536","article-title":"QuickGO: A web-based tool for Gene Ontology searching","volume":"25","author":"Binns","year":"2009","journal-title":"Bioinformatics"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/21\/23\/9211\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:40:56Z","timestamp":1760179256000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/21\/23\/9211"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,12,3]]},"references-count":102,"journal-issue":{"issue":"23","published-online":{"date-parts":[[2020,12]]}},"alternative-id":["ijms21239211"],"URL":"https:\/\/doi.org\/10.3390\/ijms21239211","relation":{},"ISSN":["1422-0067"],"issn-type":[{"type":"electronic","value":"1422-0067"}],"subject":[],"published":{"date-parts":[[2020,12,3]]}}}