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In this work, leaf transcriptomic changes were evaluated in the diploid C. canephora and its polyploid C. arabica, grown at 25 \u00b0C and at two supra-optimal temperatures (37 \u00b0C, 42 \u00b0C), under ambient (aCO2) or elevated air CO2 (eCO2). Both species expressed fewer genes as temperature rose, although a high number of differentially expressed genes (DEGs) were observed, especially at 42 \u00b0C. An enrichment analysis revealed that the two species reacted differently to the high temperatures but with an overall up-regulation of the photosynthetic machinery until 37 \u00b0C. Although eCO2 helped to release stress, 42 \u00b0C had a severe impact on both species. A total of 667 photosynthetic and biochemical related-DEGs were altered with high temperatures and eCO2, which may be used as key probe genes in future studies. This was mostly felt in C. arabica, where genes related to ribulose-bisphosphate carboxylase (RuBisCO) activity, chlorophyll a-b binding, and the reaction centres of photosystems I and II were down-regulated, especially under 42\u00b0C, regardless of CO2. Transcriptomic changes showed that both species were strongly affected by the highest temperature, although they can endure higher temperatures (37 \u00b0C) than previously assumed.<\/jats:p>","DOI":"10.3390\/ijms22063125","type":"journal-article","created":{"date-parts":[[2021,3,18]],"date-time":"2021-03-18T11:41:06Z","timestamp":1616067666000},"page":"3125","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["A Transcriptomic Approach to Understanding the Combined Impacts of Supra-Optimal Temperatures and CO2 Revealed Different Responses in the Polyploid Coffea arabica and Its Diploid Progenitor C. canephora"],"prefix":"10.3390","volume":"22","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\/0000-0001-5408-5212","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"}]},{"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"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9637-8475","authenticated-orcid":false,"given":"F\u00e1bio M.","family":"DaMatta","sequence":"additional","affiliation":[{"name":"Departamento de Biologia Vegetal, Universidade Federal Vi\u00e7osa (UFV), Vi\u00e7osa 36570-090, 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":[[2021,3,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1111\/j.1365-2486.2007.01511.x","article-title":"Effects of elevated CO2 on the protein concentration of food crops: A meta-analysis","volume":"14","author":"Taub","year":"2007","journal-title":"Glob. 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