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Ozone is formed by the interaction of sunlight, molecular oxygen and by the reactions of chemicals commonly found in industrial and automobile emissions such as nitrogen oxides and volatile organic compounds.<\/jats:p><jats:p>Although it is well known that productivity of Northern red oak (<jats:italic>Quercus rubra<\/jats:italic>) (NRO), an ecologically and economically important species in the forests of eastern North America, is reduced by exposure to O<jats:sub>3<\/jats:sub>, limited information is available on its responses to exogenous stimuli at the level of gene expression.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>RNA sequencing yielded more than 323 million high-quality raw sequence reads. De novo assembly generated 52,662 unigenes, of which more than 42,000 sequences could be annotated through homology-based searches. A total of 4140 differential expressed genes (DEGs) were detected in response to O<jats:sub>3<\/jats:sub>stress, as compared to their respective controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the O<jats:sub>3<\/jats:sub>-response DEGs revealed perturbation of several biological pathways including energy, lipid, amino acid, carbohydrate and terpenoid metabolism as well as plant-pathogen interaction.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>This study provides the first reference transcriptome for NRO and initial insights into the genomic responses of NRO to O<jats:sub>3<\/jats:sub>. Gene expression profiling reveals altered primary and secondary metabolism of NRO seedlings, including known defense responses such as terpenoid biosynthesis.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12864-020-6549-5","type":"journal-article","created":{"date-parts":[[2020,2,14]],"date-time":"2020-02-14T15:04:54Z","timestamp":1581692694000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Transcriptome profiles of Quercus rubra responding to increased O3 stress"],"prefix":"10.1186","volume":"21","author":[{"given":"Nourolah","family":"Soltani","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teo","family":"Best","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dantria","family":"Grace","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christen","family":"Nelms","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ketia","family":"Shumaker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeanne","family":"Romero-Severson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"Moses","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephan","family":"Schuster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2971-9353","authenticated-orcid":false,"given":"Margaret","family":"Staton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Carlson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimberly","family":"Gwinn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,2,14]]},"reference":[{"issue":"6","key":"6549_CR1","doi-asserted-by":"publisher","first-page":"928","DOI":"10.1086\/285581","volume":"142","author":"VL Sork","year":"1993","unstructured":"Sork VL, Stowe KA, Hochwender C. 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