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BMC Genomics

Title:		Transcriptome profiles of Quercus rubra responding to increased O(3) stress
Author(s):		Soltani N; Best T; Grace D; Nelms C; Shumaker K; Romero-Severson J; Moses D; Schuster S; Staton M; Carlson J; Gwinn K;
Address:		"The Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA. The Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA. Department of Biological & Environmental Sciences, University of West Alabama, Livingston, AL, 35470, USA. Department of Biological Sciences, Notre Dame University, 46556, Notre Dame, IN, France. Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Nanyang Technological University, Nanyang Avenue, 637551, Singapore. The Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA. mstaton1@utk.edu. The Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA. jec16@psu.edu. The Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA. kgwinn@utk.edu"
Journal Title:		BMC Genomics
Year:		2020
Volume:		20200214
Issue:		1
Page Number:		160 -
DOI:		10.1186/s12864-020-6549-5
ISSN/ISBN:		1471-2164 (Electronic) 1471-2164 (Linking)
Abstract:		"BACKGROUND: Climate plays an essential role in forest health, and climate change may increase forest productivity losses due to abiotic and biotic stress. Increased temperature leads to the increased formation of ozone (O(3)). 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. Although it is well known that productivity of Northern red oak (Quercus rubra) (NRO), an ecologically and economically important species in the forests of eastern North America, is reduced by exposure to O(3), limited information is available on its responses to exogenous stimuli at the level of gene expression. RESULTS: 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(3) stress, as compared to their respective controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the O(3)-response DEGs revealed perturbation of several biological pathways including energy, lipid, amino acid, carbohydrate and terpenoid metabolism as well as plant-pathogen interaction. CONCLUSION: This study provides the first reference transcriptome for NRO and initial insights into the genomic responses of NRO to O(3). Gene expression profiling reveals altered primary and secondary metabolism of NRO seedlings, including known defense responses such as terpenoid biosynthesis"
Keywords:		"Biosynthetic Pathways Computational Biology/methods *Gene Expression Profiling Gene Expression Regulation, Plant Gene Ontology Host-Pathogen Interactions Molecular Sequence Annotation Ozone/*metabolism Quercus/*genetics/*metabolism Signal Transduction *St;"
Notes:		"MedlineSoltani, Nourolah Best, Teo Grace, Dantria Nelms, Christen Shumaker, Ketia Romero-Severson, Jeanne Moses, Daniela Schuster, Stephan Staton, Margaret Carlson, John Gwinn, Kimberly eng PGRP-OIS-1025974/National Science Foundation/ PEN04532 1000326/National Institute of Food and Agriculture/ England 2020/02/16 BMC Genomics. 2020 Feb 14; 21(1):160. doi: 10.1186/s12864-020-6549-5"