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.
BMC Genomics. 2020 Feb 14;21(1):160. doi: 10.1186/s12864-020-6549-5.
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). 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, limited information is available on its responses to exogenous stimuli at the level of gene expression.
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 stress, as compared to their respective controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the O-response DEGs revealed perturbation of several biological pathways including energy, lipid, amino acid, carbohydrate and terpenoid metabolism as well as plant-pathogen interaction.
This study provides the first reference transcriptome for NRO and initial insights into the genomic responses of NRO to O. Gene expression profiling reveals altered primary and secondary metabolism of NRO seedlings, including known defense responses such as terpenoid biosynthesis.
气候对森林健康起着至关重要的作用，气候变化可能会增加因非生物和生物胁迫而导致的森林生产力损失。温度升高会导致臭氧（O）形成增加。臭氧是由阳光、分子氧相互作用以及工业和汽车排放物中常见的化学物质如氮氧化物和挥发性有机化合物的反应形成的。尽管众所周知，北红栎（Quercus rubra）（北美东部森林中具有生态和经济重要性的物种）的生产力会因暴露于臭氧而降低，但关于其对外源刺激的基因表达水平响应的信息有限。
RNA 测序产生了超过 3.23 亿个高质量的原始序列读数。从头组装生成了 52662 个非编码基因，其中超过 42000 个序列可以通过基于同源性的搜索进行注释。与各自的对照相比，共检测到 4140 个对臭氧胁迫有反应的差异表达基因（DEGs）。对 O 反应 DEGs 的基因本体论（GO）和京都基因与基因组百科全书（KEGG）富集分析显示，包括能量、脂质、氨基酸、碳水化合物和萜类代谢以及植物-病原体相互作用在内的几个生物学途径受到干扰。
本研究为北红栎提供了第一个参考转录组，并初步了解了北红栎对 O 的基因组响应。基因表达谱揭示了北红栎幼苗中改变的初级和次级代谢，包括萜类生物合成等已知的防御反应。
