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Open AccessArticle

De Novo Transcriptome Sequencing of Low Temperature-Treated Phlox subulata and Analysis of the Genes Involved in Cold Stress

College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163000, China
Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences (HAS), Collaborative Innovation Center for Development and Utilization of Forest Resources, Harbin 150040, China
College of Horticulture, Northeast Agricultural University, Harbin 150030, China
Author to whom correspondence should be addressed.
Academic Editor: Ann Cuypers
Int. J. Mol. Sci. 2015, 16(5), 9732-9748;
Received: 15 March 2015 / Revised: 21 April 2015 / Accepted: 22 April 2015 / Published: 29 April 2015
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
PDF [2647 KB, uploaded 29 April 2015]


Phlox subulata, a perennial herbaceous flower, can survive during the winter of northeast China, where the temperature can drop to −30 °C, suggesting that P. subulata is an ideal model for studying the molecular mechanisms of cold acclimation in plants. However, little is known about the gene expression profile of P. subulata under cold stress. Here, we examined changes in cold stress-related genes in P. subulata. We sequenced three cold-treated (CT) and control (CK) samples of P. subulata. After de novo assembly and quantitative assessment of the obtained reads, 99,174 unigenes were generated. Based on similarity searches with known proteins in public protein databases, 59,994 unigenes were functionally annotated. Among all differentially expressed genes (DEGs), 8302, 10,638 and 11,021 up-regulated genes and 9898, 17,876, and 12,358 down-regulated genes were identified after treatment at 4, 0, and −10 °C, respectively. Furthermore, 3417 up-regulated unigenes were expressed only in CT samples. Twenty major cold-related genes, including transcription factors, antioxidant enzymes, osmoregulation proteins, and Ca2+ and ABA signaling components, were identified, and their expression levels were estimated. Overall, this is the first transcriptome sequencing of this plant species under cold stress. Studies of DEGs involved in cold-related metabolic pathways may facilitate the discovery of cold-resistance genes. View Full-Text
Keywords: Phlox subulata; cold acclimation; transcriptome; differentially expressed genes Phlox subulata; cold acclimation; transcriptome; differentially expressed genes

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Qu, Y.; Zhou, A.; Zhang, X.; Tang, H.; Liang, M.; Han, H.; Zuo, Y. De Novo Transcriptome Sequencing of Low Temperature-Treated Phlox subulata and Analysis of the Genes Involved in Cold Stress. Int. J. Mol. Sci. 2015, 16, 9732-9748.

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