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- Mun, Bong-Gyu, et al.
(författare)
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Analysis of transcription factors among differentially expressed genes induced by drought stress in Populus davidiana
- 2017
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Ingår i: 3 Biotech. - : Springer. - 2190-5738 .- 2190-572X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Populus davidiana is native to the Korean Peninsula and is one of the most dominant and abundantly growing forest trees in eastern Asia. Compared to other Populus species such as P. trichocarpa, P. euphratica, and P. tremula, relatively little is known about P. davidiana. Here, we performed transcriptomic analysis of P. davidiana under drought stress induced by 10% polyethylene glycol. A total of 12,403 and 12,414 differentially expressed genes (DEGs) were successfully annotated with the P. trichocarpa reference genome after 6 and 12 h of treatment, respectively. Of these, a total of 404 genes (238 up-regulated and 166 down-regulated) after 6 h and 359 genes (187 up-regulated and 172 down-regulated) after 12 h of treatment were identified as transcription factors. Transcription factors known to be key genes for drought stress response, such as AP2-EREB, WRKY, C2H2, and NAC, were identified. This results suggesting that early induction of these genes affected initiation of transcriptional regulation in response to drought stress. Quantitative real-time PCR results of selected genes showed highly significant (R = 0.93) correlation with RNA-Seq data. Interestingly, the expression pattern of some transcription factors was P. davidiana specific. The sequence of P. davidiana ortholog of P. trichocarpa gene POPTR_0018s10230, which plays an important role in plant response to drought, was further analyzed as our RNA-Seq results showed highly significant changes in the expression of this gene following the stress treatment. Sequence of the gene was compared to P. trichocarpa gene sequence using cloning-based sequencing. Additionally, we generated a predicted 3D protein structure for the gene product. Results indicated that the amino acid sequence of P. davidiana-specific POPTR_0018s10230 is different at six different positions compared to P. trichocarpa, resulting in a significantly different structure of the protein. Identifying the transcription factors expressed in P. davidiana under drought stress will not only offer clues for understanding the underlying mechanisms involved in drought stress physiology but also serve as a basis for future molecular studies on this species.
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| 2. |
- Mun, Bong-Gyu, et al.
(författare)
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Profile and time-scale dynamics of differentially expressed genes in transcriptome of Populus davidiana under drought stress
- 2017
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Ingår i: Plant Molecular Biology Reporter. - : Springer. - 0735-9640 .- 1572-9818. ; 35:6, s. 647-660
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Tidskriftsartikel (refereegranskat)abstract
- The genus Populus contains 25–35 species of deciduous flowering plants in the family Salicaceae. It has evolved to overcome various environmental stresses including drought stress through changes in physiological processes such a stomatal movement, photosynthesis, stress signaling, defense responses, and overall growth rate. In this study, we performed RNA-seq-based transcriptome profiling of Populus davidiana in response to drought stress induced by 10% PEG at two time points (6 and 12 h). We generated over 527 million reads by applying Populus trichocarpa as reference genome. Assembly of the reads yielded 32,650 genes and 75,820 transcripts; of these, after quantile normalization, a total of 997 genes were identified with dynamic expression over time, classifying them into nine different clusters. Among them, 550 genes responded significantly to drought stress treatment after 6 h (108 genes up-regulated and 201 genes down-regulated) and 12 h (161 up-regulated and 80 down-regulated) respectively, with at least twofold change in their expression. Based on analysis of these genes, we found several differentially expressed genes (DEGs) involved in cellular transport, transcriptional regulation, protein modification, regulation of cellular redox state, and those involved in response to other stresses. We also validated RNA-seq-mediated transcriptome data by RT-qPCR analysis of eight randomly selected DEGs. It showed significantly high correlation coefficient (0.95) suggesting high reliability of RNA-seq analysis. This study presents the first RNA-seq mediated transcriptome profile of P. davidiana in response to drought stress, providing critical information necessary for understanding the mechanisms underpinning drought stress tolerance in forest trees and other plant species.
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