Analysis of transcription factors among differentially expressed genes induced by drought stress in Populus davidiana View Full Text


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Article Info

DATE

2017-06-30

AUTHORS

Bong-Gyu Mun, Sang-Uk Lee, Eung-Jun Park, Hyun-Ho Kim, Adil Hussain, Qari Muhammad Imran, In-Jung Lee, Byung-Wook Yun

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. More... »

PAGES

209

References to SciGraph publications

  • 2014-06-20. Genome-wide analysis of salt-responsive and novel microRNAs in Populus euphratica by deep sequencing in BMC GENOMIC DATA
  • 2014-06-20. Transcriptome sequencing of transgenic poplar (Populus × euramericana 'Guariento') expressing multiple resistance genes in BMC GENOMIC DATA
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  • 2010-07-15. Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa in BMC PLANT BIOLOGY
  • 2011-12-02. Comparative analysis of root transcriptome profiles of two pairs of drought-tolerant and susceptible rice near-isogenic lines under different drought stress in BMC PLANT BIOLOGY
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    PUBMED

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    25 schema:description 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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    32 C2H2
    33 Korean Peninsula
    34 NAC
    35 P. davidiana
    36 P. euphratica
    37 P. tremula
    38 P. trichocarpa
    39 P. trichocarpa reference genome
    40 PCR results
    41 Peninsula
    42 Populus davidiana
    43 Populus species
    44 Quantitative real-time PCR results
    45 RNA-seq data
    46 RNA-seq results
    47 WRKY
    48 acid sequence
    49 amino acid sequence
    50 analysis
    51 basis
    52 changes
    53 cloning-based sequencing
    54 clues
    55 correlation
    56 data
    57 davidiana
    58 different positions
    59 different structures
    60 drought
    61 drought stress
    62 drought stress physiology
    63 drought stress response
    64 early induction
    65 eastern Asia
    66 euphratica
    67 expression
    68 expression patterns
    69 factors
    70 forest trees
    71 future molecular studies
    72 gene products
    73 gene sequences
    74 genes
    75 genome
    76 glycol
    77 important role
    78 induction
    79 initiation
    80 key genes
    81 mechanism
    82 molecular studies
    83 orthologs
    84 patterns
    85 physiology
    86 plant responses
    87 polyethylene glycol
    88 position
    89 products
    90 protein
    91 protein structure
    92 real-time PCR results
    93 reference genome
    94 regulation
    95 response
    96 results
    97 role
    98 sequence
    99 sequencing
    100 significant changes
    101 species
    102 stress
    103 stress physiology
    104 stress response
    105 stress treatments
    106 structure
    107 study
    108 total
    109 transcription factors
    110 transcriptional regulation
    111 transcriptomic analysis
    112 treatment
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