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Int. J. Mol. Sci. 2017, 18(9), 2005; doi:10.3390/ijms18092005

Genome-Wide Identification of the PHD-Finger Family Genes and Their Responses to Environmental Stresses in Oryza sativa L.

1
Key Laboratory of Agricultural Biological Functional Gene, College of Life Science, Northeast Agricultural University, Harbin 150038, China
2
Crop Stress Molecular Biology Laboratory, College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China
3
LGPM, CentraleSupélec, Université Paris-Saclay, SFR Condorcet FR CNRS 3417, Centre Européen de Biotechnologie et de Bioéconomie (CEBB), 3 rue des Rouges Terres, 51110 Pomacle, France
*
Authors to whom correspondence should be addressed.
Received: 20 June 2017 / Revised: 25 August 2017 / Accepted: 14 September 2017 / Published: 19 September 2017
(This article belongs to the Special Issue Selected Papers from the 6th National Plant Protein Research Congress)
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Abstract

The PHD-finger family has been demonstrated to be involved in regulating plant growth and development. However, little information is given for its role in environmental stress responses. Here, we identified a total of 59 PHD family genes in the rice genome. These OsPHDs genes were located on eleven chromosomes and synteny analysis only revealed nine duplicated pairs within the rice PHD family. Phylogenetic analysis of all OsPHDs and PHDs from other species revealed that they could be grouped into two major clusters. Furthermore, OsPHDs were clustered into eight groups and members from different groups displayed a great divergence in terms of gene structure, functional domains and conserved motifs. We also found that with the exception of OsPHD6, all OsPHDs were expressed in at least one of the ten tested tissues and OsPHDs from certain groups were expressed in specific tissues. Moreover, our results also uncovered differential responses of OsPHDs expression to environmental stresses, including ABA (abscisic acid), water deficit, cold and high Cd. By using quantitative real-time PCR, we further confirmed the differential expression of OsPHDs under these stresses. OsPHD1/7/8/13/33 were differentially expressed under water deficit and Cd stresses, while OsPHD5/17 showed altered expression under water deficit and cold stresses. Moreover, OsPHD3/44/28 displayed differential expression under ABA and Cd stresses. In conclusion, our results provide valuable information on the rice PHD family in plant responses to environmental stress, which will be helpful for further characterizing their biological roles in responding to environmental stresses. View Full-Text
Keywords: Oryza sativa; PHD-finger transcription factors; evolutionary divergence; expression analysis; environmental stress Oryza sativa; PHD-finger transcription factors; evolutionary divergence; expression analysis; environmental stress
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Sun, M.; Jia, B.; Yang, J.; Cui, N.; Zhu, Y.; Sun, X. Genome-Wide Identification of the PHD-Finger Family Genes and Their Responses to Environmental Stresses in Oryza sativa L.. Int. J. Mol. Sci. 2017, 18, 2005.

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