Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response
Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
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Authors to whom correspondence should be addressed.
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These authors contributed equally to this work.
Academic Editor: Jianhua Zhu
Int. J. Mol. Sci. 2015, 16(10), 23517-23544; https://doi.org/10.3390/ijms161023517
Received: 20 July 2015 / Revised: 28 August 2015 / Accepted: 16 September 2015 / Published: 30 September 2015
(This article belongs to the Special Issue Plant Molecular Biology)
Plant homeodomain (PHD)-finger proteins were found universally in eukaryotes and known as key players in regulating transcription and chromatin structure. Many PHD-finger proteins have been well studied on structure and function in animals. Whereas, only a few of plant PHD-finger factors had been characterized, and majority of PHD-finger proteins were functionally unclear. In this study, a complete comprehensive analysis of maize PHD family is presented. Sixty-seven PHD-finger genes in maize were identified and further divided into ten groups according to phylogenetic analysis that was supported by motif and intron/exon analysis. These genes were unevenly distributed on ten chromosomes and contained 12 segmental duplication events, suggesting that segmental duplications were the major contributors in expansion of the maize PHD family. The paralogous genes mainly experienced purifying selection with restrictive functional divergence after the duplication events on the basis of the Ka/Ks ratio. Gene digital expression analysis showed that the PHD family had a wide expression profile in maize development. In addition, 15 potential stress response genes were detected by promoter cis-element and expression analysis. Two proteins ZmPHD14 and ZmPHD19 were located in the nucleus. These results provided a solid base for future functional genome study of the PHD-finger family in maize and afforded important clues for characterizing and cloning potentially important candidates in response to abiotic stresses.
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Keywords:
PHD family; genome-wide analysis; duplication; maize; abiotic stress
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MDPI and ACS Style
Wang, Q.; Liu, J.; Wang, Y.; Zhao, Y.; Jiang, H.; Cheng, B. Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response. Int. J. Mol. Sci. 2015, 16, 23517-23544.
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