Tags

Type your tag names separated by a space and hit enter

Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response.
Int J Mol Sci. 2015 Sep 30; 16(10):23517-44.IJ

Abstract

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.

Authors+Show Affiliations

Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China. qqwangahau@163.com.Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China. liujinyang315@163.com.Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China. yuwangahau@163.com.Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China. zhaoyang2013@ahau.edu.cn.Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China. hyjiang@ahau.edu.cn.Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China. beijiucheng@ahau.edu.cn.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

26437398

Citation

Wang, Qianqian, et al. "Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response." International Journal of Molecular Sciences, vol. 16, no. 10, 2015, pp. 23517-44.
Wang Q, Liu J, Wang Y, et al. Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response. Int J Mol Sci. 2015;16(10):23517-44.
Wang, Q., Liu, J., Wang, Y., Zhao, Y., Jiang, H., & Cheng, B. (2015). Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response. International Journal of Molecular Sciences, 16(10), 23517-44. https://doi.org/10.3390/ijms161023517
Wang Q, et al. Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response. Int J Mol Sci. 2015 Sep 30;16(10):23517-44. PubMed PMID: 26437398.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response. AU - Wang,Qianqian, AU - Liu,Jinyang, AU - Wang,Yu, AU - Zhao,Yang, AU - Jiang,Haiyang, AU - Cheng,Beijiu, Y1 - 2015/09/30/ PY - 2015/07/20/received PY - 2015/08/28/revised PY - 2015/09/16/accepted PY - 2015/10/6/entrez PY - 2015/10/6/pubmed PY - 2016/7/12/medline KW - PHD family KW - abiotic stress KW - duplication KW - genome-wide analysis KW - maize SP - 23517 EP - 44 JF - International journal of molecular sciences JO - Int J Mol Sci VL - 16 IS - 10 N2 - 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. SN - 1422-0067 UR - https://www.unboundmedicine.com/medline/citation/26437398/Systematic_Analysis_of_the_Maize_PHD_Finger_Gene_Family_Reveals_a_Subfamily_Involved_in_Abiotic_Stress_Response_ L2 - https://www.mdpi.com/resolver?pii=ijms161023517 DB - PRIME DP - Unbound Medicine ER -