Genome-wide identification of pear HD-Zip gene family and expression patterns under stress induced by drought, salinity, and pathogen

Hong Wang,Jing Lin,Xiao Gang Li,Youhong Chang

doi:10.1007/s11738-015-1933-5

Abstract

Homeodomain-leucine zipper (HD-Zip) transcription factor genes are unique in the plant kingdom. Studies have shown that HD-Zip transcription factor has four subfamilies (subfamilies I–IV), and each subfamily exerts similar or diverse functions in the growth and development as well as environmental stress responses of plants. Although a genome-wide analysis of this transcription factor has been performed in some species, systematic identification of sequences and expression patterns under biotic and abiotic stress have not been carried out in pear. In this study, we identified 52 putative HD-Zip genes within the pear genome. Based on the phylogenetic analysis, HD-Zip transcription factors were classified into four subfamilies: 18, 13, 5, and 16 members were identified separately in subfamilies I, II, III, and IV, respectively. Genes in the same subfamily shared the constituent structure and conserved motifs, thereby implying that the HD-Zip genes that shared similar structures may exert similar functions. Moreover, abundant stress-related and pathogen-related cis-elements were observed in the promoter region of the pear HD-Zip I and II genes. Transcript abundance level of 20 selected HD-Zip I and II genes were analyzed by quantitative real-time RT-PCR (qRT-PCR) during the infection of Alternaria alternata, and abiotic stress conditions such as drought and salinity treatment. The results confirmed that some genes display stress-inducible and pathogen-inducible expression patterns.

Highlights

Plants launch complex cellular, physiological, and molecular responses during their developmental processes (Sultan 2010)
According to the difference of HD sequence, HD size, and HD location, which are associated with other domains and gene structure, the HD-containing proteins are classified into six members including homeodomain-leucine zipper (HD-Zip), Wuschel-related homeobox (WOX), plant homeodomain associated to a finger domain (PHD-finger), bell domain (BELL), knotted related homeobox (KNOX), and zinc finger-homeodomain (ZF-HD) (Ariel et al 2010)
To obtain comprehensive information of PbHD-Zip genes in the pear genome, the Hidden Markov Model (HMM) profile of the homeobox and Homeodomain-leucine zipper (HD-Zip) domain (PF00046 and PF04618) were used as a query to search the database using the program HMMER3.0 (Liu et al 2014) with default E value; 118 HD-containing sequences were found in the pear genome

Summary

Introduction

Physiological, and molecular responses during their developmental processes (Sultan 2010). These responses are usually regulated by transcription factors (Nakashima et al 2009). The current studies on transcription factors are focused on NAC, AP2/ EREBP, MYB, WRKY, and HD-Zip. Homeobox is a conserved 60-amino acid motif called the homeodomain (HD), which is able to bind specific DNA sequences (Moens and Selleri 2006; Ariel et al 2010). The HD-Zip transcription factors are unique to the plant kingdom (Ariel et al 2010) They contain a highly conserved HD, and a Zip element (Schena and Davis 1992). The homeodomain is at the C-terminal end and binds to DNA, and the Zip element mediates

Methods

Results

Conclusion