Genome-wide analysis of the homeodomain-leucine zipper (HD-ZIP) gene family in peach (Prunus persica)

Abstract

ABSTRACT. In this study, 33 homeodomain-leucine zipper (HD-ZIP) genes were identified in peach using the HD-ZIP amino acid sequences of Arabidopsis thaliana as a probe. Based on the phylogenetic analysis and the individual gene or protein characteristics, the HD-ZIP gene family in peach can be classified into 4 subfamilies, HD-ZIP I, II, III, and IV, containing 14, 7, 4, and 8 members, respectively. The most closely related peach HD-ZIP members within the same subfamilies shared very similar gene structure in terms of either intron/exon numbers or lengths. Almost all members of the same subfamily shared common motif compositions, thereby implying that the HD-ZIP proteins within the same subfamily may have functional similarity. The 33 peach HD-ZIP genes were distributed across scaffolds 1 to 7. Although the primary structure varied among HD-ZIP family proteins, their tertiary structures were similar. The results from this study will 2655 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 13 (2): 2654-2668 (2014) Analysis of the HD-ZIP family in peach be useful in selecting candidate genes from specific subfamilies for functional analysis.

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

“…The HD-Zip family members were widely investigated in A. thaliana (Schena and Davis 1992), Z. mays (Zhao et al 2011), O. sativa (Agalou et al 2008), P. trichocarpa (Hu et al 2012), and other species (Liu et al 2013;Chen et al 2014;Zhang et al 2014). Until now, no genome-wide research, including gene identification, genome organization, and phylogenetic analysis, has been reported in pear.…”

“…Recent comprehensive analysis of genes encoding HD-Zip proteins from other plant species, such as Populus (Hu et al 2012), peach (Zhang et al 2014), soybean (Chen et al 2014), Arabidopsis (Olsson et al 2004), maize (Zhao et al 2011), and rice (Agalou et al 2008), enabled comparison of numbers and classification of these genes among different species. For some species, the larger the genome size of the Fig.…”

“…It is widely known that the intron/exon organization and intron types and numbers are clues of the evolution relationship within some gene families including HD-Zip genes (Zhao et al 2011). Studies in peach showed one gene of 14 HD-Zip I members without an intron (Zhang et al 2014). In Populus, 4 of 22 HD-Zip I genes had no introns (Hu et al 2012).…”

Isolation and expression analysis of four HD-ZIP III family genes targeted by microRNA166 in peach

“…Among them, miR166 is predicted to target the four genes of HD-ZIP III family, and has four nucleotide mismatches in the complementary area with three target genes (gene ID ppa001378m, ppa001343m, ppa001386m for CDS downloaded from GDR website) and three mismatches with one target gene (gene ID ppa001405m), respectively. Combined with our previous study on HD-ZIP family (Zhang et al, 2014) and NCBI BLAST using nucleotide sequences of HD-ZIP III family genes in Arabidopsis thaliana, peach genes with ID ppa001343m, ppa001405m, ppa001386m, and ppa001378m were named PpHB14, PpHB15, PpHB8, and PpREV in this work, respectively. Gene ontology (GO) annotation indicated the four genes function in nucleic acid binding and take part in many processes including meristem structural organization, anatomical structure arrangement, regulation of cell differentiation, and reproductive structure development.…”

“…Using the corresponding full-length cDNA sequences of each of the genes in peach predicted by Zhang et al (2014), specific primers were designed using Primer Premier 5.0 software (Premier Biosoft, Canada), and synthesized by Invitrogen Biotechnology Co., Ltd. Primers are listed in Table 1 Amplifications by PCR were performed in 25-µL volumes containing: 2.5 µL 10X PCR buffer; 0.5 µL 10 mM dNTP mixture, 2 µL MgCl 2 ; 0.3 µL LA Taq polymerase (5U/µL; Takara Biotechnology); 2 µL cDNA; 0.5 µL of each gene-specific primer; and 16.7 µL RNase-free water. Amplification was performed in an Eppendorf authorized thermal cycler (Eppendorf Vertrieb Deutschland GmbH, Hamburg, Germany) using the following program: 94°C pre-denaturing for 5 min; 34 cycles of 94°C for 1 min, the primer-specific melting temperature (Tm) for 1 min (shown in Table 1), and 72°C for 1 min; and 72°C for 10 min.…”