Identification and expression analysis of ZF-HD transcription factor gene family in Camellia sinensis

【Objective】Identification and analysis of ZF-HD(zinc finger homeodomain) gene family members by bioinformatics methods and detection of their expression patterns under different tissues, abiotic stresses and hormone induction were conducted, which laid theoretical basis for the functional study of tea plant ZF-HD(ZFD) family gene and improvement of tea genetic traits.【Method】ZF-HD gene family members of tea plant were identified from tea plant genome by HMMER program prediction and sequence alignment. A variety of bioinformatics analysis tools were used to analyze gene structure, promoter elements, and the physical and chemical properties, amino acid sequences, structural characteristics, evolutionary relationships, of the encoded protein. Based on RNA-Seq data, the expression patterns of members of the ZF-HD gene family in different tissues under drought stress, salt stress, and methyl jasmonate(MeJA) were analyzed.【Result】Seventeen ZF-HD gene family members(CsZHD1-CsZHD17) were identified from tea plant genome database. Coding region sequence(CDS) length was 369-2187 bp, encoding 122-728 amino acid residues. CsZHD encoded proteins with molecular weights ranging from 13.51 to 80.42 kD and theoretical isoelectric points of 6.09 to 9.19, which were all hydrophilic and unstable proteins. The secondary structure consisted of beta-turn, extended strand, alpha-helix and random-coil state. The results of subcellular localization showed that except CsZHD2, CsZHD5, and CsZHD7 proteins were localized in the cytoplasmic and CsZHD9 was localized in the extracellular, all other CsZHD proteins were localized in the nuclears. Only CsZHD2, CsZHD7, CsZHD9, CsZHD10 and CsZHD12 contained exons and introns, and the other 12 CsZHDs had no introns. CsZHD7 protein had two ZF-HD_dimer domains and the other 16 proteins had one ZF-HD_dimer domain. CsZHD1-CsZHD17 had 2-5 conserved motifs, and motif 1 and motif 3 were shared conserved motifs in CsZHDs. Tea ZH-HD family proteins could be divided into 5 subfamilies(ZHDⅠ, ZHDⅡ, ZHDⅢ, ZHDⅣand MIF), but the tea plant lacked the ZHDⅤsubfamily compared to Arabidopsis thaliana. The expression profile of the ZHD genes using RNA-Seq data showed that except for CsZHD2, CsZHD12, and CsZHD17, which were not expressed in these eight tissues or the expression levels were low, other CsZHDs genes were differentially expressed in the 8 tissues. The expression levels of CsZHD1, CsZHD2, CsZHD5, CsZHD12, CsZHD14 and CsZHD17 were always at a low level, and other CsZHDs genes showed different expressional trends under drought and salt stresses. Under MeJA treatment, most CsZHDs genes showed a downward-regulated expression except for the extremely low expression of CsZHD2, CsZHD5 and CsZHD12.【Conclusion】Seventeen members of the ZH-HD gene family were identified from the tea tree genome, and the encoded proteins have conserved zinc finger domain and homotype box domain. Tea trees lack ZHDⅤsubgroups compared to the A. thaliana ZH-HD gene family;the expression of the CsZHDs gene is tissue-specific, and most members are affected by ambiotic stress and MeJA.