Transcriptome-wide Identification and Cold Stress Expression Analysis of EfPHD-finger Family Genes in Erianthus fulvus
ZHANG Rong-Qiong1,2,*, QIAN Zhen-Feng1,2,*, GU Shu-Jie2,3, RAO Xi-Bing2,3, SHEN Qing-Qing2,3, LYU Shao-Zhi2,3, ZHAO Xue-Ting2,3, CHEN Shu-Ying2,3, WANG Xian-Hong2,3, HE Li-Lian1,2,3,**, LI Fu-Sheng1,2,3,**
1 The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming 650201, China; 2 College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; 3 Sugarcane Research Institute, Yunnan Agricultural University, Kunming 650201, China
Abstract：Erianthus fulvus, a relative wild species of sugarcane (Saccharum spp.), plays an important role in the study of sugarcane stress resistance. PHD-finger (plant homeodomain finger) protein is a transcription regulator that can respond to biological and abiotic stresses.In this study, based on the transcriptome identification of the EfPHD-finger family genes in Erianthus fulvus, bioinformatics and cold stress expression patterns were analyzed. The results showed that a total of 38 EfPHD-finger genes were identified. The number of amino acids encoded by EfPHD-finger genes ranged from 145 to 2 268, the molecular weight of EfPHD-finger proteins ranged from 16.161 0 to 251.333 7 kD, and the isoelectric point ranged from 4.35 to 9.66. The average hydrophilic coefficient ranges from -1.094 to 0.035. Subcellular localization indicated that all 37 EfPHD-finger proteins were in the nucleus, and only EfPHD24 was in the nucleus and chloroplast. Phylogenetic tree analysis demonstrated that 38 EfPHD-finger proteins were divided into 7 groups. Analysis of cold stress expression patterns based on transcriptome data revealed that 38 EfPHD-finger genes were differentially expressed under different degrees of cold stress. Among them, EfPHD13, EfPHD16, EfPHD21, EfPHD25, EfPHD28, EfPHD32, EfPHD34, and EfPHD38 were up-regulated, and EfPHD13 was sustained up-regulated, with the largest up-regulated multiple. The 8 up-regulated genes were verified by qPCR, and the correlation between the verification results and transcriptome sequencing results was analyzed. The results showed that the correlation of EfPHD25 and EfPHD28 genes was weak, and the correlation of other genes was strong (R≥0.90). Furthermore, EfPHD13 gene (GenBank No. OK356615) was cloned. Its CDS length was 1 863 bp, encoding 620 amino acids, containing PHD_MMD1_like domain, multiple phosphorylation sites, no signal peptide and transmembrane structure. This study provides reference for further research on the cold stress response function of PHD-finger family genes in Erianthus fulvus.
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