Cao Yunpeng, Han Yahui, Meng Dandan, Abdullah Muhammad, Li Dahui, Jin Qing, Lin Yi, Cai Yongping
School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
Funct Integr Genomics. 2018 Sep;18(5):519-531. doi: 10.1007/s10142-018-0609-9. Epub 2018 Apr 20.
PHD-finger proteins, which belongs to the type of zinc finger family, and that play an important role in the regulation of both transcription and the chromatin state in eukaryotes. Currently, PHD-finger proteins have been well studied in animals, while few studies have been carried out on their function in plants. In the present study, 129 non-redundant PHD-finger genes were identified from 5 Rosaceae species (pear, apple, strawberry, mei, and peach); among them, 31 genes were identified in pear. Subsequently, we carried out a bioinformatics analysis of the PHD-finger genes. Thirty-one PbPHD genes were divided into 7 subfamilies based on the phylogenetic analysis, which are consistent with the intron-exon and conserved motif analyses. In addition, we identified five segmental duplication events, implying that the segmental duplications might be a crucial role in the expansion of the PHD-finger gene family in pear. The microsynteny analysis of five Rosaceae species showed that there were independent duplication events in addition to the genome-wide duplication of the pear genome. Subsequently, ten expressed PHD-finger genes of pear fruit were identified using qRT-PCR, and one of these genes, PbPHD10, was identified as an important candidate gene for the regulation of lignin synthesis. Our research provides useful information for the further analysis of the function of PHD-finger gene family in pear.
PHD 指蛋白属于锌指家族类型，在真核生物的转录和染色质状态调控中发挥重要作用。目前，PHD 指蛋白在动物中已得到充分研究，而对其在植物中的功能研究较少。在本研究中，从 5 种蔷薇科物种（梨、苹果、草莓、梅和桃）中鉴定出 129 个非冗余 PHD 指基因；其中，在梨中鉴定出 31 个基因。随后，我们对 PHD 指基因进行了生物信息学分析。基于系统发育分析，31 个 PbPHD 基因被分为 7 个亚家族，这与内含子 - 外显子和保守基序分析结果一致。此外，我们鉴定出 5 个片段重复事件，这表明片段重复可能在梨中 PHD 指基因家族的扩张中起关键作用。对 5 种蔷薇科物种的微同源性分析表明，除了梨基因组的全基因组复制外，还存在独立的复制事件。随后，利用 qRT-PCR 鉴定出梨果实中 10 个表达的 PHD 指基因，其中一个基因 PbPHD10 被鉴定为木质素合成调控的重要候选基因。我们的研究为进一步分析梨中 PHD 指基因家族的功能提供了有用信息。
