数字农科院2.0

Genome-Wide Identification and Characterization of the PPPDE Gene Family in Rice

文献类型： 外文期刊

作者： Wangmin Lian;Xiaodeng Zhan;Daibo Chen;Weixun Wu;Qunen Liu;Yinxing Zhang;Shihua Cheng;Xiangyang Lou;Liyong Cao;Yongbo Hong

作者机构：

关键词： domestication;phylogenetic analysis;PPPDE gene family;rice;stress response

期刊名称： Agronomy

ISSN： 2073-4395

年卷期： 2024 年 14 卷 5 期

页码：

收录情况： SCIE（2024版）

摘要： Protein ubiquitination is common and crucial in cellular functions, however, little is known about how deubiquitinating enzymes (DUBs) reverse regulate the ubiquitination signaling process. PPPDE family proteins are a novel class of deubiquitinating peptidases with demonstrated deubiquitination/deSUMOylating activities. In this study, we identified 10 PPPDE genes from the rice (Oryza sativa L.) genome unevenly distributed on five chromosomes, where most of these members have not been reported to date. Based on the gene structure, the OsPPPDE family consists of three distinct subgroups within the phylogenetic tree. Cis-element analysis identified light/phytohormone-responsive, development, and abiotic stress-related elements in the promoters of OsPPPDE. Furthermore, we conducted and analyzed the transcript abundance of OsPPPDE under various tissues and stresses using the transcriptome data of 352 samples from the Rice Expression Database and GEO datasets. Moreover, OsPPPDE5 showed differential regulation of its transcript abundance during Cd and drought stress. Collinearity and syntenic analysis of 101 PPPDEs and PPPDE-like proteins in 10 plant genomes indicated that this family is evolutionarily conserved. Domestication analysis suggests that OsPPPDEs may contribute to indica–japonica divergence using the data from the 3K Rice Genome Project. Our study provides a foundation for further study on the function and molecular mechanism of the OsPPPDE gene family.

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