RNA-seq provides insights into potato deubiquitinase responses to drought stress in seedling stage

Xun Tang; Fujun Sun; Ning Zhang; Birendra Bahadur Rana; Raju Kharel; Pan Luo; Huaijun Si

doi:10.3389/fpls.2023.1268448

RNA-seq provides insights into potato deubiquitinase responses to drought stress in seedling stage

Front Plant Sci. 2023 Sep 14:14:1268448. doi: 10.3389/fpls.2023.1268448. eCollection 2023.

Authors

Xun Tang^{1

2}, Fujun Sun², Ning Zhang^{1

2}, Birendra Bahadur Rana³, Raju Kharel⁴, Pan Luo², Huaijun Si^{1

2}

Affiliations

¹ State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China.
² College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China.
³ Nepal Agricultural Research Council, National Potato Research Program, Lalitpur, Nepal.
⁴ Department of Genetics and Plant Breeding, Agricultural and Forestry University, Chitwan, Nepal.

Abstract

Ubiquitination is a specific protein degradation and reversible post-translational modification process that can be reversed by deubiquitinase (DUBs). DUBs can hydrolyze and release ubiquitin in the substrate protein so that the substrate can avoid degradation or change its activity, and it has an impact on plant growth and development, cell cycle, abiotic stress response, and other biological processes. Transcript sequences of potato varieties "DM1-3", "Atlantic" and "Cooperation-88" downloaded from Potato Genome Resources were used for genome-wide identification of the DUB gene family using Hidden Markov Models and verified in the NCBI CD-Search tool. The characteristics of DUB genes from different potato varieties were analyzed including subcellular localization, gene structural motifs, phylogenetic tree, and sequence homology. Polyethylene glycol 6000 (PEG6000) induced drought stress transcriptome analysis was performed on the "Atlantic", and differentially expressed genes were screened, with emphasis on the characterization of deubiquitinase. DUB genes have a complex gene structure, often with a large number of exons and alternative splicing. Their promoters contain abundant abiotic stress-responsive elements, such as 425 MYC, 325 ABRE, and 320 MYB. There are also a large number of orthologous genes in the DUBs of the three potato varieties, and these genes are often clustered in similar regions on the genome. We performed transcriptome sequencing of the potato under PEG-induced drought stress and analyzed it for the first time using the Atlantic as a reference genome. We identified a total of 6067 down-regulated differentially expressed genes (DEGs) and 4950 up-regulated DEGs under PEG-induced drought stress. We screened the expression of DUBs and observed that 120 DUBs were up-regulated where most of them functioned in the nucleus, and the interacting proteins of DUBs were also localized in the nucleus. We have comprehensively identified and analyzed potato DUBs, and the accurately aligned transcriptome data which will further deepen the understanding of DUBs involved in the regulation of osmotic stress.

Keywords: RNA-Seq; Solanum tuberosum L; abiotic stress; deubiquitinase; deubiquitination; genome-wide analysis.

Grants and funding

The authors declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the Natural Science Foundation of Gansu Province (21JR7RA847), Project of Key Research Base of Social Science in Sichuan Province (MLS1908) and the Key Program of Natural Science Foundation of Gansu Province (No. 22JR5RA832).