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

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.

Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

“…More recently, Jian et al. (2022) and Tang et al. (2023) delved into the molecular responses of potatoes to drought stress and ubiquitination, respectively.…”

“…The study identified 5,508 DEGs and highlighted the significant enrichment of categories related to nucleic acid binding, transporter activity, ion/molecule transport, ion binding, kinase activity, and oxidative phosphorylation. More recently, Jian et al (2022) and Tang et al (2023) delved into the molecular responses of potatoes to drought stress and ubiquitination, respectively. Jian et al identified 12,798 DEGs in response to simulated drought stress, elucidating pathways such as galactose metabolism, fatty acid metabolism, and plant-pathogen interaction.…”

Differentially Expressed Genes Identification of Kohlrabi Seedlings (Brassica oleracea var. caulorapa L.) under Polyethylene Glycol Osmotic Stress and AP2/ERF Transcription Factor Family Analysis

“…Therefore, it is of great significance to study response mechanisms to physiological drought caused by osmotic stress and excavate differentially expressed genes of different crops. Relying on transcriptome sequencing approach, a large number of differentially expressed genes (DEGs) in response to Polyethylene Glycol (PEG) osmotic stress were identified [ 13 , 14 ]. In root and tuber crops, Karanja et al [ 15 ] reported that the RsERF045 , RsERF104 and RsERF184 genes were highly responsive to PEG in radish.…”