Comparative genomic analysis of expansin superfamily gene members in zucchini and cucumber and their expression profiles under different abiotic stresses

Arslan, Büşra; İncili, Çınar Yiğit; Ulu, Ferhat; Horuz, Erdoğan; Uğurlu, Aslı; Öçal, Mustafa; Kalyoncuoğlu, Elif; Baloğlu, Mehmet Cengiz; Altunoğlu, Yasemin Çelik

doi:10.1007/s12298-021-01108-w

Cited by 6 publications

(1 citation statement)

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“…Expansin genes encode for plant cell wall-related proteins which control plant cell division and contribute to the growth regulation of plant tissues 70 . CsEXPB-04 and CsEXPA-11 which are expansin genes are confirmed to play a role in abiotic stress responses in cucumber based on expression analysis 71 . The loosening of cell wall polysaccharides by loosening enzymes like expansins implies its importance under drought, osmotic, or salt stress to continue the growth of stressed cells and organs 41 .…”

Section: Discussionmentioning

confidence: 96%

Deciphering the molecular basis of abiotic stress response in cucumber (Cucumis sativus L.) using RNA-Seq meta-analysis, systems biology, and machine learning approaches

Zinati

Nazari

2023

Sci Rep

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Abiotic stress in cucumber (Cucumis sativus L.) may trigger distinct transcriptome responses, resulting in significant yield loss. More insight into the molecular underpinnings of the stress response can be gained by combining RNA-Seq meta-analysis with systems biology and machine learning. This can help pinpoint possible targets for engineering abiotic tolerance by revealing functional modules and key genes essential for the stress response. Therefore, to investigate the regulatory mechanism and key genes, a combination of these approaches was utilized in cucumber subjected to various abiotic stresses. Three significant abiotic stress-related modules were identified by gene co-expression network analysis (WGCNA). Three hub genes (RPL18, δ-COP, and EXLA2), ten transcription factors (TFs), one transcription regulator, and 12 protein kinases (PKs) were introduced as key genes. The results suggest that the identified PKs probably govern the coordination of cellular responses to abiotic stress in cucumber. Moreover, the C2H2 TF family may play a significant role in cucumber response to abiotic stress. Several C2H2 TF target stress-related genes were identified through co-expression and promoter analyses. Evaluation of the key identified genes using Random Forest, with an area under the curve of ROC (AUC) of 0.974 and an accuracy rate of 88.5%, demonstrates their prominent contributions in the cucumber response to abiotic stresses. These findings provide novel insights into the regulatory mechanism underlying abiotic stress response in cucumber and pave the way for cucumber genetic engineering toward improving tolerance ability under abiotic stress.

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Section: Discussionmentioning

confidence: 96%