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Related Experiment Video

Updated: Oct 28, 2025

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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The DUB family in Populus: identification, characterization, evolution and expression patterns.

Wenqing Zheng1,2, Liang Du3,4

  • 1Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 10083, China.

BMC Genomics
|July 16, 2021
PubMed
Summary
This summary is machine-generated.

This study identified 88 deubiquitinase (DUB) genes in Populus trichocarpa, revealing their evolutionary relationships and distinct expression patterns. Many PtrUBP genes showed upregulation in response to phytohormones, suggesting a role in abiotic stress.

Keywords:
DeubiquitinasesEvolutionExpressionPopulus

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Area of Science:

  • Plant molecular biology
  • Genomics
  • Biochemistry

Background:

  • Deubiquitinase (DUB) enzymes regulate protein stability and ubiquitination, impacting crucial cellular processes like cell division and DNA repair.
  • While DUBs are vital in many organisms, their roles and characteristics in woody plants remain largely uncharacterized.

Purpose of the Study:

  • To comprehensively identify and characterize the deubiquitinase (DUB) gene family in the woody model plant, Populus trichocarpa.
  • To investigate the evolutionary relationships, gene structure, and expression patterns of these DUB genes.
  • To explore the potential involvement of specific DUB genes, particularly PtrUBP, in abiotic stress responses.

Main Methods:

  • Bioinformatic analysis to identify DUB family genes in the Populus trichocarpa genome.
  • Phylogenetic analysis to classify DUB genes into subfamilies and assess evolutionary relationships.
  • Analysis of gene structure, conserved motifs, and promoter cis-regulatory elements.
  • Examination of DUB gene expression profiles using existing transcriptome data.
  • Phytohormone treatment (abscisic acid, methyl jasmonate, salicylic acid) on selected PtrUBP genes.

Main Results:

  • Identification of 88 DUB genes in Populus trichocarpa, categorized into PtrUBP, PtrUCH, PtrOTU, PtrMJD, and PtrJAMM subfamilies.
  • Phylogenetic analysis revealed distinct groupings within each subfamily, with conserved gene structures and motifs.
  • Synteny analysis provided insights into the evolutionary history of DUB genes across different plant species.
  • Expression profiling indicated tissue-specific patterns for DUB genes.
  • A majority of the 16 tested PtrUBP genes were upregulated following foliar application of abscisic acid, methyl jasmonate, and salicylic acid.

Conclusions:

  • This study significantly expands the understanding of the DUB gene family in woody plants, specifically Populus.
  • The comprehensive analysis of gene structure, conserved elements, and expression provides a foundation for functional studies.
  • The results suggest a potential role for PtrUBP genes in the abiotic stress response mechanisms of Populus.