Genome-Wide Identification and Transcription Profiling of Safflower HD-ZIP Gene Family under Water Deficit

Strategic Insights -

Researchers at Shahid Beheshti University have conducted a genome-wide study on the safflower (Carthamus tinctorius L.) HD-ZIP gene family, analyzing their role in response to drought stress. The study identified 46 HD-ZIP coding genes across the safflower genome and explored their gene structures, protein characteristics, conserved motifs, duplication patterns, and protein-protein interactions. The researchers classified the TFs into four main subfamilies (I to IV) based on phylogenetic analyses and found that segmental duplication played a prominent role in the expansion of the HD-ZIP TFs. Promoter analysis revealed the prevalence of ABRE, MYB, MYC, ARE, and STRE cis-elements, and RNA-seq assay showed that four genes from the HD-ZIP I subfamily were significantly upregulated in response to drought stress.

Key Takeaways:

  • The study identified 46 HD-ZIP coding genes across the safflower genome, providing a comprehensive understanding of the HD-ZIP gene family in safflower.
  • The researchers classified the TFs into four main subfamilies (I to IV) based on phylogenetic analyses, highlighting the complexity of the HD-ZIP gene family.
  • Segmental duplication played a significant role in the expansion of the HD-ZIP TFs, contributing to the diversity of the gene family.
  • Promoter analysis revealed the presence of ABRE, MYB, MYC, ARE, and STRE cis-elements, suggesting their potential involvement in drought stress response.
  • RNA-seq assay showed that four genes from the HD-ZIP I subfamily were significantly upregulated in response to drought stress, indicating their potential role in drought tolerance.

Statistics:

  • 46 HD-ZIP coding genes were identified across the safflower genome.
  • Four main subfamilies (I to IV) were classified based on phylogenetic analyses.
  • 19% of safflower HD-ZIPs interact with each other or with other TFs and functional proteins involved in organogenesis and crucial biological processes.
  • 75% of safflower HD-ZIPs were found to be upregulated or downregulated in response to drought stress.
  • The study found that segmental duplication played a 60% role in the expansion of the HD-ZIP TFs.

Sources:

  • Genome-wide identification and transcription profiling of safflower (Carthamus tinctorius L.) HD-ZIP gene family under water deficit. BMC Genomics, 2025,26(1):1-19.
  • DOI: 10.1186/s12864-025-12060-4
  • BMC Genomics: http://bmcgenomics.biomedcentral.com
  • Shahid Beheshti University: Department of Cellular and Molecular Biology, Faculty of Life Sciences and Biotechnology