Revisiting the role of transcription factors in coordinating the defense response against Citrus bark cracking viroid infection in commercial hop (Humulus lupulus L.)

Nath, Vishnu Sukumari (author), Kumar Mishra, Ajay (author), Kumar, Atul (author), Matoušek, Jaroslav (author), Jakše, Jernej (author)

Transcription factors (TFs) play a major role in controlling gene expression by intricately regulating diverse biological processes such as growth and development, the response to external stimuli and the activation of defense responses. The systematic identification and classification of TF genes are essential to gain insight into their evolutionary history, biological roles, and regulatory networks. In this study, we performed a global mining and characterization of hop TFs and their involvement in Citrus bark cracking viroid CBCVd infection by employing a digital gene expression analysis. Our systematic analysis resulted in the identification of a total of 3,818 putative hop TFs that were classified into 99 families based on their conserved domains. A phylogenetic analysis classified the hop TFs into several subgroups based on a phylogenetic comparison with reference TF proteins from Arabidopsis thaliana providing glimpses of their evolutionary history. Members of the same subfamily and subgroup shared conserved motif compositions. The putative functions of the CBCVd-responsive hop TFs were predicted using their orthologous counterparts in A. thaliana. The analysis of the expression profiling of the CBCVd-responsive hop TFs revealed a massive differential modulation, and the expression of the selected TFs was validated using qRT-PCR. Together, the comprehensive integrated analysis in this study provides better insights into the TF regulatory networks associated with CBCVd infections in the hop, and also offers candidate TF genes for improving the resistance in hop against viroids.

• Language: English
• Keywords: transcriptional reprogramming, viroid pathogenesis, hop stunt disease, management
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2019
• Number of pages: 19 str.
• Numbering: Vol. 11, iss. 5, art. 419
• PID: 20.500.12556/RUL-132325
• UDC: 577.2
• ISSN on article: 1999-4915
• DOI: 10.3390/v11050419
• COBISS.SI-ID: 9229433
• Publication date in RUL: 21.10.2021

Record is a part of a journal

• Title: Viruses
• Shortened title: Viruses
• Publisher: MDPI
• ISSN: 1999-4915
• COBISS.SI-ID: 517597977

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
• Licensing start date: 05.05.2019

Secondary language

• Language: Slovenian
• Keywords: genetske transformacije, viroid razpokanosti skorje agrumov, CBCVd, huda viroidna zakrnelost hmelja, Humulus lupulus, hmelj, transkriptomska analiza, različno izraženi geni