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Revisiting the role of transcription factors in coordinating the defense response against Citrus bark cracking viroid infection in commercial hop (Humulus lupulus L.)
ID Nath, Vishnu Sukumari (Author), ID Kumar Mishra, Ajay (Author), ID Kumar, Atul (Author), ID Matoušek, Jaroslav (Author), ID Jakše, Jernej (Author)

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Abstract
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 This link opens in a new window
UDC:577.2
ISSN on article:1999-4915
DOI:10.3390/v11050419 This link opens in a new window
COBISS.SI-ID:9229433 This link opens in a new window
Publication date in RUL:21.10.2021
Views:660
Downloads:122
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Record is a part of a journal

Title:Viruses
Shortened title:Viruses
Publisher:MDPI
ISSN:1999-4915
COBISS.SI-ID:517597977 This link opens in a new window

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

Projects

Funder:Drugi - Drug financer ali več financerjev
Funding programme:Operational Programme Research, Development and Education
Project number:CZ.02.2.69/0.0/0.0/16_027/0008357
Acronym:MEMOBIC

Funder:Drugi - Drug financer ali več financerjev
Funding programme:Czech Science foundation
Project number:18-10515J/DFG STE 465/10-1

Funder:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
Project number:P4-0077
Name:Kmetijske rastline - genetika in sodobne tehnologije

Funder:Drugi - Drug financer ali več financerjev
Project number:RVO:60077344

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