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Genetic Regulation of Biotic Stress Responses
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Genetic Regulation of Biotic Stress Responses

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (15 August 2024) | Viewed by 17693

Special Issue Editor

Prof. Dr. Zhuo Chen

E-Mail Website
Guest Editor
Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
Interests: phytopathogenic fungi; fungal disease; genetic; genomics; coding RNA and no-coding RNA; fungicide
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant diseases caused by phytopathogens can seriously affect the productivity and quality of crops. A large number of studies have focused on the genes of resistance or susceptibility, as well as the action mechanisms of crop disease. The study of plant–pathogen interactions would contribute to our understanding of resistance responses of the plant host and the infection mechanism of the phytopathogens. This would also help us to discover novel resistance genes, then raise novel resistance varieties and develop pesticides with novel action targets. At present, the sequencing of whole-genome, whole-transcriptome, degradome, metabolome, and some bioinformatics methods involved with predicting resistance genes could be used in studying the resistance responses of the host. These would contribute to revealing the response mechanisms. This Special Issue will publish research articles detailing the response mechanisms of a plant host during infection, and also review the latest advances in plant–pathogen interactions. We expect to publish sixteen to eighteen research articles and two or three review articles in this Special Issue.

Prof. Dr. Zhuo Chen
Guest Editor

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Keywords

  • plant diseases
  • biotic stress
  • resistance genes
  • genetic
  • genomics
  • plant host

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Published Papers (8 papers)

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Research

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16 pages, 1767 KiB  
Communication
Transcriptome-Based Comparative Expression Profiling of Sweet Potato during a Compatible Response with Root-Knot Nematode Meloidogyne incognita Infection
by Yeon Woo Sung, Jaewook Kim, Jung-Wook Yang, Donghwan Shim and Yun-Hee Kim
Genes 2023, 14(11), 2074; https://doi.org/10.3390/genes14112074 - 13 Nov 2023
Cited by 4 | Viewed by 1277
Abstract
M. incognita, a root-knot nematode (RKN), infects the roots of several important food crops, including sweet potato (Ipomoea batatas Lam.), and severely reduces yields. However, the molecular mechanisms underlying infection remain unclear. Previously, we investigated differential responses to RKN invasion in [...] Read more.
M. incognita, a root-knot nematode (RKN), infects the roots of several important food crops, including sweet potato (Ipomoea batatas Lam.), and severely reduces yields. However, the molecular mechanisms underlying infection remain unclear. Previously, we investigated differential responses to RKN invasion in susceptible and resistant sweet potato cultivars through RNA-seq-based transcriptome analysis. In this study, gene expression similarities and differences were examined in RKN-susceptible sweet potato cultivars during the compatible response to RKN infection. Three susceptible cultivars investigated in previous research were used: Dahomi (DHM), Shinhwangmi (SHM), and Yulmi (YM). Of the three cultivars, YM had the highest number of genes with altered expression in response to infection. YM was also the cultivar with the highest susceptibility to RKN. Comparisons among cultivars identified genes that were regulated in more than one cultivar upon infection. Pairwise comparisons revealed that YM and DHM shared the most regulated genes, whereas YM and SHM shared the lowest number of regulated genes. Five genes were up-regulated, and two were down-regulated, in all three cultivars. Among these, four genes were highly up-regulated in all cultivars: germin-like protein, anthranilate synthase α subunit, isocitrate lyase, and uncharacterized protein. Genes were also identified that were uniquely regulated in each cultivar in response to infection, suggesting that susceptible cultivars respond to infection through shared and cultivar-specific pathways. Our findings expand the understanding of the compatible response to RKN invasion in sweet potato roots and provide useful information for further research on RKN defense mechanisms. Full article
(This article belongs to the Special Issue Genetic Regulation of Biotic Stress Responses)
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13 pages, 13403 KiB  
Article
Genome-Wide Identification and Characterization of the WRKY Gene Family in Cucurbita maxima
by Qin Zhou, Ziqing Guo, Xiaojun Zhou, Lei Zhou, Duanhua Wang, Kailiang Bo and Pu Zhu
Genes 2023, 14(11), 2030; https://doi.org/10.3390/genes14112030 - 31 Oct 2023
Viewed by 1503
Abstract
In higher plants, WRKY transcription factors are broadly involved in a variety of life activities and play an important role in both biotic and abiotic stress responses. However, little is known about the functions of WRKY genes in the popular species, such as [...] Read more.
In higher plants, WRKY transcription factors are broadly involved in a variety of life activities and play an important role in both biotic and abiotic stress responses. However, little is known about the functions of WRKY genes in the popular species, such as Cucurbita maxima (pumpkin), which is planted worldwide. In the present study, 102 CmWRKY genes were identified in the C. maxima genome. Chromosome location, multiple sequence alignment, phylogenetic analysis, and synteny analysis of the CmWRKYs were performed. Notably, we found that silencing CmWRKY22 promoted cucumber mosaic virus (CMV) infection, whereas overexpression of CmWRKY22 inhibited the CMV infection. Subsequently, an electrophoretic mobility shift assay (EMSA) confirmed that CmWRKY22 was able to bind to the W-box at the promoter of CmPR1b, which is a responsive gene of the salicylic acid (SA) signaling pathway. In summary, this study has provided a foundation for the antiviral functions of WRKY transcription factors in C. maxima. Full article
(This article belongs to the Special Issue Genetic Regulation of Biotic Stress Responses)
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12 pages, 1825 KiB  
Article
Transcriptomic Analysis of Tobacco Plants in Response to Whitefly Infection
by Xin Wang, Zhuang-Xin Ye, Yi-Zhe Wang, Xiao-Jing Wang, Jian-Ping Chen and Hai-Jian Huang
Genes 2023, 14(8), 1640; https://doi.org/10.3390/genes14081640 - 18 Aug 2023
Cited by 3 | Viewed by 1652
Abstract
The whitefly Bemisia tabaci is one of the most destructive pests worldwide, and causes tremendous economic losses. Tobacco Nicotiana tabacum serves as a model organism for studying fundamental biological processes and is severely damaged by whiteflies. Hitherto, our knowledge of how tobacco perceives [...] Read more.
The whitefly Bemisia tabaci is one of the most destructive pests worldwide, and causes tremendous economic losses. Tobacco Nicotiana tabacum serves as a model organism for studying fundamental biological processes and is severely damaged by whiteflies. Hitherto, our knowledge of how tobacco perceives and defends itself against whiteflies has been scare. In this study, we analyze the gene expression patterns of tobacco in response to whitefly infestation. A total of 244 and 2417 differentially expressed genes (DEGs) were identified at 12 h and 24 h post whitefly infestation, respectively. Enrichment analysis demonstrates that whitefly infestation activates plant defense at both time points, with genes involved in plant pattern recognition, transcription factors, and hormonal regulation significantly upregulated. Notably, defense genes are more intensely upregulated at 24 h post infestation than at 12 h, indicating an increased immunity induced by whitefly infestation. In contrast, genes associated with energy metabolism, carbohydrate metabolism, ribosomes, and photosynthesis are suppressed, suggesting impaired plant development. Taken together, our study provides comprehensive insights into how plants respond to phloem-feeding insects, and offers a theoretical basis for better research on plant–insect interactions. Full article
(This article belongs to the Special Issue Genetic Regulation of Biotic Stress Responses)
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16 pages, 5967 KiB  
Article
Genome-Wide Identification and Functional Analysis of NAP1 in Triticum aestivum
by Huimin Feng, Mila Wu, Ziqiong Wang, Xia Wang, Jianping Chen, Jian Yang and Peng Liu
Genes 2023, 14(5), 1041; https://doi.org/10.3390/genes14051041 - 4 May 2023
Viewed by 1869
Abstract
As a main molecular chaperone of histone H2A-H2B, nucleosome assembly protein 1 (NAP1) has been widely researched in many species. However, there is little research investigating the function of NAP1 in Triticum aestivum. To understand the capabilities of the family of NAP1 [...] Read more.
As a main molecular chaperone of histone H2A-H2B, nucleosome assembly protein 1 (NAP1) has been widely researched in many species. However, there is little research investigating the function of NAP1 in Triticum aestivum. To understand the capabilities of the family of NAP1 genes in wheat and the relationship between TaNAP1 genes and plant viruses, we performed comprehensive genome-wide analysis and quantitative real-time polymerase chain reaction (qRT-PCR) for testing expression profiling under hormonal and viral stresses. Our results showed that TaNAP1 was expressed at different levels in different tissues, with higher expression in tissues with high meristematic capacity, such as roots. Furthermore, the TaNAP1 family may participate in plant defense mechanisms. This study provides a systematic analysis of the NAP1 gene family in wheat and lays the foundation for further studies on the function of TaNAP1 in the response of wheat plants to viral infection. Full article
(This article belongs to the Special Issue Genetic Regulation of Biotic Stress Responses)
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12 pages, 7034 KiB  
Article
Molecular Cloning and Characterization of WRKY12, A Pathogen Induced WRKY Transcription Factor from Akebia trifoliata
by Feng Wen, Xiaozhu Wu, Lishen Zhang, Jiantao Xiao, Tongjian Li and Mingliang Jia
Genes 2023, 14(5), 1015; https://doi.org/10.3390/genes14051015 - 29 Apr 2023
Cited by 5 | Viewed by 1857
Abstract
WRKY transcription factors (TFs), which are plant-specific TFs, play significant roles in plant defense. Here, a pathogen-induced WRKY gene, named AktWRKY12, which was the homologous gene of AtWRKY12, was isolated from Akebia trifoliata. The AktWRKY12 gene has a total length [...] Read more.
WRKY transcription factors (TFs), which are plant-specific TFs, play significant roles in plant defense. Here, a pathogen-induced WRKY gene, named AktWRKY12, which was the homologous gene of AtWRKY12, was isolated from Akebia trifoliata. The AktWRKY12 gene has a total length of 645 nucleotides and an open reading frame (ORF) encoding 214 amino acid polypeptides. The characterizations of AktWRKY12 were subsequently performed with the ExPASy online tool Compute pI/Mw, PSIPRED and SWISS-MODEL softwares. The AktWRKY12 could be classified as a member of WRKY group II-c TFs based on sequence alignment and phylogenetic analysis. The results of tissue-specific expression analysis revealed that the AktWRKY12 gene was expressed in all the tested tissues, and the highest expression level was detected in A. trifoliata leaves. Subcellular localization analysis showed that AktWRKY12 was a nuclear protein. Results showed that the expression level of AktWRKY12 significantly increased in A. trifoliata leaves with pathogen infection. Furthermore, heterologous over-expression of AktWRKY12 in tobacco resulted in suppressed expression of lignin synthesis key enzyme genes. Based on our results, we speculate that AktWRKY12 might play a negative role in A. trifoliata responding to biotic stress by regulating the expression of lignin synthesis key enzyme genes during pathogen infection. Full article
(This article belongs to the Special Issue Genetic Regulation of Biotic Stress Responses)
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16 pages, 5296 KiB  
Article
Comprehensive Analysis of NAC Genes Reveals Differential Expression Patterns in Response to Pst DC3000 and Their Overlapping Expression Pattern during PTI and ETI in Tomato
by Songzhi Xu, Zhiyao Zhang, Jiajing Zhou, Xiao Han, Kun Song, Haiying Gu, Suqin Zhu and Lijun Sun
Genes 2022, 13(11), 2015; https://doi.org/10.3390/genes13112015 - 2 Nov 2022
Cited by 5 | Viewed by 2333
Abstract
NAC (NAM/ATAF/CUC) transcription factors belong to a unique gene family in plants, which play vital roles in regulating diverse biological processes, including growth, development, senescence, and in response to biotic and abiotic stresses. Tomato (Solanum lycopersicum), as the most highly valued [...] Read more.
NAC (NAM/ATAF/CUC) transcription factors belong to a unique gene family in plants, which play vital roles in regulating diverse biological processes, including growth, development, senescence, and in response to biotic and abiotic stresses. Tomato (Solanum lycopersicum), as the most highly valued vegetable and fruit crop worldwide, is constantly attacked by Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), causing huge losses in production. Thus, it is essential to conduct a comprehensive identification of the SlNAC genes involved in response to Pst DC3000 in tomato. In this study, a complete overview of this gene family in tomato is presented, including genome localization, protein domain architectures, physical and chemical features, and nuclear location score. Phylogenetic analysis identified 20 SlNAC genes as putative stress-responsive genes, named SSlNAC 1–20. Expression profiles analysis revealed that 18 of these 20 SSlNAC genes were significantly induced in defense response to Pst DC3000 stress. Furthermore, the RNA-seq data were mined and analyzed, and the results revealed the expression pattern of the 20 SSlNAC genes in response to Pst DC3000 during the PTI and ETI. Among them, SSlNAC3, SSlNAC4, SSlNAC7, SSlNAC8, SSlNAC12, SSlNAC17, and SSlNAC19 were up-regulated against Pst DC3000 during PTI and ETI, which suggested that these genes may participate in both the PTI and ETI pathway during the interaction between tomato and Pst DC3000. In addition, SSlNAC genes induced by exogenous hormones, including indole-3-acetic acid (IAA), abscisic acid (ABA), salicylic acid (SA), and methyl jasmonic acid (MeJA), were also recovered. These results implied that SSlNAC genes may participate in the Pst DC3000 stress response by multiple regulatory pathways of the phytohormones. In all, this study provides important clues for further functional analysis and of the regulatory mechanism of SSlNAC genes under Pst DC3000 stress. Full article
(This article belongs to the Special Issue Genetic Regulation of Biotic Stress Responses)
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Review

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43 pages, 2514 KiB  
Review
Advances in CircRNAs in the Past Decade: Review of CircRNAs Biogenesis, Regulatory Mechanisms, and Functions in Plants
by Dongqin Zhang, Yue Ma, Misbah Naz, Nazeer Ahmed, Libo Zhang, Jing-Jiang Zhou, Ding Yang and Zhuo Chen
Genes 2024, 15(7), 958; https://doi.org/10.3390/genes15070958 - 21 Jul 2024
Viewed by 1375
Abstract
Circular RNA (circRNA) is a type of non-coding RNA with multiple biological functions. Whole circRNA genomes in plants have been identified, and circRNAs have been demonstrated to be widely present and highly expressed in various plant tissues and organs. CircRNAs are highly stable [...] Read more.
Circular RNA (circRNA) is a type of non-coding RNA with multiple biological functions. Whole circRNA genomes in plants have been identified, and circRNAs have been demonstrated to be widely present and highly expressed in various plant tissues and organs. CircRNAs are highly stable and conserved in plants, and exhibit tissue specificity and developmental stage specificity. CircRNAs often interact with other biomolecules, such as miRNAs and proteins, thereby regulating gene expression, interfering with gene function, and affecting plant growth and development or response to environmental stress. CircRNAs are less studied in plants than in animals, and their regulatory mechanisms of biogenesis and molecular functions are not fully understood. A variety of circRNAs in plants are involved in regulating growth and development and responding to environmental stress. This review focuses on the biogenesis and regulatory mechanisms of circRNAs, as well as their biological functions during growth, development, and stress responses in plants, including a discussion of plant circRNA research prospects. Understanding the generation and regulatory mechanisms of circRNAs is a challenging but important topic in the field of circRNAs in plants, as it can provide insights into plant life activities and their response mechanisms to biotic or abiotic stresses as well as new strategies for plant molecular breeding and pest control. Full article
(This article belongs to the Special Issue Genetic Regulation of Biotic Stress Responses)
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29 pages, 3513 KiB  
Review
Mode of Action of Heat Shock Protein (HSP) Inhibitors against Viruses through Host HSP and Virus Interactions
by Shuang Wu, Yongtian Zhao, Delu Wang and Zhuo Chen
Genes 2023, 14(4), 792; https://doi.org/10.3390/genes14040792 - 25 Mar 2023
Cited by 7 | Viewed by 5097
Abstract
Misfolded proteins after stress-induced denaturation can regain their functions through correct re-folding with the aid of molecular chaperones. As a molecular chaperone, heat shock proteins (HSPs) can help client proteins fold correctly. During viral infection, HSPs are involved with replication, movement, assembly, disassembly, [...] Read more.
Misfolded proteins after stress-induced denaturation can regain their functions through correct re-folding with the aid of molecular chaperones. As a molecular chaperone, heat shock proteins (HSPs) can help client proteins fold correctly. During viral infection, HSPs are involved with replication, movement, assembly, disassembly, subcellular localization, and transport of the virus via the formation of macromolecular protein complexes, such as the viral replicase complex. Recent studies have indicated that HSP inhibitors can inhibit viral replication by interfering with the interaction of the virus with the HSP. In this review, we describe the function and classification of HSPs, the transcriptional mechanism of HSPs promoted by heat shock factors (HSFs), discuss the interaction between HSPs and viruses, and the mode of action of HSP inhibitors at two aspects of inhibiting the expression of HSPs and targeting the HSPs, and elaborate their potential use as antiviral agents. Full article
(This article belongs to the Special Issue Genetic Regulation of Biotic Stress Responses)
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