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Genetic, Genomics and Big Data Analysis of the Interaction between...
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Genetic, Genomics and Big Data Analysis of the Interaction between Pathogenic Fungi and Plants

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: 31 December 2024 | Viewed by 5363

Special Issue Editors

Dr. Houxiang Kang

E-Mail Website
Guest Editor
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Interests: genomics; genetics; plant pathology; the application of artificial intelligence in crop breeding
Prof. Dr. Wei Li

E-Mail Website
Guest Editor
1. Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
2. College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
Interests: molecular plant–microbe interactions; plant pathogenic fungi; molecular plant pathology; genomics analysis; plant diseases
Dr. Zhigang Li

E-Mail Website
Guest Editor
Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou 570228, China
Interests: bioinformatics; computational biology and system biology exploring plant-pathogen interaction; population genetic structure and evolutionary potential

Special Issue Information

Dear Colleagues,

This Special Issue focuses on the genetic, genomics, and big data analysis of the interaction between pathogenic fungi and their hosts. The aim is to explore the intricate relationships between these organisms and uncover valuable insights that can aid in the development of effective strategies for disease management.

This Special Issue plans to bring together a series of research papers that delve into various aspects of this interaction. Starting from the fundamental data of genetics and multi-omics, including genomics, transcriptomics, proteomics, and metabolomics, the aim is to decipher the complex molecular networks at play during the interaction between the host and the pathogen. These analyses provide a holistic view of the complex biological processes and offer potential targets for disease control, considering both the pathogen and the host.

Overall, the main objective of this Special Issue is to provide a comprehensive overview of the genetic, genomics, and big data analysis pertaining to the interaction between pathogenic fungi and plants. The research presented in this Special Issue aims to enhance our understanding of the molecular mechanisms underlying pathogenicity, ultimately offering valuable insights for the development of innovative strategies to effectively combat fungal diseases in agriculture and promote plant health.

Dr. Houxiang Kang
Prof. Dr. Wei Li
Dr. Zhigang Li
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Fungi is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genetic
  • genomics
  • big data analysis
  • pathogenic fungi
  • plant–pathogen interaction

Published Papers (6 papers)

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Research

14 pages, 3657 KiB  
Article
Phytophthora sojae Effector PsAvh113 Targets Transcription Factors in Nicotiana benthamiana
by Shuai Wu, Jinxia Shi, Qi Zheng, Yuqin Ma, Wenjun Zhou, Chengjie Mao, Chengjie Chen, Zhengwu Fang, Rui Xia and Yongli Qiao
J. Fungi 2024, 10(5), 318; https://doi.org/10.3390/jof10050318 - 27 Apr 2024
Viewed by 376
Abstract
Phytophthora sojae is a type of pathogenic oomycete that causes Phytophthora root stem rot (PRSR), which can seriously affect the soybean yield and quality. To subvert immunity, P. sojae secretes a large quantity of effectors. However, the molecular mechanisms regulated by most P. [...] Read more.
Phytophthora sojae is a type of pathogenic oomycete that causes Phytophthora root stem rot (PRSR), which can seriously affect the soybean yield and quality. To subvert immunity, P. sojae secretes a large quantity of effectors. However, the molecular mechanisms regulated by most P. sojae effectors, and their host targets remain unexplored. Previous studies have shown that the expression of PsAvh113, an effector secreted by Phytophthora sojae, enhances viral RNA accumulations and symptoms in Nicotiana benthamiana via VIVE assay. In this study, we analyzed RNA-sequencing data based on disease symptoms in N. benthamiana leaves that were either mocked or infiltrated with PVX carrying the empty vector (EV) and PsAvh113. We identified 1769 differentially expressed genes (DEGs) dependent on PsAvh113. Using stricter criteria screening and Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analysis of DEGs, we found that 38 genes were closely enriched in response to PsAvh113 expression. We selected three genes of N. benthamiana (NbNAC86, NbMyb4, and NbERF114) and found their transcriptional levels significantly upregulated in N. benthamiana infected with PVX carrying PsAvh113. Furthermore, individual silencing of these three genes promoted P. capsici infection, while their overexpression increased resistance to P. capsici in N. benthamiana. Our results show that PsAvh113 interacts with transcription factors NbMyb4 and NbERF114 in vivo. Collectively, these data may help us understand the pathogenic mechanism of effectors and manage PRSR in soybeans. Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction between Pathogenic Fungi and Plants)
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20 pages, 10669 KiB  
Article
Transcriptome-Wide Identification and Expression Analysis of Genes Encoding Defense-Related Peptides of Filipendula ulmaria in Response to Bipolaris sorokiniana Infection
by Ekaterina A. Istomina, Tatyana V. Korostyleva, Alexey S. Kovtun, Marina P. Slezina and Tatyana I. Odintsova
J. Fungi 2024, 10(4), 258; https://doi.org/10.3390/jof10040258 - 28 Mar 2024
Viewed by 675
Abstract
Peptides play an essential role in plant development and immunity. Filipendula ulmaria, belonging to the Rosaceae family, is a medicinal plant which exhibits valuable pharmacological properties. F. ulmaria extracts in vitro inhibit the growth of a variety of plant and human pathogens. The [...] Read more.
Peptides play an essential role in plant development and immunity. Filipendula ulmaria, belonging to the Rosaceae family, is a medicinal plant which exhibits valuable pharmacological properties. F. ulmaria extracts in vitro inhibit the growth of a variety of plant and human pathogens. The role of peptides in defense against pathogens in F. ulmaria remains unknown. The objective of this study was to explore the repertoire of antimicrobial (AMPs) and defense-related signaling peptide genes expressed by F. ulmaria in response to infection with Bipolaris sorokiniana using RNA-seq. Transcriptomes of healthy and infected plants at two time points were sequenced on the Illumina HiSeq500 platform and de novo assembled. A total of 84 peptide genes encoding novel putative AMPs and signaling peptides were predicted in F. ulmaria transcriptomes. They belong to known, as well as new, peptide families. Transcriptional profiling in response to infection disclosed complex expression patterns of peptide genes and identified both up- and down-regulated genes in each family. Among the differentially expressed genes, the vast majority were down-regulated, suggesting suppression of the immune response by the fungus. The expression of 13 peptide genes was up-regulated, indicating their possible involvement in triggering defense response. After functional studies, the encoded peptides can be used in the development of novel biofungicides and resistance inducers. Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction between Pathogenic Fungi and Plants)
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12 pages, 3224 KiB  
Article
Genetic Diversity and Reproduction Trends of Phytophthora infestans in Estonia: EU_41_A2 Detected without an Indication of Clonal Reproduction
by Britt Puidet, Mati Koppel and Riinu Kiiker
J. Fungi 2024, 10(3), 233; https://doi.org/10.3390/jof10030233 - 21 Mar 2024
Viewed by 800
Abstract
This study explores the population dynamics of Phytophthora infestans in Estonia from 2005 to 2022, focusing on genetic diversity and potential shifts in reproductive strategies. In total, 153 P. infestans isolates were collected throughout Estonia over ten growing seasons. Genotyping revealed considerable genetic [...] Read more.
This study explores the population dynamics of Phytophthora infestans in Estonia from 2005 to 2022, focusing on genetic diversity and potential shifts in reproductive strategies. In total, 153 P. infestans isolates were collected throughout Estonia over ten growing seasons. Genotyping revealed considerable genetic diversity, with most isolates not corresponding to known multilocus genotypes (MLGs). Still, instances of invasive clonal lineages were observed, notably EU_41_A2. The data indicate the likelihood of random mating rather than clonal reproduction in all the analyzed years. The principal coordinate analysis (PCoA) results revealed no distinct clustering among the sampling years. Statistical analysis and the minimum spanning network (MSN) indicated low genetic differentiation between years with minimal fluctuations in allele frequencies. The continuous monitoring of P. infestans populations is essential for detecting any changes from the current evolutionary trajectory and implement effective disease management strategies, especially considering the recent emergence of EU_41_A2 in the Nordics and the potential impacts of climate change. Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction between Pathogenic Fungi and Plants)
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15 pages, 6932 KiB  
Article
Dual RNA-Seq Reveals Temperature-Mediated Gene Reprogramming and Molecular Crosstalk between Grapevine and Lasiodiplodia theobromae
by Junbo Peng, Yonghua Li, Qikai Xing, Caiping Huang and Jiye Yan
J. Fungi 2023, 9(12), 1197; https://doi.org/10.3390/jof9121197 - 14 Dec 2023
Viewed by 1004
Abstract
High temperatures associated with a fluctuating climate profoundly accelerate the occurrence of a myriad of plant diseases around the world. A comprehensive insight into how plants respond to pathogenic microorganisms under high-temperature stress is required for plant disease management, whereas the underlying mechanisms [...] Read more.
High temperatures associated with a fluctuating climate profoundly accelerate the occurrence of a myriad of plant diseases around the world. A comprehensive insight into how plants respond to pathogenic microorganisms under high-temperature stress is required for plant disease management, whereas the underlying mechanisms behind temperature-mediated plant immunity and pathogen pathogenicity are still unclear. Here, we evaluated the effect of high temperature on the development of grapevine canker disease and quantified the contribution of temperature variation to the gene transcription reprogramming of grapevine and its pathogenic agent Lasiodiplodia theobromae using a dual RNA-seq approach. The results showed that both grapevine and the pathogen displayed altered transcriptomes under different temperatures, and even the transcription of a plethora of genes from the two organisms responded in different directions and magnitudes. The transcription variability that arose due to temperature oscillation allowed us to identify a total of 26 grapevine gene modules and 17 fungal gene modules that were correlated with more than one gene module of the partner organism, which revealed an extensive web of plant–pathogen gene reprogramming during infection. More importantly, we identified a set of temperature-responsive genes that were transcriptionally orchestrated within the given gene modules. These genes are predicted to be involved in multiple cellular processes including protein folding, stress response regulation, and carbohydrate and peptide metabolisms in grapevine and porphyrin- and pteridine-containing compound metabolisms in L. theobromae, implying that in response to temperature oscillation, a complex web of signaling pathways in two organism cells is activated during infection. This study describes a co-transcription network of grapevine and L. theobromae in the context of considering temperature variation, which provides novel insights into deciphering the molecular mechanisms underlying temperature-modulated disease development. Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction between Pathogenic Fungi and Plants)
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18 pages, 4574 KiB  
Article
Nano-Silicon Triggers Rapid Transcriptomic Reprogramming and Biochemical Defenses in Brassica napus Challenged with Sclerotinia sclerotiorum
by Qiuping Zhang, Jiaqi Wang, Jiajia Wang, Mulan Liu, Xiao Ma, Yang Bai, Qiang Chen, Song Sheng and Feng Wang
J. Fungi 2023, 9(11), 1108; https://doi.org/10.3390/jof9111108 - 16 Nov 2023
Viewed by 986
Abstract
Stem rot caused by Sclerotinia sclerotiorum poses a significant threat to global agriculture, leading to substantial economic losses. To explore innovative integrated pest management strategies and elucidate the underlying mechanisms, this study examined the impact of nano-silicon on enhancing resistance to Sclerotinia sclerotiorum [...] Read more.
Stem rot caused by Sclerotinia sclerotiorum poses a significant threat to global agriculture, leading to substantial economic losses. To explore innovative integrated pest management strategies and elucidate the underlying mechanisms, this study examined the impact of nano-silicon on enhancing resistance to Sclerotinia sclerotiorum in Brassica napus. Bacteriostatic assays revealed that nano-silicon effectively inhibited the mycelial growth of Sclerotinia sclerotiorum in a dose-dependent manner. Field trials corroborated the utility of nano-silicon as a fertilizer, substantially bolstering resistance in the Brassica napus cultivar Xiangyou 420. Specifically, the disease index was reduced by 39–52% across three distinct geographical locations when compared to untreated controls. This heightened resistance was attributed to nano-silicon’s role in promoting the accumulation of essential elements such as silicon (Si), potassium (K), and calcium (Ca), while concurrently reducing sodium (Na) absorption. Furthermore, nano-silicon was found to elevate the levels of soluble sugars and lignin, while reducing cellulose content in both leaves and stems. It also enhanced the activity levels of antioxidant enzymes. Transcriptomic analysis revealed 22,546 differentially expressed genes in Si-treated Brassica napus post-Sclerotinia inoculation, with the most pronounced transcriptional changes observed one day post-inoculation. Weighted gene co-expression network analysis identified a module comprising 45 hub genes that are implicated in signaling, transcriptional regulation, metabolism, and defense mechanisms. In summary, nano-silicon confers resistance to Brassica napus against Sclerotinia sclerotiorum by modulating biochemical defenses, enhancing antioxidative activities, and rapidly reprogramming key resistance-associated genes. These findings contribute to our mechanistic understanding of Si-mediated resistance against necrotrophic fungi and offer valuable insights for the development of stem-rot-resistant Brassica napus cultivars. Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction between Pathogenic Fungi and Plants)
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14 pages, 3708 KiB  
Article
The Difference in Diversity between Endophytic Microorganisms in White and Grey Zizania latifolia
by Yipeng Li, Cailin Hu, Ruiqi Song, Zhihui Yin, Lingyun Wang, Lin Shi, Wei Li, Zhaisheng Zheng and Mengfei Yang
J. Fungi 2023, 9(11), 1067; https://doi.org/10.3390/jof9111067 - 1 Nov 2023
Viewed by 1034
Abstract
The Zizania latifolia is usually infected by the obligate parasitic fungus Ustilago esculenta to form an edible fleshy stem which is an aquatic vegetable called Jiaobai in China. The infection by the teliospore (T) strain of U. esculenta induces Z. latifolia forming gray [...] Read more.
The Zizania latifolia is usually infected by the obligate parasitic fungus Ustilago esculenta to form an edible fleshy stem which is an aquatic vegetable called Jiaobai in China. The infection by the teliospore (T) strain of U. esculenta induces Z. latifolia forming gray fleshy stems, while the mycelia-teliospore (MT) strain of U. esculenta induces white fleshy stems which are more suitable for edibility than gray fleshy stems. The mechanism of this phenomenon is still largely unknown. One of the possible causes is the diversity of endophytic microbial communities between these two fleshy stems. Therefore, we utilized fungal ITS1 and bacterial 16S rDNA amplicon sequencing to investigate the diversity of endophytic microbial communities in the two different fleshy stems of Z. latifolia. The results revealed that the α diversity and richness of endophytic fungi in white Z. latifolia were significantly greater than in gray Z. latifolia. The dominant fungal genus in both fleshy stems was U. esculenta, which accounted for over 90% of the endophytic fungi. The community composition of endophytic fungi in gray and white Z. latifolia was different except for U. esculenta, and a negative correlation was observed between U. esculenta and other endophytic fungi. In addition, the dominant bacterial genus in gray Z. latifolia was Alcaligenaceae which is also negatively correlated with other bacterium communities. Additionally, the co-occurrence network of white Z. latifolia was found to have a stronger scale, connectivity, and complexity compared to that of gray Z. latifolia. And the detected beneficial bacteria and pathogens in the stems of Z. latifolia potentially compete for resources. Furthermore, the function of endophytic bacteria is more abundant than endophytic fungi in Z. latifolia. This research investigated the correlation between the development of Z. latifolia fleshy stems and endophytic microbial communities. Our findings indicate that the composition of endophytic microbial communities is closely related to the type of Z. latifolia fleshy stems. This research also suggests the potential utilization of specific microbial communities to enhance the growth and development of Z. latifolia, thereby contributing to the breeding of Z. latifolia. Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction between Pathogenic Fungi and Plants)
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