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Forests
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Forest Tree Diseases Genomics: Growing Resources and Applications
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Forest Tree Diseases Genomics: Growing Resources and Applications

A special issue of Forests (ISSN 1999-4907). This special issue belongs to the section "Forest Health".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 8671

Special Issue Editors

Dr. Tingting Dai

E-Mail Website
Guest Editor
Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
Interests: detection; fungi and oomycetes; phylogeny; whole genome sequencing
Dr. Jiajia Chen

E-Mail Website
Guest Editor
College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China
Interests: fungi and oomycetes; phylogeny; whole genome sequencing
Dr. Simon Francis Shamoun

E-Mail Website
Guest Editor
Canadian Forest Service, Pacific Forestry Centre, Natural Resources Canada, Government of Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
Interests: forest pathology; forest invasive alien and indigenous pathogens; molecular ecology and diagnostics; mycoviruses; biological control science and technology

Special Issue Information

Dear Colleagues,

A large number of fungi and oomycetes are of Tree Pathology. On one hand, fungi and oomycetes are among the dominant causal agents of plant diseases; on the other hand, fungi or oomycetes are also biological control agents of pathogens. Our understanding of the diversity, host range and specificity of fungi and oomycetes has improved with the enrichment of knowledge surrounding taxonomy and phylogeny over the years; however, many unknowns remain.

Fungi and oomycetes genomes are easily obtained, and have been used as models for genome evolution and the reconstruction of the phylogenetic relationship using genome-scale data. In these models, groundbreaking comparative genomic studies making use of these features have already been published. These breakthroughs are leading the way in fungi and oomycetes research.

The aim of this research topic is to collect articles focusing on the biodiversity, molecular systematics, and taxonomy of fungi and oomycetes all over the world. Additionally, approaches to the diagnosis of fungal and oomycete plant diseases, including advances in the field of molecular diagnosis of fungi and oomycetes, are welcome. Research involving diagnostic techniques should demonstrate improvements in diagnostic accuracy and time.

For these above reasons, we sincerely encourage experts and researchers to contribute original research articles, reviews, and communications that address the following topics:

  1. Phylogeny and diversity of fungi and oomycetes.
  2. Morphological and molecular characterization of plant pathogens.
  3. Genomics, transcriptomics, proteomics, and epigenomics data analyses.
  4. Molecular diagnostics of fungi and oomycetes.

Dr. Tingting Dai
Dr. Jiajia Chen
Dr. Simon Francis Shamoun
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. Forests 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

  • detection
  • fungi and oomycetes
  • phylogeny
  • taxonomy
  • whole genome sequencing

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Published Papers (6 papers)

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16 pages, 7616 KiB  
Article
Functional Characterization of the Sterol-Synthesis-Related Gene CgCYP51 in the Poplar Anthracnose-Causing Fungus Colletotrichum gloeosporioides
by Manyang Zhang, Fuhan Li and Fanli Meng
Forests 2024, 15(11), 1888; https://doi.org/10.3390/f15111888 - 26 Oct 2024
Viewed by 690
Abstract
Poplar is an economically and ecologically valuable tree species. Anthracnose, which severely affects poplar tree growth, is mainly caused by Colletotrichum gloeosporioides. In the infestation cycle of poplar anthracnose, the entry of C. gloeosporioides into the host tissue depends on the formation [...] Read more.
Poplar is an economically and ecologically valuable tree species. Anthracnose, which severely affects poplar tree growth, is mainly caused by Colletotrichum gloeosporioides. In the infestation cycle of poplar anthracnose, the entry of C. gloeosporioides into the host tissue depends on the formation of an appressorium. The subsequent development of the appressorium determines the pathogenesis of poplar anthracnose and the degree of damage. Previous studies have found that the transcription factor CgSte12 affects appressorium formation and development by regulating the expression of a series of genes, including the sterol-synthesis-related gene CgCYP51, which influences appressorium formation and development. In this study, knockout and functional analyses of CgCYP51 revealed decreases in differentiation, darkening rate, and turgor pressure of appressoria in mutants. Additionally, compared with the wild-type appressorium, mutant appressoria secreted less mucus and exhibited abnormal penetration pore formation, ultimately leading to decreased pathogenicity. Moreover, CgCyp51 affected the sensitivity of C. gloeosporioides to sterol biosynthesis inhibitors. Considered together, the study findings indicate CgCYP51 is a key CgSte12-regulated gene that affects C. gloeosporioides appressorium formation and development. Furthermore, the study data provide new insights into the molecular basis of C. gloeosporioides appressorium formation and development. Full article
(This article belongs to the Special Issue Forest Tree Diseases Genomics: Growing Resources and Applications)
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13 pages, 4148 KiB  
Article
Transcriptomic Profiling Reveals That the Differentially Expressed PtNAC9 Transcription Factor Stimulates the Salicylic Acid Pathway to Enhance the Defense Response against Bursaphelenchus xylophilus in Pines
by Tong-Yue Wen, Xin-Yu Wang, Xiao-Qin Wu and Jian-Ren Ye
Forests 2024, 15(9), 1538; https://doi.org/10.3390/f15091538 - 1 Sep 2024
Viewed by 1056
Abstract
Pinus, a conifer, dominates the world’s forest ecosystems. But it is seriously infected with pine wood nematode (PWN). Transcription factors (TFs) are key regulators in regulating plant resistance. However, the molecular mechanism of TFs remains thus far unresolved in P. thunbergii inoculated [...] Read more.
Pinus, a conifer, dominates the world’s forest ecosystems. But it is seriously infected with pine wood nematode (PWN). Transcription factors (TFs) are key regulators in regulating plant resistance. However, the molecular mechanism of TFs remains thus far unresolved in P. thunbergii inoculated with Bursaphelenchus xylophilus. Here, we used RNA-seq technology to identify differentially expressed TFs in resistant and susceptible pines. The results show that a total of 186 differentially expressed transcription factors (DETFs), including 99 upregulated and 87 downregulated genes were identified. Gene ontology (GO) enrichment showed that the highly enriched differentially expressed TFs were responsible for secondary biosynthetic processes. According to KEGG pathway analysis, the differentially expressed TFs were related to chaperones and folding catalysts, phenylpropanoid biosynthesis, and protein processing in the endoplasmic reticulum. Many TFs such as NAC, LBD, MYB, bHLH, and WRKY were determined to be quite abundant in the DETFs. Moreover, the NAC transcription factor PtNAC9 was upregulated in PWN-resistant and susceptible P. thunbergii and especially distinctly upregulated in resistant pines. By purifying recombinant PtNAC9 protein in vitro, we found that overexpression of PtNAC9 at the early stage of B. xylophilus infection could reduce the degree of disease. We also demonstrated the content of salicylic acid (SA) and the related genes were increased in the PtNAC9 protein-treated plants. These results could be helpful in enhancing our understanding of the resistance mechanism underlying different resistant pine. Full article
(This article belongs to the Special Issue Forest Tree Diseases Genomics: Growing Resources and Applications)
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22 pages, 14329 KiB  
Article
Colletotrichum Species Causing Cyclocarya paliurus Anthracnose in Southern China
by Xiang-Rong Zheng, Mao-Jiao Zhang and Feng-Mao Chen
Forests 2024, 15(3), 490; https://doi.org/10.3390/f15030490 - 6 Mar 2024
Viewed by 1406
Abstract
Cyclocarya paliurus, native to China, is a medicinal and edible plant with important health benefits. Anthracnose is an emerging disease in southern China that causes severe economic losses and poses a great threat to the C. paliurus tea industry. However, to date, [...] Read more.
Cyclocarya paliurus, native to China, is a medicinal and edible plant with important health benefits. Anthracnose is an emerging disease in southern China that causes severe economic losses and poses a great threat to the C. paliurus tea industry. However, to date, the species diversity of pathogens causing C. paliurus anthracnose has remained limited. From 2018 to 2022, a total of 331 Colletotrichum isolates were recovered from symptomatic leaves in eight major C. paliurus planting provinces of southern China. Phylogenetic analyses based on nine loci (ITS, GAPDH, ACT, CHS-1, TUB, CAL, HIS3, GS and ApMat) coupled with phenotypic characteristics revealed that 43 representative isolates belonged to seven known Colletotrichum species, including C. brevisporum, C. fructicola, C. gloeosporioides sensu stricto, C. godetiae, C. nymphaeae, C. plurivorum and C. sojae. Pathogenicity tests demonstrated that all species described above were pathogenic to wounding detached leaves of C. paliurus, with C. fructicola being the most aggressive species. However, C. brevisporum, C. plurivorum and C. sojae were not pathogenic to the intact plant of C. paliurus. These findings reveal the remarkable species diversity involved in C. paliurus anthracnose and will facilitate further studies on implementing effective control of C. paliurus anthracnose in China. Full article
(This article belongs to the Special Issue Forest Tree Diseases Genomics: Growing Resources and Applications)
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13 pages, 1817 KiB  
Article
The New Report of Root Rot on Fatsia japonica Caused by Phytophthora nicotianae in China
by Jing Zhou, Tingyan Xu, Xiaoqiao Xu, Tingting Dai and Tingli Liu
Forests 2023, 14(7), 1459; https://doi.org/10.3390/f14071459 - 17 Jul 2023
Cited by 4 | Viewed by 2796
Abstract
As an ornamental plant, Fatsia japonica has been widely used in gardens. From April 2021 to 2022, a disease that caused the wilting and root rot of F. japonica in a large area was observed, which eventually led to the plants wilting and [...] Read more.
As an ornamental plant, Fatsia japonica has been widely used in gardens. From April 2021 to 2022, a disease that caused the wilting and root rot of F. japonica in a large area was observed, which eventually led to the plants wilting and dying, while the leaves did not fall off. This disease greatly reduced the landscape effect of plants. An oomycete species was isolated from the roots of the infected plants. This colony morphology was slightly radial to stellate, and the aerial mycelium was flocculent. Oval sporangia with papillae, apical chlamydospores and zoospores formed in sporangia were observed. The morphological characteristics were consistent with Phytophthora. For accurate identification, the internal transcribed spacer (ITS), cytochrome oxidase subunit II (COXII) and large ribosomal subunit (LSU) genes were amplified and sequenced. The species was identified as Phytophthora nicotianae using phylogenetic analysis. Finally, the disease was reproduced by inoculating healthy F. japonica with a zoospore suspension; the symptoms were consistent with those of natural infections, and the isolate obtained from artificially infected plants had the same morphological characteristics as the inoculated isolate. The results demonstrated that P. nicotianae is the pathogenic factor of root rot. of F. japonica. This is the first report of root rot on F. japonica caused by P. nicotianae in China. Full article
(This article belongs to the Special Issue Forest Tree Diseases Genomics: Growing Resources and Applications)
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11 pages, 3028 KiB  
Brief Report
First Report of Anthracnose Caused by Colletotrichum gloeosporioides on Lucky Bamboo in China
by Yulin Qian, Xueying Wang, Xiaoying Zhai, Xuehui Hu, Tao Li, Yuyang Li and Qin Xiong
Forests 2025, 16(1), 128; https://doi.org/10.3390/f16010128 - 11 Jan 2025
Viewed by 471
Abstract
Lucky bamboo (Dracaena sanderiana hort. ex. Mast. = Dracaena braunii) is a popular decorative plant in China. In March 2022, a severe outbreak of anthracnose disease occurred on the stems of lucky bamboo plants in a nursery garden in Nanjing, Jiangsu [...] Read more.
Lucky bamboo (Dracaena sanderiana hort. ex. Mast. = Dracaena braunii) is a popular decorative plant in China. In March 2022, a severe outbreak of anthracnose disease occurred on the stems of lucky bamboo plants in a nursery garden in Nanjing, Jiangsu Province, China. Thirty-two fungal isolates were obtained from the infected stem tissues and were morphologically identified as Colletotrichum species. A multilocus phylogenetic analysis based on the internal transcribed spacer (ITS) region, the actin (ACT) gene, and the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene indicated the isolate FGZ-1 as Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. The pathogenicity of isolate FGZ-1 was verified by inoculating mycelial plugs on stem segments and spraying spores on the whole one-year-old lucky bamboo plants. Koch’s postulates were fulfilled via the re-isolation of C. gloeosporioides from the diseased tissues. To the best of our knowledge, this is the first report of C. gloeosporioides causing anthracnose on lucky bamboo in China. The detection of C. gloeosporioides on lucky bamboo in China expands the range of Colletotrichum species that are associated with anthracnose in this popular ornamental plant. This study lays a solid foundation for future investigations into the pathogenic mechanisms of anthracnose on D. sanderiana and control strategies for this disease, such as biocontrol agents and the construction of resistant cultivars. Full article
(This article belongs to the Special Issue Forest Tree Diseases Genomics: Growing Resources and Applications)
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10 pages, 3512 KiB  
Brief Report
Protein Disulfide Isomerase CfPdi1 Is Required for Response to ER Stress, Autophagy, and Pathogenicity in Colletotrichum fructicola
by Sizheng Li, Jiajia Chen and He Li
Forests 2023, 14(8), 1597; https://doi.org/10.3390/f14081597 - 7 Aug 2023
Viewed by 1315
Abstract
Camellia oleifera, a woody plant indigenous to China, is primarily utilized for the production of cooking oil. However, it is frequently afflicted by anthracnose, a highly detrimental disease that leads to significant annual losses. Colletotrichum fructicola is the predominant etiological agent responsible [...] Read more.
Camellia oleifera, a woody plant indigenous to China, is primarily utilized for the production of cooking oil. However, it is frequently afflicted by anthracnose, a highly detrimental disease that leads to significant annual losses. Colletotrichum fructicola is the predominant etiological agent responsible for anthracnose in Ca. oleifera. Additionally, our investigation has revealed that a bZIP transcription factor CfHac1 in C. fructicola governs the pathogenicity and response to endoplasmic reticulum stress. In this study, we conducted an investigation of the role of the CfPDI1 gene in C. fructicola, which was significantly downregulated in ΔCfhac1 under endoplasmic reticulum stress. The CfPDI1 gene was deleted, resulting in reduced vegetative growth, conidiation, appressoria formation, and appressorium turgor generation. Furthermore, it was observed that the ΔCfpdi1 mutant exhibited impaired responsiveness to endoplasmic reticulum stresses, and the expression of UPR-related genes in C. fructicola was influenced by CfPdi1. Cytological investigations indicated that CfPdi1 is localized in the endoplasmic reticulum. Further analysis revealed that the ΔCfpdi1 mutant displays significantly reduced pathogenicity in Ca. oleifera. Taken together, this study illustrated crucial functions of CfPdi1 in development, response to ER stress, autophagy, and pathogenicity in C. fructicola. Full article
(This article belongs to the Special Issue Forest Tree Diseases Genomics: Growing Resources and Applications)
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