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Wang G, Zhang G, Lv X, Wang Y, Long Y, Wang X, Liu H. First complete mitogenome of Massarineae and its contribution to phylogenetic implications in Pleosporales. Sci Rep 2023; 13:22431. [PMID: 38104200 PMCID: PMC10725480 DOI: 10.1038/s41598-023-49822-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023] Open
Abstract
Endophytic fungi play an important role in the growth and development of traditional Chinese medicine plants. We isolated a strain of Acrocalymma vagum from the endophytic fungi of the traditional Chinese plants Paris. To accurately identify this endophytic fungal species of interest, we sequenced the mitochondrial genome of A. vagum, which is the first discovered mitochondrial genome in Massarineae. The A. vagum mitochondrial genome consists of a 35,079-bp closed circular DNA molecule containing 36 genes. Then, we compared the general sequence characteristics of A. vagum with those of Pleosporales, and the second structure of the 22 tRNAs was predicted. The phylogenetic relationship of A. vagum was constructed using two different data sets (protein-coding genes and amino acids). The phylogenetic tree shows that A. vagum is located at the root of Pleosporales. The analysis of introns shows that the number of introns increases with the increase in branch length. The results showed that monophyly was confirmed for all families in Pleosporales except for Pleosporaceae. A. vagum is an ancient species in the Pleosporales, and Pleosporaceae may require further revision. In Pleosporales, the number of introns is positively correlated with branch length, providing data for further study on the origin of introns.
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Affiliation(s)
- Guangying Wang
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Gongyou Zhang
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guiyang, China
| | - Xiaoying Lv
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Yaping Wang
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guiyang, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Yaohang Long
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guiyang, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Xianyi Wang
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang, China.
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guiyang, China.
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China.
| | - Hongmei Liu
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang, China.
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guiyang, China.
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China.
- School of Basic Medicine Science, Guizhou Medical University, Guiyang, China.
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Xu N, Lu H, Yi X, Peng S, Huang X, Zhang Y, He C. Potential of Alpha-(α)-Solanine as a Natural Inhibitor of Fungus Causing Leaf Spot Disease in Strawberry. Life (Basel) 2023; 13:life13020450. [PMID: 36836807 PMCID: PMC9961337 DOI: 10.3390/life13020450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 02/09/2023] Open
Abstract
Curvularia trifolii is an important pathogenic fungus that causes leaf spot disease in strawberry and other crops. Increased resistance in pathogenic fungi against chemical fungicides necessitates the search for biological alternatives to control plant fungal diseases. The present study aimed to perform transcriptome and metabolome analysis of C. trifolii fungi. We evaluated the potential of an alkaloid, namely alpha (α)-solanine, to inhibit the growth of Curvularia under in vitro conditions. Furthermore, transcriptomic and metabolomic analysis of treated C. trifolii was performed to identify the differential genes and metabolites. Results revealed that treatment with α-solanine resulted in the poor growth and development of fungal spores. The transcriptome analysis revealed that 1413 genes were differentially expressed (DEGs), among which 340 unigenes were up-regulated, 100 unigenes were down-regulated, and the rest were unaffected in treated samples. Gene ontology analysis revealed that the majority of the genes were related to oxidative stress in the fungus. Additionally, using ultra-high performance liquid chromatography-tandem mass spectrometry, we identified 455 metabolites, among which the majority of metabolites were related to lipid biosynthesis. The high number of genes related to lipid biosynthesis and reactive oxygen species revealed that α-solanine causes oxidative stress in Curvularia, leading to growth inhibition, and can be potentially used as an alternative to chemical fungicides.
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Affiliation(s)
- Ning Xu
- College of Horticulture, Hunan Agricultural University, Nongda Road No.1, Changsha 410128, China
- Institute of Hunan Edible Fungi, Shuangtang Road No. 107, Changsha 410013, China
| | - Huan Lu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, No. 1000, Jinqi Road, Shanghai 201403, China
| | - Xueqian Yi
- Hunan Institute of Traffic Engineering, Jiefang Road No. 430, Hengyang 421200, China
| | - Simin Peng
- College of Horticulture, Hunan Agricultural University, Nongda Road No.1, Changsha 410128, China
| | - Xiaohui Huang
- College of Horticulture, Hunan Agricultural University, Nongda Road No.1, Changsha 410128, China
| | - Yu Zhang
- College of Horticulture, Hunan Agricultural University, Nongda Road No.1, Changsha 410128, China
| | - Changzheng He
- College of Horticulture, Hunan Agricultural University, Nongda Road No.1, Changsha 410128, China
- Correspondence:
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Ogaji YO, Lee RC, Sawbridge TI, Cocks BG, Daetwyler HD, Kaur S. De Novo Long-Read Whole-Genome Assemblies and the Comparative Pan-Genome Analysis of Ascochyta Blight Pathogens Affecting Field Pea. J Fungi (Basel) 2022; 8:jof8080884. [PMID: 36012871 PMCID: PMC9410150 DOI: 10.3390/jof8080884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Ascochyta Blight (AB) is a major disease of many cool-season legumes globally. In field pea, three fungal pathogens have been identified to be responsible for this disease in Australia, namely Peyronellaea pinodes, Peyronellaea pinodella and Phoma koolunga. Limited genomic resources for these pathogens have been generated, which has hampered the implementation of effective management strategies and breeding for resistant cultivars. Using Oxford Nanopore long-read sequencing, we report the first high-quality, fully annotated, near-chromosome-level nuclear and mitochondrial genome assemblies for 18 isolates from the Australian AB complex. Comparative genome analysis was performed to elucidate the differences and similarities between species and isolates using phylogenetic relationships and functional diversity. Our data indicated that P. pinodella and P. koolunga are heterothallic, while P. pinodes is homothallic. More homology and orthologous gene clusters are shared between P. pinodes and P. pinodella compared to P. koolunga. The analysis of the repetitive DNA content showed differences in the transposable repeat composition in the genomes and their expression in the transcriptomes. Significant repeat expansion in P. koolunga’s genome was seen, with strong repeat-induced point mutation (RIP) activity being evident. Phylogenetic analysis revealed that genetic diversity can be exploited for species marker development. This study provided the much-needed genetic resources and characterization of the AB species to further drive research in key areas such as disease epidemiology and host–pathogen interactions.
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Affiliation(s)
- Yvonne O. Ogaji
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Robert C. Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Tim I. Sawbridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Benjamin G. Cocks
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Hans D. Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- Correspondence:
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Shen MC, Shi YZ, Bo GD, Liu XM. Fungal Inhibition of Agricultural Soil Pathogen Stimulated by Nitrogen-Reducing Fertilization. Front Bioeng Biotechnol 2022; 10:866419. [PMID: 35497365 PMCID: PMC9039341 DOI: 10.3389/fbioe.2022.866419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Plant health is the fundamental of agricultural production, which is threatened by plant pathogens severely. The previous studies exhibited the effects of different pathogen control strategies (physical, chemical, and microbial methods), which resulted from bringing in exogenous additives, on microbial community structures and functions. Nevertheless, few studies focused on the potential inhibitory abilities of native microbial community in the soil, which could be activated or enhanced by different fertilization strategies. In this study, three plant diseases (TMV, TBS, and TBW) of tobacco, fungal community of tobacco rhizosphere soil, and the correlation between them were researched. The results showed that nitrogen-reducing fertilization strategies could significantly decrease the occurrence rate and the disease index of three tobacco diseases. The results of bioinformatics analyses revealed that the fungal communities of different treatments could differentiate the nitrogen-reducing fertilization group and the control group (CK). Furthermore, key genera which were responsible for the variation of fungal community were explored by LEfSe analysis. For instance, Tausonia and Trichocladium increased, while Naganishia and Fusicolla decreased under nitrogen-reducing fertilization conditions. Additionally, the correlation between tobacco diseases and key genera was verified using the Mantel test. Moreover, the causal relationship between key genera and tobacco diseases was deeply explored by PLS–PM analysis. These findings provide a theoretical basis for a nitrogen-reducing fertilization strategy against tobacco diseases without exogenous additives and make contributions to revealing the microbial mechanism of native-valued fungal key taxa against tobacco diseases, which could be stimulated by agricultural fertilization management.
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Affiliation(s)
- Min-Chong Shen
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - You-Zhi Shi
- Cigar Institute of China Tobacco Hubei Industrial Co., Ltd., Yichang, China
| | - Guo-Dong Bo
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Xin-Min Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- *Correspondence: Xin-Min Liu,
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