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Pant P, Negi A, Rawat J, Kumar R. Characterization of rhizospheric fungi and their in vitro antagonistic potential against myco-phytopathogens invading Macrotyloma uniflorum plants. Int Microbiol 2024:10.1007/s10123-024-00520-y. [PMID: 38616239 DOI: 10.1007/s10123-024-00520-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024]
Abstract
Microorganisms have become more resistant to pesticides, which increases their ability to invade and infect crops resulting in decreased crop productivity. The rhizosphere plays a crucial role in protecting plants from harmful invaders. The purpose of the study was to investigate the antagonistic efficiency of indigenous rhizospheric fungal isolates against phytopathogens of M. uniflorum plants so that they could be further used as potent Biocontrol agents. Thirty rhizospheric fungal isolates were collected from the roots of the Macrotyloma uniflorum plant and initially described morphologically for the present study. Further, in vitro tests were conducted to evaluate the antifungal activity of these strains against four myco-phytopathogens namely Macrophamina phaseolina, Phomopsis sp. PhSFX-1, Nigrospora oryzae, and Boeremia exigua. These pathogens are known to infect the same crop plant, M. uniflorum, and cause declines in crop productivity. Fifteen fungal strains out of the thirty fungal isolates showed some partial antagonistic activity against the myco-phytopathogens. The potent fungal isolates were further identified using molecular techniques, specifically based on the internal transcribed spacer (ITS) region sequencing. Penicillium mallochii, Cladosporium pseudocladosporioides, Aspergillus chevalieri, Epicoccum nigrum, Metarhizium anisopliae, and Mucor irregularis were among the strains that were identified. These potent fungal strains showed effective antagonistic activity against harmful phytopathogens. Current findings suggest that these strains may be taken into consideration as synthetic fungicides which are frequently employed to manage plant diseases alternatives.
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Affiliation(s)
- Pooja Pant
- Department of Biotechnology, Sir J. C. Bose Technical Campus, Bhimtal, Kumaun University, Nainital, India.
| | - Ankit Negi
- Department of Biotechnology, Sir J. C. Bose Technical Campus, Bhimtal, Kumaun University, Nainital, India
| | - Jyoti Rawat
- Department of Food Science and Technology, Graphic Era (Deemed to Be) University, Dehradun, 248002, India
| | - Rishendra Kumar
- Department of Biotechnology, Sir J. C. Bose Technical Campus, Bhimtal, Kumaun University, Nainital, India.
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Hosseini B, Voegele RT, Link TI. Diagnosis of Soybean Diseases Caused by Fungal and Oomycete Pathogens: Existing Methods and New Developments. J Fungi (Basel) 2023; 9:jof9050587. [PMID: 37233298 DOI: 10.3390/jof9050587] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/03/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Soybean (Glycine max) acreage is increasing dramatically, together with the use of soybean as a source of vegetable protein and oil. However, soybean production is affected by several diseases, especially diseases caused by fungal seed-borne pathogens. As infected seeds often appear symptomless, diagnosis by applying accurate detection techniques is essential to prevent propagation of pathogens. Seed incubation on culture media is the traditional method to detect such pathogens. This method is simple, but fungi have to develop axenically and expert mycologists are required for species identification. Even experts may not be able to provide reliable type level identification because of close similarities between species. Other pathogens are soil-borne. Here, traditional methods for detection and identification pose even greater problems. Recently, molecular methods, based on analyzing DNA, have been developed for sensitive and specific identification. Here, we provide an overview of available molecular assays to identify species of the genera Diaporthe, Sclerotinia, Colletotrichum, Fusarium, Cercospora, Septoria, Macrophomina, Phialophora, Rhizoctonia, Phakopsora, Phytophthora, and Pythium, causing soybean diseases. We also describe the basic steps in establishing PCR-based detection methods, and we discuss potentials and challenges in using such assays.
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Affiliation(s)
- Behnoush Hosseini
- Department of Phytopathology, Institute of Phytomedicine, Faculty of Agricultural Sciences, University of Hohenheim, Otto-Sander-Str. 5, 70599 Stuttgart, Germany
| | - Ralf Thomas Voegele
- Department of Phytopathology, Institute of Phytomedicine, Faculty of Agricultural Sciences, University of Hohenheim, Otto-Sander-Str. 5, 70599 Stuttgart, Germany
| | - Tobias Immanuel Link
- Department of Phytopathology, Institute of Phytomedicine, Faculty of Agricultural Sciences, University of Hohenheim, Otto-Sander-Str. 5, 70599 Stuttgart, Germany
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Rapid and Accurate Detection of Gnomoniopsis smithogilvyi the Causal Agent of Chestnut Rot, through an Internally Controlled Multiplex PCR Assay. Pathogens 2022; 11:pathogens11080907. [PMID: 36015028 PMCID: PMC9415963 DOI: 10.3390/pathogens11080907] [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: 07/08/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
The fungus Gnomoniopsis smithogilvyi is a significant threat to the production of sweet chestnut (Castanea sativa) nuts in Australia and worldwide. The pathogen causes nut rot, which leads to substantial production losses. Early and accurate diagnosis of the disease is essential to delineate and implement control strategies. A specific and sensitive multiplex PCR was developed based on the amplification of three barcode sequences of G. smithogilvyi. The assay reliability was enhanced by including the amplification of a host gene as an internal control. Primers were thoroughly evaluated in silico before assessing them in vitro. Primer annealing temperature and concentration were optimised to enhance the assay sensitivity and specificity. The assay detection limit ranged between 0.1 and 1.0 pg (5 and 50 fg/μL) of genomic DNA per reaction. No cross-reactivity was observed with genomic DNA from closely and distantly related fungal species. We also characterised Australian G. smithogilvyi isolates phenotypically and genotypically and found significant differences in morphologic and virulence traits of the isolates. An understanding of the virulence of G. smithogilvyi and the availability of a reliable and accurate diagnostic technique will enable earlier detection of the pathogen, which will contribute to effective control strategies for the disease.
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Genetic Diversity and Population Structure of Head Blight Disease Causing Fungus Fusarium graminearum in Northern Wheat Belt of India. J Fungi (Basel) 2022; 8:jof8080820. [PMID: 36012808 PMCID: PMC9409692 DOI: 10.3390/jof8080820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
Head blight or scab caused by Fusarium graminearum (FG), once ranked as a minor disease in wheat, is now emerging as one of the economically important diseases in India. The present study represents the first in-depth population genetic analysis of the FG from the northern wheat belt of India. In this study, multiple conserved gene sequences comprised of β-tubulin (TUB), translation elongation factor 1-α (TEF), and histone-3 (HIS) regions were used for multi-locus phylogenetic analysis of 123 geographically distinct F. graminearum isolates collected from four different states (Haryana (HR), Punjab (PB), Rajasthan (RJ) and West Bengal (WB)) of India. The phylogenetic and haplotype analysis showed the presence of thirty haplotypes in all the analyzed populations. The haplotypic diversity in the RJ population (Hd = 0.981) was higher than in the HR (Hd = 0.972), PB (Hd = 0.965) and WB population (Hd = 0.962). Recombination events (Rm = 12) and mutation events (485) were also detected. Analysis of molecular variance (AMOVA) indicated that genetic diversity was exclusively due to the differences within populations. The haplotype network was widely dispersed and not associated with specific populations, as a single common haplotype was not detected. The PB population contained both unique (H9, H10 and H11) and shared haplotypes (27 haplotypes) in a higher number in comparison to other geographical locations. Except for haplotype H22 (contains highly aggressive isolates), there was no specific linkage noticed between the isolate aggressiveness and haplotype. The concatenated sequences of all the three genes demonstrated a low level of genetic differentiation (Fst = −0.014 to 0.02) in the analyzed population. Positive values for the neutrality tests in PB, HR and RJ reveal a balancing selection mechanism behind the FG population structure. The WB population showed both positive and negative values of neutrality indices, indicating the role of both population expansion as well as balancing selection in structuring the FG population.
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Chaisiri C, Liu X, Lin Y, Luo C. Diaporthe citri: A Fungal Pathogen Causing Melanose Disease. PLANTS (BASEL, SWITZERLAND) 2022; 11:1600. [PMID: 35736750 PMCID: PMC9227384 DOI: 10.3390/plants11121600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/25/2022] [Accepted: 06/12/2022] [Indexed: 11/16/2022]
Abstract
Citrus melanose is a fungal disease caused by Diaporthe citri F.A. Wolf. It is found in various citrus-growing locations across the world. The host range of D. citri is limited to plants of the Citrus genus. The most economically important hosts are Citrus reticulata (mandarin), C. sinensis (sweet orange), C. grandis or C. maxima (pumelo), and C. paradisi (grapefruit). In the life cycle of D. citri throughout the citrus growing season, pycnidia can be seen in abundance on dead branches, especially after rain, with conidia appearing as slimy masses discharged from the dead twigs. Raindrops can transmit conidia to leaves, twigs, and fruits, resulting in disease dispersion throughout small distances. Persistent rains and warm climatic conditions generally favor disease onset and development. The melanose disease causes a decline in fruit quality, which lowers the value of fruits during marketing and exportation. High rainfall areas should avoid planting susceptible varieties. In this article, information about the disease symptoms, history, geographic distribution, epidemiology, impact, and integrated management practices, as well as the pathogen morphology and identification, was reviewed and discussed.
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Affiliation(s)
- Chingchai Chaisiri
- Key Lab of Horticultural Plant Biology, Ministry of Education, Wuhan 430070, China; (C.C.); (X.L.)
- Hubei Key Lab of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China;
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangyu Liu
- Key Lab of Horticultural Plant Biology, Ministry of Education, Wuhan 430070, China; (C.C.); (X.L.)
- Hubei Key Lab of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China;
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Lin
- Hubei Key Lab of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China;
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaoxi Luo
- Key Lab of Horticultural Plant Biology, Ministry of Education, Wuhan 430070, China; (C.C.); (X.L.)
- Hubei Key Lab of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China;
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Abstract
Citrus essential oils (EOs) are widely used as flavoring agents in food, pharmaceutical, cosmetical and chemical industries. For this reason, their demand is constantly increasing all over the world. Besides industrial applications, the abundance of EOs in the epicarp is particularly relevant for the quality of citrus fruit. In fact, these compounds represent a natural protection against postharvest deteriorations due to their remarkable antimicrobial, insecticidal and antioxidant activities. Several factors, including genotype, climatic conditions and cultural practices, can influence the assortment and accumulation of EOs in citrus peels. This review is focused on factors influencing variation of the EOs’ composition during ripening and on the implications on postharvest quality of the fruit.
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Peng W, Yang Y, Xu J, Peng E, Dai S, Dai L, Wang Y, Yi T, Wang B, Li D, Song N. TALE Transcription Factors in Sweet Orange ( Citrus sinensis): Genome-Wide Identification, Characterization, and Expression in Response to Biotic and Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2022; 12:814252. [PMID: 35126435 PMCID: PMC8811264 DOI: 10.3389/fpls.2021.814252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Three-amino-acid-loop-extension (TALE) transcription factors comprise one of the largest gene families in plants, in which they contribute to regulation of a wide variety of biological processes, including plant growth and development, as well as governing stress responses. Although sweet orange (Citrus sinensis) is among the most commercially important fruit crops cultivated worldwide, there have been relatively few functional studies on TALE genes in this species. In this study, we investigated 18 CsTALE gene family members with respect to their phylogeny, physicochemical properties, conserved motif/domain sequences, gene structures, chromosomal location, cis-acting regulatory elements, and protein-protein interactions (PPIs). These CsTALE genes were classified into two subfamilies based on sequence homology and phylogenetic analyses, and the classification was equally strongly supported by the highly conserved gene structures and motif/domain compositions. CsTALEs were found to be unevenly distributed on the chromosomes, and duplication analysis revealed that segmental duplication and purifying selection have been major driving force in the evolution of these genes. Expression profile analysis indicated that CsTALE genes exhibit a discernible spatial expression pattern in different tissues and differing expression patterns in response to different biotic/abiotic stresses. Of the 18 CsTALE genes examined, 10 were found to be responsive to high temperature, four to low temperature, eight to salt, and four to wounding. Moreover, the expression of CsTALE3/8/12/16 was induced in response to infection with the fungal pathogen Diaporthe citri and bacterial pathogen Candidatus Liberibacter asiaticus, whereas the expression of CsTALE15/17 was strongly suppressed. The transcriptional activity of CsTALE proteins was also verified in yeast, with yeast two-hybrid assays indicating that CsTALE3/CsTALE8, CsTALE3/CsTALE11, CsTALE10/CsTALE12, CsTALE14/CsTALE8, CsTALE14/CsTALE11 can form respective heterodimers. The findings of this study could lay the foundations for elucidating the biological functions of the TALE family genes in sweet orange and contribute to the breeding of stress-tolerant plants.
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Affiliation(s)
- Weiye Peng
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Yang Yang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Jing Xu
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Erping Peng
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Suming Dai
- Horticulture College, Hunan Agricultural University, Changsha, China
- National Center for Citrus Improvement Changsha, Changsha, China
| | - Liangying Dai
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Yunsheng Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Tuyong Yi
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Bing Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Dazhi Li
- Horticulture College, Hunan Agricultural University, Changsha, China
- National Center for Citrus Improvement Changsha, Changsha, China
| | - Na Song
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
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K N, Dubey SC, Kamil D. Diversity analysis of different Diaporthe ( Phomopsis) species and development of molecular marker to identify quarantine important species Phomopsis phaseolorum. 3 Biotech 2022; 12:31. [PMID: 35070621 PMCID: PMC8714617 DOI: 10.1007/s13205-021-03075-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 10/09/2021] [Indexed: 01/03/2023] Open
Abstract
The genus Diaporthe Nitschke (Phomopsis Sacc. & Harter) infect various agricultural and horticultural important crops and cause diseases such as damping off, leaf spots, blights, canker, dieback, wilt, root and fruit rots. P. vexans, P. helianthi and P. phaseolorum are the important species within genus causing huge yield and economic loss. Being primarily seed borne it also hinders import and export of germplasm and seeds. Therefore, extensive characterization is required to diagnose and manage the disease. Seventeen isolates collected from ITCC, IARI and ICAR-NBPGR belonging to eight species were morphological and molecularly characterized and diversity was analyzed. Several morphological and cultural characters were studied and analyzed. Due to lack of sufficient morphological variation to identify/differentiate species, molecular characterization using house-keeping genes, internal transcriber spacer (ITS) was carried out. ITS produced amplicon of ~ 600 bp in the isolates of Phomopsis and phylogenetic tree obtained revealed that isolates of a species belonging same geographic region had more sequence similarity than isolates belonging to different geographic regions this might be due to population adaption under varied environments. Development of EF-1alpha-based marker specific to P. phaseolorum helps in easily detection of pathogen in quarantine stations. In addition, species of Phomopsis were previously named based on host association which has led to misidentification and proliferation of species. Cross pathogenicity of isolates on three important hosts, brinjal, soybean and chilli revealed its broad host range and naming only basis of host association is unjustified.
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Affiliation(s)
- Nishmitha K
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Deeba Kamil
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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Abundant Genetic Diversity and Extensive Differentiation among Geographic Populations of the Citrus Pathogen Diaporthe citri in Southern China. J Fungi (Basel) 2021; 7:jof7090749. [PMID: 34575787 PMCID: PMC8468327 DOI: 10.3390/jof7090749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 11/29/2022] Open
Abstract
The fungal pathogen Diaporthe citri is a major cause of diseases in citrus. One common disease is melanose, responsible for large economic losses to the citrus fruit industry. However, very little is known about the epidemiology and genetic structure of D. citri. In this study, we analyzed 339 isolates from leaves and fruits with melanose symptoms from five provinces in southern China at 14 polymorphic simple sequence repeat (SSR) loci and the mating type idiomorphs. The genetic variations were analyzed at three levels with separate samples: among provinces, among orchards within one county, and among trees within one orchard. The five provincial populations from Fujian, Zhejiang, Jiangxi, Hunan, and Guizhou were significantly differentiated, while limited differences were found among orchards from the same county or among trees from the same orchard. STRUCTURE analysis detected two genetic clusters in the total sample, with different provincial subpopulations showing different frequencies of isolates in these two clusters. Mantel analysis showed significant positive correlation between genetic and geographic distances, consistent with geographic separation as a significant barrier to gene flow in D. citri in China. High levels of genetic diversity were found within individual subpopulations at all three spatial scales of analyses. Interestingly, most subpopulations at all three spatial scales had the two mating types in similar frequencies and with alleles at the 14 SSR loci not significantly different from linkage equilibrium. Indeed, strains with different mating types and different multilocus genotypes were frequently isolated from the same leaves and fruits. The results indicate that sexual reproduction plays an important role in natural populations of D. citri in southern China and that its ascospores likely represent an important contributor to citrus disease.
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Ariyawansa HA, Tsai I, Wang JY, Withee P, Tanjira M, Lin SR, Suwannarach N, Kumla J, Elgorban AM, Cheewangkoon R. Molecular Phylogenetic Diversity and Biological Characterization of Diaporthe Species Associated with Leaf Spots of Camellia sinensis in Taiwan. PLANTS (BASEL, SWITZERLAND) 2021; 10:1434. [PMID: 34371637 PMCID: PMC8309328 DOI: 10.3390/plants10071434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022]
Abstract
Camellia sinensis is one of the major crops grown in Taiwan and has been widely cultivated around the island. Tea leaves are prone to various fungal infections, and leaf spot is considered one of the major diseases in Taiwan tea fields. As part of a survey on fungal species causing leaf spots on tea leaves in Taiwan, 19 fungal strains morphologically similar to the genus Diaporthe were collected. ITS (internal transcribed spacer), tef1-α (translation elongation factor 1-α), tub2 (beta-tubulin), and cal (calmodulin) gene regions were used to construct phylogenetic trees and determine the evolutionary relationships among the collected strains. In total, six Diaporthe species, including one new species, Diaporthe hsinchuensis, were identified as linked with leaf spot of C. sinensis in Taiwan based on both phenotypic characters and phylogeny. These species were further characterized in terms of their pathogenicity, temperature, and pH requirements under laboratory conditions. Diaporthe tulliensis, D. passiflorae, and D. perseae were isolated from C. sinensis for the first time. Furthermore, pathogenicity tests revealed that, with wound inoculation, only D. hongkongensis was pathogenic on tea leaves. This investigation delivers the first assessment of Diaporthe taxa related to leaf spots on tea in Taiwan.
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Affiliation(s)
- Hiran A. Ariyawansa
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan; (I.T.); (J.-Y.W.)
| | - Ichen Tsai
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan; (I.T.); (J.-Y.W.)
- Biodiversity and Climate Research Centre (BiK-F), 60325 Frankfurt am Main, Germany
- Department of Biological Science, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Jian-Yuan Wang
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan; (I.T.); (J.-Y.W.)
| | - Patchareeya Withee
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (P.W.); (M.T.)
| | - Medsaii Tanjira
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (P.W.); (M.T.)
| | - Shiou-Ruei Lin
- Department of Tea Agronomy, Tea Research and Extension Station, Taoyuan 32654, Taiwan;
| | - Nakarin Suwannarach
- Research Centre of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (N.S.); (J.K.)
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jaturong Kumla
- Research Centre of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (N.S.); (J.K.)
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Abdallah M. Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Ratchadawan Cheewangkoon
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (P.W.); (M.T.)
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
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Liu XY, Chaisiri C, Lin Y, Yin WX, Luo CX. Whole-Genome Sequence of Diaporthe citri Isolate NFHF-8-4, the Causal Agent of Citrus Melanose. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:845-847. [PMID: 33761784 DOI: 10.1094/mpmi-01-21-0004-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Diaporthe species are the causal agents of melanose, stem-end rot, and gummosis diseases of citrus. D. citri is the predominant species on different citrus varieties. These diseases exceedingly reduce quality and marketability of fresh fruits. Melanose on fruits especially causes massive economic losses. The infection mechanisms of D. citri are still unclear and the genome sequence of D. citri has not been released. In order to systemically explore the interaction between citrus and D. citri, we sequenced the whole-genome of D. citri NFHF-8-4, which was isolated from a sample with melanose in Jiangxi Province. The NFHF-8-4 genome sequence will provide valuable information for studying the development process, infection process, and resistance to fungicides mechanisms in D. citri.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Xiang-Yu Liu
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science & Technology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chingchai Chaisiri
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science & Technology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Lin
- College of Plant Science & Technology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei-Xiao Yin
- College of Plant Science & Technology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao-Xi Luo
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science & Technology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
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12
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Gai Y, Xiong T, Xiao X, Li P, Zeng Y, Li L, Riely BK, Li H. The Genome Sequence of the Citrus Melanose Pathogen Diaporthe citri and Two Citrus-Related Diaporthe Species. PHYTOPATHOLOGY 2021; 111:779-783. [PMID: 33315476 DOI: 10.1094/phyto-08-20-0376-sc] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Melanose disease is one the most widely distributed and economically important fungal diseases of citrus worldwide. The causative agent is the filamentous fungus Diaporthe citri (syn. Phomopsis citri). Here, we report the genome assemblies of three strains of D. citri, namely strains ZJUD2, ZJUD14, and Q7, which were generated using a combination of PacBio Sequel long-read and Illumina paired-end sequencing data. The assembled genomes of D. citri ranged from 52.06 to 63.61 Mb in genome size, containing 15,977 to 16,622 protein-coding genes. We also sequenced and annotated the genome sequences of two citrus-related Diaporthe species, D. citriasiana and D. citrichinensis. In addition, a database for citrus-related Diaporthe genomes was established to provide a public platform to access genome sequences, genome annotation and comparative genomics data of these Diaporthe species. The described genome sequences and the citrus-related Diaporthe genomes database provide a useful resource for the study of fungal biology, pathogen-host interaction, molecular diagnostic marker development, and population genomic analyses of Diaporthe species. The database will be updated regularly when the genomes of newly isolated Diaporthe species are sequenced. The citrus-related Diaporthe genomes database is freely available for nonprofit use at zjudata.com/blast/diaporthe.php.
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Affiliation(s)
- Yunpeng Gai
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Tao Xiong
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaoe Xiao
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Pudong Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yating Zeng
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Lei Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Brendan K Riely
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Hongye Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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Chaisiri C, Liu X, Lin Y, Fu Y, Zhu F, Luo C. Phylogenetic and Haplotype Network Analyses of Diaporthe eres Species in China Based on Sequences of Multiple Loci. BIOLOGY 2021; 10:179. [PMID: 33804529 PMCID: PMC8000818 DOI: 10.3390/biology10030179] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 11/17/2022]
Abstract
Diaporthe eres is considered one of the most important causal agents of many plant diseases, with a broad host range worldwide. In this study, multiple sequences of ribosomal internal transcribed spacer region (ITS), translation elongation factor 1-α gene (EF1-α), beta-tubulin gene (TUB2), calmodulin gene (CAL), and histone-3 gene (HIS) were used for multi-locus phylogenetic analysis. For phylogenetic analysis, maximum likelihood (ML), maximum parsimony (MP), and Bayesian inferred (BI) approaches were performed to investigate relationships of D. eres with closely related species. The results strongly support that the D. eres species falls into a monophyletic lineage, with the characteristics of a species complex. Phylogenetic informativeness (PI) analysis showed that clear boundaries could be proposed by using EF1-α, whereas ITS showed an ineffective reconstruction and, thus, was unsuitable for speciating boundaries for Diaporthe species. A combined dataset of EF1-α, CAL, TUB2, and HIS showed strong resolution for Diaporthe species, providing insights for the D. eres complex. Accordingly, besides D. biguttusis, D. camptothecicola, D. castaneae-mollissimae, D. cotoneastri, D. ellipicola, D. longicicola, D. mahothocarpus, D. momicola, D. nobilis, and Phomopsis fukushii, which have already been previously considered the synonymous species of D. eres, another three species, D. henanensis, D. lonicerae and D. rosicola, were further revealed to be synonyms of D. eres in this study. In order to demonstrate the genetic diversity of D. eres species in China, 138 D. eres isolates were randomly selected from previous studies in 16 provinces. These isolates were obtained from different major plant species from 2006 to 2020. The genetic distance was estimated with phylogenetic analysis and haplotype networks, and it was revealed that two major haplotypes existed in the Chinese populations of D. eres. The haplotype networks were widely dispersed and not uniquely correlated to specific populations. Overall, our analyses evaluated the phylogenetic identification for D. eres species and demonstrated the population diversity of D. eres in China.
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Affiliation(s)
- Chingchai Chaisiri
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (C.C.); (X.L.)
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Xiangyu Liu
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (C.C.); (X.L.)
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Yang Lin
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Yanping Fu
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Fuxing Zhu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Chaoxi Luo
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (C.C.); (X.L.)
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
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Chaisiri C, Liu XY, Yin WX, Luo CX, Lin Y. Morphology Characterization, Molecular Phylogeny, and Pathogenicity of Diaporthe passifloricola on Citrus reticulata cv. Nanfengmiju in Jiangxi Province, China. PLANTS (BASEL, SWITZERLAND) 2021; 10:218. [PMID: 33498730 PMCID: PMC7911537 DOI: 10.3390/plants10020218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/21/2021] [Accepted: 01/21/2021] [Indexed: 11/24/2022]
Abstract
The Nanfengmiju (Citrus reticulata cv. Nanfengmiju), a high-quality local variety of mandarin, is one of the major fruit crops in Jiangxi Province, China. Citrus melanose and stem-end rot, two common fungal diseases of Nanfengmiju, are both caused by Diaporthe spp. (syn. Phomopsis spp.). Identification of the Diaporthe species is essential for epidemiological studies, quarantine measures, and management of diseases caused by these fungi. Melanose disease was observed on Nanfengmiju fruit in Jiangxi Province of China in 2016. Based on morphological characterization and multi-locus phylogenetic analyses, three out of 39 isolates from diseased samples were identified as D. passifloricola. Since these three isolates did not cause melanose on citrus fruit in the pathogenicity tests, they were presumed to be endophytic fungi present in the diseased tissues. However, our results indicate that D. passifloricola may persist as a symptom-less endophyte in the peel of citrus fruit, yet it may cause stem-end if it invades the stem end during fruit storage. To the best of our knowledge, this is the first report of D. passifloricola as the causal agent of the stem-end rot disease in Citrus reticulata cv. Nanfengmiju.
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Affiliation(s)
- Chingchai Chaisiri
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (C.C.); (X.-Y.L.); (W.-X.Y.); (C.-X.L.)
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang-Yu Liu
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (C.C.); (X.-Y.L.); (W.-X.Y.); (C.-X.L.)
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei-Xiao Yin
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (C.C.); (X.-Y.L.); (W.-X.Y.); (C.-X.L.)
| | - Chao-Xi Luo
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (C.C.); (X.-Y.L.); (W.-X.Y.); (C.-X.L.)
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (C.C.); (X.-Y.L.); (W.-X.Y.); (C.-X.L.)
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Paenibacillus brasilensis YS-1: A Potential Biocontrol Agent to Retard Xinyu Tangerine Senescence. AGRICULTURE 2020. [DOI: 10.3390/agriculture10080330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Xinyu tangerine (Citrus reticulata Blanco) is a non-climacteric fruit that is widely cultivated and consumed in China but highly susceptible to fungal infections. Antagonistic microorganisms can control postharvest diseases and extend the storage life of citrus fruits. However, little work has been done to investigate the effects of applying Paenibacillus brasilensis YS-1 by immersion to enhance the cold storability of Xinyu tangerines. Fruits were soaked with P. brasilensis YS-1 fermented filtrates for 10 min and in sterile water as the control. The decay incidence, weight loss, nutrient content, respiration rate, malondialdehyde (MDA) content, and defensive enzymes activities in citrus fruit were measured during cold storage at 5 ± 0.5 °C. The results showed that P. brasilensis YS-1 treatment significantly reduced postharvest decay and effectively maintained the nutritional quality compared to the control under cold storage. The weight loss, respiration rate, and MDA content were lower in P. brasilensis YS-1-treated fruits than the control fruits, indicating that P. brasilensis YS-1 treatment increased the activities of superoxide dismutase (SOD), peroxidase (POD), polyphenol oxidase (PPO), and phenylalnine ammonia-lyase (PAL). According to the results, a postharvest application of P. brasilensis YS-1 can control the postharvest decay and maintain fruit quality, as well as increase the defensive enzyme activity, so as to achieve the purpose of retarding postharvest senescence in citrus fruit.
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