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Sajjan U, Hubballi M, Pandey AK, Devappa V, Maheswarappa HP. Characterizations of Ganoderma species causing basal stem rot disease in coconut tree. 3 Biotech 2024; 14:104. [PMID: 38464612 PMCID: PMC10923766 DOI: 10.1007/s13205-023-03872-w] [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: 02/11/2023] [Accepted: 11/30/2023] [Indexed: 03/12/2024] Open
Abstract
The basal stem rot disease incidence ranged from 0 to 5% in Karnataka India during the year 2019-20. Twenty pathogenic isolates of Ganoderma sp varied with cultural characteristics and virulence on coconut seedlings of the variety Tipatur Tall. The identity of each isolate was confirmed through morphological characters and through ITS sequencing. Two isolates viz., G4 and G5 were identified as Ganoderma applanatum and remaining all isolates were identified as G. lucidum. The genetic diversity analysis of Ganoderma isolates was done using ten Random Amplified Polymorphic DNA (RAPD) and fifteen Inter Simple Sequence Repeat (ISSR) primers. Among the ten RAPD primers, only eight primers recorded polymorphism (33.30-66.70%). The primer SBS-Q3 exhibited the highest polymorphism of 66.70%. In case of ISSR primers, all primers recorded polymorphism (33.30-60.00%). The primer UBC866 was the most polymorphic primer with 60.0% polymorphism. RAPD and ISSR markers were compared for their efficacy in assessing the genetic diversity by taking the band frequency, Shannon's index, polymorphic information content, resolving power, and mean resolving power into consideration, and it was concluded that ISSR was marker of choice over RAPD. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03872-w.
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Affiliation(s)
- Umesh Sajjan
- University of Horticultural Sciences, Bagalkot, Karnataka 587104 India
| | | | - Abhay K. Pandey
- Department of Mycology and Microbiology, Tea Research Association, North Bengal Regional, R and D Center, Nagrakata, 735225 West Bengal India
| | - V. Devappa
- University of Horticultural Sciences, Bagalkot, Karnataka 587104 India
| | - H. P. Maheswarappa
- Department of Mycology and Microbiology, Tea Research Association, North Bengal Regional, R and D Center, Nagrakata, 735225 West Bengal India
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Nagappan J, Ooi SE, Chan KL, Kadri F, Nurazah Z, Halim MAA, Angel LPL, Sundram S, Chin CF, May ST, Low ETL. Transcriptional effects of carbon and nitrogen starvation on Ganoderma boninense, an oil palm phytopathogen. Mol Biol Rep 2024; 51:212. [PMID: 38273212 DOI: 10.1007/s11033-023-09054-4] [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: 05/22/2023] [Accepted: 10/24/2023] [Indexed: 01/27/2024]
Abstract
BACKGROUND Ganoderma boninense is a phytopathogen of oil palm, causing basal and upper stem rot diseases. METHODS The genome sequence was used as a reference to study gene expression during growth in a starved carbon (C) and nitrogen (N) environment with minimal sugar and sawdust as initial energy sources. This study was conducted to mimic possible limitations of the C-N nutrient sources during the growth of G. boninense in oil palm plantations. RESULTS Genome sequencing of an isolate collected from a palm tree in West Malaysia generated an assembly of 67.12 Mb encoding 19,851 predicted genes. Transcriptomic analysis from a time course experiment during growth in this starvation media identified differentially expressed genes (DEGs) that were found to be associated with 29 metabolic pathways. During the active growth phase, 26 DEGs were related to four pathways, including secondary metabolite biosynthesis, carbohydrate metabolism, glycan metabolism and mycotoxin biosynthesis. G. boninense genes involved in the carbohydrate metabolism pathway that contribute to the degradation of plant cell walls were up-regulated. Interestingly, several genes associated with the mycotoxin biosynthesis pathway were identified as playing a possible role in pathogen-host interaction. In addition, metabolomics analysis revealed six metabolites, maltose, xylobiose, glucooligosaccharide, glycylproline, dimethylfumaric acid and arabitol that were up-regulated on Day2 of the time course experiment. CONCLUSIONS This study provides information on genes expressed by G. boninense in metabolic pathways that may play a role in the initial infection of the host.
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Affiliation(s)
- Jayanthi Nagappan
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Siew-Eng Ooi
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Faizun Kadri
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Zain Nurazah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Mohd Amin Ab Halim
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Lee Pei Lee Angel
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Shamala Sundram
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Chiew-Foan Chin
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Sean T May
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nr Loughborough, LE12 5RD, UK
| | - Eng Ti Leslie Low
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
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Induced expression of Ganoderma boninense Lanosterol 14α-Demethylase (ERG11) during interaction with oil palm. Mol Biol Rep 2023; 50:2367-2379. [PMID: 36580194 DOI: 10.1007/s11033-022-08131-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 11/16/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND The basidiomycete fungus, Ganoderma boninense is the main contributor to oil palm Basal Stem Rot (BSR) in Malaysia and Indonesia. Lanosterol 14α-Demethylase (ERG11) is a key enzyme involved in biosynthesis of ergosterol, which is an important component in the fungal cell membrane. The Azole group fungicides are effective against pathogenic fungi including G. boninense by inhibiting the ERG11 activity. However, the work on molecular characterization of G. boninense ERG11 is still unavailable today. METHODS AND RESULTS This study aimed to isolate and characterize the full-length cDNA encoding ERG11 from G. boninense. The G. boninense ERG11 gene expression during interaction with oil palm was also studied. A full-length 1860 bp cDNA encoding ERG11 was successfully isolated from G. boninense. The G. boninense ERG11 shared 91% similarity to ERG11 from other basidiomycete fungi. The protein structure homology modeling of GbERG11 was analyzed using the SWISS-MODEL workspace. Southern blot and genome data analyses showed that there is only a single copy of ERG11 gene in the G. boninense genome. Based on the in-vitro inoculation study, the ERG11 gene expression in G. boninense has shown almost 2-fold upregulation with the presence of oil palm. CONCLUSION This study provided molecular information and characterization study on the G. boninense ERG11 and this knowledge could be used to design effective control measures to tackle the BSR disease of oil palm.
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Dat TD, Nguyen Phan Thi Cam C, Nguyen Minh A, Nguyen Duc V, Vuong Hoai T, Nguyen Huynh Bach Son L, Huynh Ngoc O, Hoang Minh N, Mai PT, Hieu NH. Application of ultrasound‐assisted enzymatic extraction to enhance triterpenoid content and the biological properties of Vietnamese
Ganoderma lucidum
extract. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tran Do Dat
- VNU‐HCM, Key Laboratory of Chemical Engineering and Petroleum Processing (Key CEPP Lab) Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Faculty of Chemical Engineering Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City (VNU‐HCM) Ho Chi Minh City Vietnam
| | - Chuong Nguyen Phan Thi Cam
- VNU‐HCM, Key Laboratory of Chemical Engineering and Petroleum Processing (Key CEPP Lab) Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Faculty of Chemical Engineering Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City (VNU‐HCM) Ho Chi Minh City Vietnam
| | - Anh Nguyen Minh
- VNU‐HCM, Key Laboratory of Chemical Engineering and Petroleum Processing (Key CEPP Lab) Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Faculty of Chemical Engineering Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City (VNU‐HCM) Ho Chi Minh City Vietnam
| | - Viet Nguyen Duc
- VNU‐HCM, Key Laboratory of Chemical Engineering and Petroleum Processing (Key CEPP Lab) Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Faculty of Chemical Engineering Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City (VNU‐HCM) Ho Chi Minh City Vietnam
| | - Thanh Vuong Hoai
- VNU‐HCM, Key Laboratory of Chemical Engineering and Petroleum Processing (Key CEPP Lab) Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Faculty of Chemical Engineering Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City (VNU‐HCM) Ho Chi Minh City Vietnam
| | | | - Oanh Huynh Ngoc
- VNU‐HCM, Key Laboratory of Chemical Engineering and Petroleum Processing (Key CEPP Lab) Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Faculty of Chemical Engineering Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City (VNU‐HCM) Ho Chi Minh City Vietnam
| | - Nam Hoang Minh
- VNU‐HCM, Key Laboratory of Chemical Engineering and Petroleum Processing (Key CEPP Lab) Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Faculty of Chemical Engineering Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City (VNU‐HCM) Ho Chi Minh City Vietnam
| | - Phong Thanh Mai
- VNU‐HCM, Key Laboratory of Chemical Engineering and Petroleum Processing (Key CEPP Lab) Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Faculty of Chemical Engineering Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City (VNU‐HCM) Ho Chi Minh City Vietnam
| | - Nguyen Huu Hieu
- VNU‐HCM, Key Laboratory of Chemical Engineering and Petroleum Processing (Key CEPP Lab) Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Faculty of Chemical Engineering Ho Chi Minh City University of Technology (HCMUT) Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City (VNU‐HCM) Ho Chi Minh City Vietnam
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Stefanova P, Brazkova M, Angelova G. Comparative study of DNA extraction methods for identification of medicinal mushrooms. BIO WEB OF CONFERENCES 2022. [DOI: 10.1051/bioconf/20224502007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The isolation of high quantity and intact DNA is of a great significance for molecular identification of higher fungi. The aim of this study was to compare two DNA extraction methods for isolation of DNA from medicinal mushrooms of Agaricomycetes class. A modified CTAB method and a modified SDS method were compared by the yield and purity of the extracted DNA, its fragmentation state and suitability for amplification. The results demonstrated high efficiency of both methods in regard to DNA yield (14.18 -144.28 ng DNA/mg biomass with CTAB method and 15.03 -108.34 ng DNA/mg biomass with SDS method). The CTAB method provided DNA extracts with higher purity (A260/A280 ranged from 1.83 to 1.99) in comparison with the SDS method (A260/A280 = 1.53 -1.86). The modified CTAB method produced amplifiable DNA from all mushroom isolates, while the SDS method demonstrated suitability for amplification only in 50% of the samples. Therefore, the modified CTAB method could be the method of choice for DNA extraction from medicinal mushrooms. The analyzed isolates were subjected to molecular identification by ITS1-5.8S-ITS2 rRNA gene sequence analysis and were identified as Ganoderma resinaceum, Trametes versicolor, Fomitopsis pinicola and Inonotus hispidus.
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Nóbrega BB, Soares DMM, Zamuner CK, Stevani CV. Optimized methodology for obtention of high-yield and -quality RNA from the mycelium of the bioluminescent fungus Neonothopanus gardneri. J Microbiol Methods 2021; 191:106348. [PMID: 34699864 DOI: 10.1016/j.mimet.2021.106348] [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: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 10/20/2022]
Abstract
Neonothopanus gardneri, also known as coconut flower mushroom (flor-de-coco), is a Brazilian bioluminescent basidiomycete found in Palm Forest, a transitional biome between the Amazonian Forest and Caatinga (Savanna-like vegetation) in Northeast Brazil, especially in Piauí State. Recent advances toward the elucidation of fungal bioluminescence have contributed to the discovery of four genes (hisps, h3h, luz and cph) involved with the bioluminescence process, the so-called Caffeic Acid Cycle (CAC) and to develop biotechnological applications such autoluminescent tobacco plants and luciferase-based reporter genes. High-yield and -quality RNA-extraction methods are required for most of these purposes. Herein, four methods for RNA isolation from the mycelium of N. gardneri were evaluated: RNeasy® kit (QIAGEN), TRI+, TRI18G+, and TRI26G+. Highest RNA yield was observed for TRI18G+ and TRI26G+ methods, an increase of ~130% in comparison to the RNeasy® method and of ~40% to the TRI+ protocol. All the RNA samples showed good purity and integrity, except by gDNA contamination in RNA samples produced with the RNeasy® method. High quality of RNA samples was confirmed by successful cDNA synthesis and PCR amplification of the coding sequence of h3h gene, responsible for the hydroxylation of the precursor of fungal luciferin (3-hydroxyhispidin). Similarly, RT-qPCR amplification of ef-tu gene, related to the protein biosynthesis in the cell, was demonstrated from RNA samples. This is the first report of a reproducible, time-saving and low-cost optimized method for isolation of high-quality and -yield, DNA-free RNA from a bioluminescent fungus, but that can also be useful for other basidiomycetes.
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Affiliation(s)
- Bianca B Nóbrega
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil; Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Douglas M M Soares
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
| | - Caio K Zamuner
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Cassius V Stevani
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
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Lim FH, Rasid OA, Idris AS, As'wad AWM, Vadamalai G, Parveez GKA, Wong MY. Enhanced polyethylene glycol (PEG)-mediated protoplast transformation system for the phytopathogenic fungus, Ganoderma boninense. Folia Microbiol (Praha) 2021; 66:677-688. [PMID: 34041694 DOI: 10.1007/s12223-021-00852-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/04/2021] [Indexed: 11/26/2022]
Abstract
The basidiomycete fungus, Ganoderma boninense, has been identified as the main causal agent of oil palm basal stem rot (BSR) disease which has caused significant economic losses to the industry especially in Malaysia and Indonesia. Various efforts have been initiated to understand the disease and this plant pathogen especially at the molecular level. This is the first study of its kind on the development of a polyethylene glycol (PEG)-mediated protoplast transformation system for G. boninense. Based on the minimal inhibitory concentration study, 60 µg/mL and above of hygromycin were effective to completely inhibit G. boninense growth. Approximately 5.145 × 107 cells/mL of protoplasts with the viability of 97.24% was successfully obtained from G. boninense mycelium tissue. The PEG-mediated G. boninense protoplast transformation using 1 µg of transformation vector, 25% of PEG solution, 10 min of pre-transformation incubation, and 30 min of post-transformation incubation has improved the transformation rate as compared with the previous reported protocols for other basidiomycete fungi. Optimization of four transformation parameters has improved the transformation efficiency of G. boninense from an average of 2 to 67 putative transformants. The presence of hygromycin phosphotransferase (hpt) and enhanced green fluorescent protein (eGFP) genes in the putative transformants was detected by PCR and verified by gene sequence analysis. Southern hybridization result further confirmed the integration of hpt gene in G. boninense transformants, and the green fluorescent signal was detected in the G. boninense transformants under the microscopic analysis. The establishment of this transformation system will accelerate the gene function studies of G. boninense especially those genes that may contribute to the pathogenesis of this fungus in oil palm.
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Affiliation(s)
- Fook-Hwa Lim
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
| | - Omar Abd Rasid
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Abu Seman Idris
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Abdul Wahab Mohd As'wad
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Ganesan Vadamalai
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Institute of Plantation Studies, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | | | - Mui-Yun Wong
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
- Institute of Plantation Studies, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
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