Importance of Molecular and Phylogenetic Analyses for Identification of Basidiomycetes

Sarwar, Samina; Firdous, Qudsia; Khalid, Abdul Nasir

doi:10.5772/intechopen.80671

Cited by 7 publications

(4 citation statements)

References 28 publications

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“…Implementation of molecular fungal identification needs to be done to identify fungal species through phylogenetic analysis to get correct results. However, morphological observation of fungi can be used as supporting data for the characteristics of a fungus (Sarwar et al 2019). Fungal isolates that based on morphological identified as Sarocladium sp., DNA sequencing were also carried out by ITS rDNA gene sequence to correctly identify species.…”

Section: Resultsmentioning

confidence: 99%

Short Communication: Sarocladium oryzae associated with sheath rot disease of rice in Indonesia

et al. 2020

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Abstract. Pramunadipta S, Widiastuti A, Wibowo A, Suga H, Priyatmojo A. 2020. Short Communication: Sarocladium oryzae associated with sheath rot disease of rice in Indonesia. Biodiversitas 21: 1243-1249. One of the obstacles in increasing rice production is the presence of sheath rot pathogen infection, which causes changes in color on the rice sheath to brown or reddish-brown, sometimes does not produce rice grain. The major fungal pathogens that cause sheath rot disease are Sarocladium oryzae and Fusarium spp. The loss of rice yields reaches 85%. The disease found in six provinces, some of which are the largest rice-producing centers in Indonesia. A total of twenty-four Sarocladium sp. were isolated from leaf sheath symptom on potato dextrose agar and water agar medium. Sheath rot pathogen identification based on molecular method was performed using internal transcribed spacer (ITS) rDNA gene sequencing. Necrosis occurs after artificial inoculation in Ciherang rice variety was observed and showed that all isolates were pathogenic. Morphological characterization of the isolates identified them as Sarocladium sp. Molecular identification showed that six representatives isolates belonging to S. oryzae. These findings are important information about the fungal pathogen that causes sheath rot disease in Indonesia, and in studies for formulating control measures of the pathogen in the future to prevent the disease epidemic on rice. This is the first report about the existence of sheath rot disease, morphological characterization and molecular identification of S. oryzae in various rice fields in Indonesia.

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Section: Resultsmentioning

confidence: 99%

Short Communication: Sarocladium oryzae associated with sheath rot disease of rice in Indonesia

et al. 2020

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“…as an endophyte is not rare; it has been isolated from several medicinal plants with potent biological activity against several drug-resistant pathogens (Lu et al, 2000;Arivudainambi et al, 2011;Sharma et al, 2017;Kim and Shim, 2019). Molecular tools including phylogenetic analyses that aid along with the traditional techniques have been proven to be successful for correct identification of fungi and have further revolutionized the fungal classification (Sarwar et al, 2019). Moreover, the ITS region which consists of a highly conserved 5.8S rRNA and variable regions ITS1 and, ITS2, is one of the widely used phylogenetic markers for fungal species identification (Tamura et al, 2004;Xu and Adamowicz, 2016).…”

Section: Discussionmentioning

confidence: 99%

Isolation and Characterization of an Endophytic Fungus Colletotrichum coccodes Producing Tyrosol From Houttuynia cordata Thunb. Using ITS2 RNA Secondary Structure and Molecular Docking Study

Talukdar

Padhi

Kumar

et al. 2021

Front. Bioeng. Biotechnol.

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An endophytic fungus isolated from healthy leaf tissues of Houttuynia cordata Thunb., an ethnomedicinal plant of North East India, showed a considerable amount of antimicrobial activity. The ethyl acetate extract of the fungal culture filtrates displayed promising antimicrobial activity against a panel of clinically significant pathogens including Candida albicans, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. Bioassay guided purification of the organic extract using column and thin layer chromatography yielded a pure homogenous compound which was identified using spectroscopic methods (essentially by 1H NMR and MS) as tyrosol, a well-known phenylethanoid present in several natural sources. Besides, molecular docking studies against tyrosyl tRNA synthetases (TyrRS) of S. aureus (PDB ID: 1JIL) and E. coli (PDB ID: 1VBM), and CYP45014α-lanosterol demethylase (CYP51) of C. albicans (PDB ID: 5FSA) revealed tyrosol has a strong binding affinity with the enzyme active site residues. The fungus was identified as Colletotrichum sp. and characterized by its genomic ITS rDNA and ITS2 sequences. Phylogenetic analyses showed clustering of our isolate with Colletotrichum coccodes. Species of Colletotrichum are also reported to be plant pathogens. Therefore, to confirm the endophytic lifestyle of the isolate, ITS2 RNA secondary structure study was undertaken. The result indicated our isolate exhibited differences in the folding pattern as well as in motif structures when compared to those of pathogenic C. coccodes. The findings indicated that endophytic fungi harboring H. cordata could be explored as a potent source of antimicrobial agents.

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“…These methods involve DNA or RNA analysis to determine genetic relationships and species boundaries. DNA barcoding, a molecular tool that targets specific genetic markers, has gained popularity for its rapid and precise identification (Sarwar et al 2019). This approach involves comparing DNA sequences from mushrooms genes to reference databases, allowing for precise species identification.…”

Section: Mushroom Identificationmentioning

confidence: 99%

Complete mitochondrial genomes of edible mushrooms: features, evolution, and phylogeny

Zeb,

Aziz,

Azizullah

et al. 2024

Physiologia Plantarum

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Edible mushrooms are an important food source with high nutritional and medicinal value. They are a useful source for studying phylogenetic evolution and species divergence. The exploration of the evolutionary relationships among these species conventionally involves analyzing sequence variations within their complete mitochondrial genomes, which range from 31,854 bp (Cordyceps militaris) to 197,486 bp (Grifolia frondosa). The study of the complete mitochondrial genomes of edible mushrooms has emerged as a critical field of research, providing important insights into fungal genetic makeup, evolution, and phylogenetic relationships. This review explores the mitochondrial genome structures of various edible mushroom species, highlighting their unique features and evolutionary adaptations. By analyzing these genomes, robust phylogenetic frameworks are constructed to elucidate mushrooms lineage relationships. Furthermore, the exploration of different variations of mitochondrial DNA presents novel opportunities for enhancing mushroom cultivation biotechnology and medicinal applications. The mitochondrial genomic features are essential for improving agricultural practices and ensuring food security through improved crop productivity, disease resistance, and nutritional qualities. The current knowledge about the mitochondrial genomes of edible mushrooms is summarized in this review, emphasising their significance in both scientific research and practical applications in bioinformatics and medicine.

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Importance of Molecular and Phylogenetic Analyses for Identification of Basidiomycetes

Cited by 7 publications

References 28 publications

Short Communication: Sarocladium oryzae associated with sheath rot disease of rice in Indonesia

Short Communication: Sarocladium oryzae associated with sheath rot disease of rice in Indonesia

Isolation and Characterization of an Endophytic Fungus Colletotrichum coccodes Producing Tyrosol From Houttuynia cordata Thunb. Using ITS2 RNA Secondary Structure and Molecular Docking Study

Complete mitochondrial genomes of edible mushrooms: features, evolution, and phylogeny

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