Fungal Genomic Resources for Strain Identification and Diversity Analysis of 1900 Fungal Species

Iquebal, Mir Asif; Jaiswal, Sarika; Mishra, Vineet Kumar; Jasrotia, Rahul Singh; Angadi, U. B.; Passari, Ajit Kumar; Deka, Purbajyoti; Prabha, Ratna; Singh, Dhananjaya P.; Gupta, Vijai Kumar; Tomar, R. S.; Oberoi, Harinder Singh; Rai, Anil; Kumar, Dinesh

doi:10.3390/jof7040288

Cited by 7 publications

(3 citation statements)

References 60 publications

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“…It supports custom in silico analyses through advanced bioinformatics tools and a Galaxy-based workspace for comprehensive data analyses like RNA sequencing (RNA-Seq) and variant calling [ 45 , 46 , 47 ]. This integration enhances the utility of FungiDB for comparative genomics and evolutionary studies, complementing the resources provided by Ensembl Fungi [ 48 , 49 ].…”

Section: Methodsmentioning

confidence: 99%

Revealing Hidden Genes in Botrytis cinerea: New Insights into Genes Involved in the Biosynthesis of Secondary Metabolites

Suárez,

Collado,

Garrido

2024

IJMS

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Utilizing bioinformatics tools, this study expands our understanding of secondary metabolism in Botrytis cinerea, identifying novel genes within polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), sesquiterpene cyclase (STC), diterpene cyclase (DTC), and dimethylallyltryptophan synthase (DMATS) families. These findings enrich the genetic framework associated with B. cinerea’s pathogenicity and ecological adaptation, offering insights into uncharted metabolic pathways. Significantly, the discovery of previously unannotated genes provides new molecular targets for developing targeted antifungal strategies, promising to enhance crop protection and advance our understanding of fungal biochemistry. This research not only broadens the scope of known secondary metabolites but also opens avenues for future exploration into B. cinerea’s biosynthetic capabilities, potentially leading to novel antifungal compounds. Our work underscores the importance of integrating bioinformatics and genomics for fungal research, paving the way for sustainable agricultural practices by pinpointing precise molecular interventions against B. cinerea. This study sets a foundation for further investigations into the fungus’s secondary metabolism, with implications for biotechnology and crop disease management.

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Section: Methodsmentioning

confidence: 99%

Revealing Hidden Genes in Botrytis cinerea: New Insights into Genes Involved in the Biosynthesis of Secondary Metabolites

Suárez,

Collado,

Garrido

2024

IJMS

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“…Moreover, FungiDB's integration with EuPathDB highlights its commitment to supporting the fungal research community by providing access to a wealth of genomic resources. This collaboration enhances the database's utility, making it an indispensable tool for researchers aiming to conduct comparative genomics studies, understand evolutionary relationships, and develop targeted interventions for fungal diseases [43]. In this way, FungiDB complements the genomic data and analytical tools provided by Ensembl Fungi, together offering a comprehensive suite of resources for the genetic exploration of fungal pathogens and their interactions with hosts and environments.…”

Section: Genomic Database Capabilitiesmentioning

confidence: 96%

Revealing Hidden Genes in <em>Botrytis cinerea</em>: New Insights into Genes Involved in the Biosynthesis of Secondary Metabolites

Suárez,

Collado,

Garrido

2024

Preprint

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Utilizing bioinformatics tools, this study expands our understanding of secondary metabolism in Botrytis cinerea, identifying novel genes within polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), sesquiterpene cyclase (STC), diterpene cyclase (DTC), and dimethylal-lyltryptophan synthase (DMATS) families. These findings enrich the genetic framework associ-ated with B. cinerea's pathogenicity and ecological adaptation, offering insights into uncharted metabolic pathways. Significantly, the discovery of previously unannotated genes provides new molecular targets for developing targeted antifungal strategies, promising to enhance crop pro-tection and advance our understanding of fungal biochemistry. This research not only broadens the scope of known secondary metabolites but also opens avenues for future exploration into B. cinerea's biosynthetic capabilities, potentially leading to novel antifungal compounds. Our work underscores the importance of integrating bioinformatics and genomics for fungal research, paving the way for sustainable agricultural practices by pinpointing precise molecular interven-tions against B. cinerea. This study sets a foundation for further investigations into the fungus's secondary metabolism, with implications for biotechnology and crop disease management.

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“…Fungi are the largest group of eukaryotes with the estimated number of species exceeding five million (Iquebal et al, 2021). The identification of fungal species is a paramount milestone in numerous fields including taxonomy, ecology, agriculture, industry, as well as health sciences.…”

Section: Molecular Identification Of the Aspergillus Neoniveusmentioning

confidence: 99%

Anti-prostate cancer metabolites from the soil-derived Aspergillus neoniveus

et al. 2022

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Prostate cancer (PCa) ranks as one of the most commonly diagnosed malignancies worldwide. Toxicity, lack of clinical efficacy, and development of resistance phenotypes are the main challenges in the control of prostate malignancies. Notably, castration-resistance prostate cancer (CRPCa) is a highly aggressive and metastatic phenotype of the disease with a poor prognosis and very limited therapeutic options. Herein, we report the isolation and genotypic identification of a soil-derived fungus Aspergillus neoniveus using the PCR-based internal transcribed spacer (ITS) region amplification approach. HPLC/MS investigation of the metabolic profile of the ethyl acetate extract from the fungal biomass revealed tentative identification of forty-five compounds belonging to various chemical classes including γ-butyrolactones, alkaloids, phenolics, and quinoids. Furthermore, the chromatographic purification of microbial extract enabled the identification of nervonic acid methyl ester (1) for the first time from endophytic fungi, as well as acetyl aszonalenin (2), and butyrolactone II (3) for the first time from A. neoniveus. The chemical frameworks of the isolated compounds were identified via extensive spectral analysis including 1 and 2D NMR and MS. The X-ray crystal structure and absolute configuration of acetyl aszonalenin (2) were also determined. Additionally, screening of in vitro anticancer activity of the fungal extract revealed its potential antiproliferative and anti-migratory activities against five different prostate cancer cells (PC3, PC-3M, DU-145, CWR-R1ca, and 22Rv1), including different cells with the castration-resistance phenotype. Moreover, the isolated metabolites significantly inhibited the proliferation, migration, and colonization of human prostate cancer cells at low micromolar levels, thus providing credence for future investigation of these metabolites in relevant anti-prostate cancer animal models. Furthermore, computational target prediction tools identified the cannabinoid G-protein coupled receptors type 1 (CB1) as a potential biological target mediating, at least in part, the anticancer effects of acetylaszonalenin (2). Moreover, molecular modeling and docking studies revealed a favorable binding pose at the CB1 receptor orthosteric ligand pocket aided by multiple polar and hydrophobic interactions with critical amino acids. In conclusion, the Aspergillus neoniveus-derived prenylated indole alkaloid acetylaszonalenin has promising anticancer activity and is amenable to further hit-to-lead optimization for the control of prostate malignancies via modulating CB1 receptors

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Fungal Genomic Resources for Strain Identification and Diversity Analysis of 1900 Fungal Species

Cited by 7 publications

References 60 publications

Revealing Hidden Genes in Botrytis cinerea: New Insights into Genes Involved in the Biosynthesis of Secondary Metabolites

Revealing Hidden Genes in Botrytis cinerea: New Insights into Genes Involved in the Biosynthesis of Secondary Metabolites

Revealing Hidden Genes in <em>Botrytis cinerea</em>: New Insights into Genes Involved in the Biosynthesis of Secondary Metabolites

Anti-prostate cancer metabolites from the soil-derived Aspergillus neoniveus

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