Morpho-Molecular and Genomic Characterization of <i>Penicillium mexicanum</i> Isolates Retrieved from a Forsaken Gold Mine
During the ongoing studies designed to examine the fungal diversity present within the abandoned and flooded Escádia Grande gold mine (Góis, Portugal), we repeatedly isolated several specimens belonging to a <i>Penicillium</i> species. Molecular phylogenetic analysis, coupled with morpho...
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2024-11-01
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| author | João Trovão Fabiana Soares Diana Sofia Paiva António Portugal |
| author_facet | João Trovão Fabiana Soares Diana Sofia Paiva António Portugal |
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| description | During the ongoing studies designed to examine the fungal diversity present within the abandoned and flooded Escádia Grande gold mine (Góis, Portugal), we repeatedly isolated several specimens belonging to a <i>Penicillium</i> species. Molecular phylogenetic analysis, coupled with morphological observations, positioned this fungus within subgen. <i>Penicillium</i> sect. <i>Paradoxa</i>, series <i>Atramentosa</i>, pinpointing its identity as <i>Penicillium mexicanum</i> (the first record for mining soils and the country). Given the limited research conducted on <i>Penicillia</i> isolated from similar environments, the species genome was sequenced utilizing the Oxford Nanopore<sup>®</sup> MinION<sup>™</sup> methodology and studied through bioinformatic analysis. The obtained genome has a size of 29.62 Mb, containing a 47.72% GC content, 10,156 genes, with 44 rRNAs and 178 tRNAs/tmRNAs, providing the first genomic resource for this microorganism. Bioinformatic analysis allowed us to identify multiple genomic traits that can contribute towards this species survival in these extreme environments, including the presence of high levels of major facilitator transporters (MFS), Zn (2)-C6 fungal-type DNA-binding domains, P-loop containing nucleoside triphosphate hydrolases, specific fungal transcription factors and sugar transporters. Furthermore, putative advantageous metabolic traits, such as methylotrophy, assimilatory nitrate and sulfate reduction abilities, were also detected. In addition, the results also highlighted a strong genomic and metabolic organization and investment towards arsenic detoxification (transport and oxidation). Lastly, thirty-two putative biosynthetic gene clusters were predicted, including some with high similarity values to monascorubrin, nidulanin A, histidyltryptophanyldiketopiperazine/dehydrohistidyltryptophanyldiketopiperazine/roquefortine D/roquefortine C/glandicoline A/glandicoline B/meleagrine, YWA1 and choline. Overall, this study expands the current <i>Penicillia</i> knowledge from mining environments while also enhancing our understanding regarding fungal arsenic resistance. |
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| spelling | doaj-art-dc92a0f6daf44291b6eb69502feebd8e2025-08-20T02:26:54ZengMDPI AGApplied Sciences2076-34172024-11-0114221060010.3390/app142210600Morpho-Molecular and Genomic Characterization of <i>Penicillium mexicanum</i> Isolates Retrieved from a Forsaken Gold MineJoão Trovão0Fabiana Soares1Diana Sofia Paiva2António Portugal3Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, PortugalCentre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, PortugalCentre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, PortugalCentre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, PortugalDuring the ongoing studies designed to examine the fungal diversity present within the abandoned and flooded Escádia Grande gold mine (Góis, Portugal), we repeatedly isolated several specimens belonging to a <i>Penicillium</i> species. Molecular phylogenetic analysis, coupled with morphological observations, positioned this fungus within subgen. <i>Penicillium</i> sect. <i>Paradoxa</i>, series <i>Atramentosa</i>, pinpointing its identity as <i>Penicillium mexicanum</i> (the first record for mining soils and the country). Given the limited research conducted on <i>Penicillia</i> isolated from similar environments, the species genome was sequenced utilizing the Oxford Nanopore<sup>®</sup> MinION<sup>™</sup> methodology and studied through bioinformatic analysis. The obtained genome has a size of 29.62 Mb, containing a 47.72% GC content, 10,156 genes, with 44 rRNAs and 178 tRNAs/tmRNAs, providing the first genomic resource for this microorganism. Bioinformatic analysis allowed us to identify multiple genomic traits that can contribute towards this species survival in these extreme environments, including the presence of high levels of major facilitator transporters (MFS), Zn (2)-C6 fungal-type DNA-binding domains, P-loop containing nucleoside triphosphate hydrolases, specific fungal transcription factors and sugar transporters. Furthermore, putative advantageous metabolic traits, such as methylotrophy, assimilatory nitrate and sulfate reduction abilities, were also detected. In addition, the results also highlighted a strong genomic and metabolic organization and investment towards arsenic detoxification (transport and oxidation). Lastly, thirty-two putative biosynthetic gene clusters were predicted, including some with high similarity values to monascorubrin, nidulanin A, histidyltryptophanyldiketopiperazine/dehydrohistidyltryptophanyldiketopiperazine/roquefortine D/roquefortine C/glandicoline A/glandicoline B/meleagrine, YWA1 and choline. Overall, this study expands the current <i>Penicillia</i> knowledge from mining environments while also enhancing our understanding regarding fungal arsenic resistance.https://www.mdpi.com/2076-3417/14/22/10600arsenic resistance<i>Eurotiomycetes</i>extreme environmentsgenomic analysisgold mine mycobiome<i>Penicillium mexicanum</i> |
| spellingShingle | João Trovão Fabiana Soares Diana Sofia Paiva António Portugal Morpho-Molecular and Genomic Characterization of <i>Penicillium mexicanum</i> Isolates Retrieved from a Forsaken Gold Mine Applied Sciences arsenic resistance <i>Eurotiomycetes</i> extreme environments genomic analysis gold mine mycobiome <i>Penicillium mexicanum</i> |
| title | Morpho-Molecular and Genomic Characterization of <i>Penicillium mexicanum</i> Isolates Retrieved from a Forsaken Gold Mine |
| title_full | Morpho-Molecular and Genomic Characterization of <i>Penicillium mexicanum</i> Isolates Retrieved from a Forsaken Gold Mine |
| title_fullStr | Morpho-Molecular and Genomic Characterization of <i>Penicillium mexicanum</i> Isolates Retrieved from a Forsaken Gold Mine |
| title_full_unstemmed | Morpho-Molecular and Genomic Characterization of <i>Penicillium mexicanum</i> Isolates Retrieved from a Forsaken Gold Mine |
| title_short | Morpho-Molecular and Genomic Characterization of <i>Penicillium mexicanum</i> Isolates Retrieved from a Forsaken Gold Mine |
| title_sort | morpho molecular and genomic characterization of i penicillium mexicanum i isolates retrieved from a forsaken gold mine |
| topic | arsenic resistance <i>Eurotiomycetes</i> extreme environments genomic analysis gold mine mycobiome <i>Penicillium mexicanum</i> |
| url | https://www.mdpi.com/2076-3417/14/22/10600 |
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