IMA genome-F18

Visagie, Cobus M.; Magistà, Donato; Ferrara, Massimo; Balocchi, Felipe; Duong, Tuan A.; Eichmeier, Ales; Gramaje, David; Aylward, Janneke; Baker, Scott E.; Barnes, Irene; Calhoun, Sara; De Angelis, Maria; Frisvad, Jens C.; Hakalova, Eliska; Hayes, Richard D.; Houbraken, Jos; Grigoriev, Igor V.; LaButti, Kurt; Leal, Catarina; Lipzen, Anna; Ng, Vivian; Pangilinan, Jasmyn; Pecenka, Jakub; Perrone, Giancarlo; Piso, Anja; Savage, Emily; Spetik, Milan; Wingfield, Michael J.; Zhang, Yu; Wingfield, Brenda D.

doi:10.1186/s43008-023-00121-w

Cited by 3 publications

(2 citation statements)

References 148 publications

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“…The gene count is within the anticipated range of 9000 to 14,000 for other recently published Penicillium spp. [ 10 , 36 , 37 ]. A BUSCO analysis of the proteins encoded by the annotated genes found the genome to be 97.9% complete.…”

Section: Resultsmentioning

confidence: 99%

“…However, the three later genomes did not offer a substantial improvement in genome quality. With the availability of third-generation sequencing technologies, achieving chromosomal-scale and nearly complete genome assemblies of fungi is possible [ 9 , 10 ]. Herein, we present the genome assembly and annotation of P. fuscoglaucum based on third-generation sequencing, resulting in a highly contiguous assembly.…”

Section: Introductionmentioning

confidence: 99%

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The Near-Gapless Penicillium fuscoglaucum Genome Enables the Discovery of Lifestyle Features as an Emerging Post-Harvest Phytopathogen

Luciano-Rosario,

Jurick,

Gottschalk

2024

JoF

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Penicillium spp. occupy many diverse biological niches that include plant pathogens, opportunistic human pathogens, saprophytes, indoor air contaminants, and those selected specifically for industrial applications to produce secondary metabolites and lifesaving antibiotics. Recent phylogenetic studies have established Penicillium fuscoglaucum as a synonym for Penicillium commune, which is an indoor air contaminant and toxin producer and can infect apple fruit during storage. During routine culturing on selective media in the lab, we obtained an isolate of P. fuscoglaucum Pf_T2 and sequenced its genome. The Pf_T2 genome is far superior to available genomic resources for the species. Our assembly exhibits a length of 35.1 Mb, a BUSCO score of 97.9% complete, and consists of five scaffolds/contigs representing the four expected chromosomes. It was determined that the Pf_T2 genome was colinear with a type specimen P. fuscoglaucum and contained a lineage-specific, intact cyclopiazonic acid (CPA) gene cluster. For comparison, a highly virulent postharvest apple pathogen, P. expansum strain TDL 12.1, was included and showed a similar growth pattern in culture to our Pf_T2 isolate but was far more aggressive in apple fruit than P. fuscoglaucum. The genome of Pf_T2 serves as a major improvement over existing resources, has superior annotation, and can inform forthcoming omics-based work and functional genetic studies to probe secondary metabolite production and disparities in aggressiveness during apple fruit decay.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The Near-Gapless Penicillium fuscoglaucum Genome Enables the Discovery of Lifestyle Features as an Emerging Post-Harvest Phytopathogen

Luciano-Rosario,

Jurick,

Gottschalk

2024

JoF

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Cultures as types and the utility of viable specimens for fungal nomenclature

Yurkov,

Visagie,

Crous

et al. 2024

IMA Fungus

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The debates over the requirement of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) for a viable specimen to represent the name-bearing type material for a species or infraspecific taxon have a long history. Taxonomy of fungi commonly studied as living cultures exemplified by yeasts and moulds, strongly depend on viable reference material. The availability of viable cultures is also particularly useful for several groups of filamentous and dimorphic fungi. While the preservation of metabolically inactive cultures is permitted and recommended by the ICNafp, there is room for improvement. Below, we review the history and current status of cultures as the name-bearing type material under the Code. We also present a roadmap with tasks to be achieved in order to establish a stable nomenclatural system that properly manages taxa typified by viable specimens. Furthermore, we propose setting up rules and defining the nomenclatural status of ex-type cultures under Chapter F, the section of the ICNafp that includes provisions specific to names of fungi.

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Morpho-Molecular and Genomic Characterization of Penicillium mexicanum Isolates Retrieved from a Forsaken Gold Mine

Trovão,

Soares,

Paiva

et al. 2024

Applied Sciences

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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 Penicillium species. Molecular phylogenetic analysis, coupled with morphological observations, positioned this fungus within subgen. Penicillium sect. Paradoxa, series Atramentosa, pinpointing its identity as Penicillium mexicanum (the first record for mining soils and the country). Given the limited research conducted on Penicillia isolated from similar environments, the species genome was sequenced utilizing the Oxford Nanopore® MinION™ 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 Penicillia knowledge from mining environments while also enhancing our understanding regarding fungal arsenic resistance.

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IMA genome-F18

Cited by 3 publications

References 148 publications

The Near-Gapless Penicillium fuscoglaucum Genome Enables the Discovery of Lifestyle Features as an Emerging Post-Harvest Phytopathogen

The Near-Gapless Penicillium fuscoglaucum Genome Enables the Discovery of Lifestyle Features as an Emerging Post-Harvest Phytopathogen

Cultures as types and the utility of viable specimens for fungal nomenclature

Morpho-Molecular and Genomic Characterization of Penicillium mexicanum Isolates Retrieved from a Forsaken Gold Mine

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