Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

Berg, M. A.; Albang, Richard; Albermann, Kaj; Badger, Jonathan H.; Daran, Jean‐Marc; Driessen, Arnold J. M.; Estrada, Carlos García; Fedorova, Natalie D.; Harris, Diana M.; Heijne, Wilbert H. M.; Joardar, Vinita; Kiel, Jan A.K.W.; Kovalchuk, Andriy; Martı́n, Juan F.; Nierman, William C.; Nijland, Jeroen G.; Pronk, Jack T.; Roubos, Johannes A.; Klei, Ida J. van der; Peij, Noël N. M. E. van; Veenhuis, Marten; Döhren, Hans von; Wagner, Christian; Wortman, Jennifer; Bovenberg, Roel A. L.

doi:10.1038/nbt.1498

Cited by 431 publications

(435 citation statements)

References 44 publications

Supporting

Mentioning

401

Contrasting

Unclassified

Order By: Relevance

“…We attribute this discrepancy to a lack of resolution of the larger chromosomes by pulse field electrophoresis. The estimated size of the genome (36.2 Mb) is consistent with results obtained for other related fungi, such as Penicillium chrysogenum (van den Berg et al 2008) and Aspergillus flavus (37 Mb) (Nierman et al 2015). …”

Section: Resultssupporting

confidence: 87%

The genome sequence of the soft-rot fungusPenicillium purpurogenumreveals a high gene dosage for lignocellulolytic enzymes

et al. 2018

View full text Add to dashboard Cite

The high lignocellulolytic activity displayed by the soft-rot fungus Penicillium purpurogenum has made it a target for the study of novel lignocellulolytic enzymes. We have obtained a reference genome of 36.2 Mb of non-redundant sequence (11,057 protein-coding genes). The 49 largest scaffolds cover 90% of the assembly, and Core Eukaryotic Genes Mapping Approach (CEGMA) analysis reveals that our assembly captures almost all protein-coding genes. RNA-seq was performed and 93.1% of the reads aligned to the assembled genome. These data, plus the independent sequencing of a set of genes of lignocellulose-degrading enzymes, validate the quality of the genome sequence. P. purpurogenum shows a higher number of proteins with CAZy motifs, transcription factors and transporters as compared to other sequenced Penicillia. These results demonstrate the great potential for lignocellulolytic activity of this fungus and the possible use of its enzymes in related industrial applications.

show abstract

Section: Resultssupporting

confidence: 87%

The genome sequence of the soft-rot fungusPenicillium purpurogenumreveals a high gene dosage for lignocellulolytic enzymes

et al. 2018

View full text Add to dashboard Cite

show abstract

“…We have selected (a) 14 popular white rot fungal strains – Ceriporiopsis subvermispora B (Fernandez-Fueyo et al 2012), Heterobasidion annosum v2.0 (Olson et al 2012), Fomitiporia mediterranea v1.0 (Floudas et al 2012), Phanerochaete carnosa HHB-10118 (Suzuki et al 2012), Pycnoporus cinnabarinus BRFM 137 (Levasseur et al 2014), Phanerochaete chrysosporium R78 v2.2 (Martinez et al 2004; Ohm et al 2014), Dichomitus squalens LYAD-421 SS1 (Floudas et al 2012), Trametes versicolor v1.0 (Floudas et al 2012), Punctularia strigosozonata v1.0 (Floudas et al 2012), Phlebia brevispora HHB-7030 SS6 (Binder et al 2013), Botrytis cinerea v1.0 (Amselem et al 2011), Pleurotus ostreatus PC15 v2.0 (Riley et al 2014; Alfaro et al 2016; Castanera et al 2016), Stereum hirsutum FP-91666 SS1 v1.0 (Floudas et al 2012), Pleurotus eryngii ATCC90797 (Guillen et al 1992; Camarero et al 1999; Ruiz‐Dueñas et al 1999; Matheny et al 2006); (b) 15 popular brown rot fungal strains – Postia placenta MAD 698-R v1.0 (Martinez et al 2009), Fibroporia radiculosa TFFH 294 (Tang et al 2012), Wolfiporia cocos MD-104 SS10 v1.0 (Floudas et al 2012), Dacryopinax primogenitus DJM 731 SSP1 v1.0 (Floudas et al 2012), Daedalea quercina v1.0 (Nagy et al 2015), Laetiporus sulphureus var v1.0 (Nagy et al 2015), Postia placenta MAD-698-R-SB12 v1.0 (Martinez et al 2009), Neolentinus lepideus v1.0 (Nagy et al 2015), Serpula lacrymans S7.9 v2.0 (Eastwood et al 2011), Calocera cornea v1.0 (Eastwood et al 2011), Gloeophyllum trabeum v1.0 (Floudas et al 2012), Fistulina hepatica v1.0 (Floudas et al 2015), Fomitopsis pinicola FP-58527 SS1 (Floudas et al 2015), Hydnomerulius pinastri v2.0 (Kohler et al 2015) and Coniophora puteana v1.0 (Kohler et al 2015); (c) 13 popular soft rot fungal strains – Trichoderma reesei v 2.0 (Martinez et al 2008), Rhizopus oryzae 99-880 from Broad (Ma et al 2009), Aspergillus wentii v1.0 (De Vries et al 2017), Penicillium chrysogenum Wisconsin 54-1255 (Van Den Berg et al 2008), Daldinia eschscholzii EC12 v1.0, Hypoxylon sp. CI-4A v1.0 (Wu et al 2017), Aspergillus niger ATCC 1015 v4.0 (Andersen et al 2011), Hypoxylon sp.…”

Section: Methodsmentioning

confidence: 99%

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

2017

View full text Add to dashboard Cite

We have conducted a genome-level comparative study of basidiomycetes wood-rotting fungi (white, brown and soft rot) to understand the total plant biomass (lignin, cellulose, hemicellulose and pectin) -degrading abilities. We have retrieved the genome-level annotations of well-known 14 white rot fungi, 15 brown rot fungi and 13 soft rot fungi. Based on the previous literature and the annotations obtained from CAZy (carbohydrate-active enzyme) database, we have separated the genome-wide CAZymes of the selected fungi into lignin-, cellulose-, hemicellulose- and pectin-degrading enzymes. Results obtained in our study reveal that white rot fungi, especially Pleurotus eryngii and Pleurotus ostreatus potentially possess high ligninolytic ability, and soft rot fungi, especially Botryosphaeria dothidea and Fusarium oxysporum sp., potentially possess high cellulolytic, hemicellulolytic and pectinolytic abilities. The total number of genes encoding for cytochrome P450 monooxygenases and metabolic processes were high in soft and white rot fungi. We have tentatively calculated the overall lignocellulolytic abilities among the selected wood-rotting fungi which suggests that white rot fungi possess higher lignin and soft rot fungi potentially possess higher cellulolytic, hemicellulolytic and pectinolytic abilities. This approach can be applied industrially to efficiently find lignocellulolytic and aromatic compound-degrading fungi based on their genomic abilities.

show abstract

“…Also, continued random mutagenesis and high-throughput screening can lead to undesirable deleterious mutations and genetic instability in producer strains (41). For example, production strains of P. chrysogenum contain multiple point mutations as well as major amplifications and deletions compared with the genome sequence of the progenitor Wisconsin strain (42). By contrast, sexual reproduction allows recombination of traits without introducing further mutations and offers a means to restore the fitness of industrial strains and eliminate ku70/ku80 mutations that can lead to genome instability (43).…”

Section: Discussionmentioning

confidence: 99%

Sexual reproduction and mating-type–mediated strain development in the penicillin-producing fungus Penicillium chrysogenum

Böhm

Hoff

O’Gorman

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

119

View full text Add to dashboard Cite

Penicillium chrysogenum is a filamentous fungus of major medical and historical importance, being the original and present-day industrial source of the antibiotic penicillin. The species has been considered asexual for more than 100 y, and despite concerted efforts, it has not been possible to induce sexual reproduction, which has prevented sexual crosses being used for strain improvement. However, using knowledge of mating-type (MAT) gene organization, we now describe conditions under which a sexual cycle can be induced leading to production of meiotic ascospores. Evidence of recombination was obtained using both molecular and phenotypic markers. The identified heterothallic sexual cycle was used for strain development purposes, generating offspring with novel combinations of traits relevant to penicillin production. Furthermore, the MAT1-1-1 mating-type gene, known primarily for a role in governing sexual identity, was also found to control transcription of a wide range of genes with biotechnological relevance including those regulating penicillin production, hyphal morphology, and conidial formation. These discoveries of a sexual cycle and MAT gene function are likely to be of broad relevance for manipulation of other asexual fungi of economic importance.sexual recombination | secondary metabolism | ascomycete

show abstract

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

Cited by 431 publications

References 44 publications

The genome sequence of the soft-rot fungusPenicillium purpurogenumreveals a high gene dosage for lignocellulolytic enzymes

The genome sequence of the soft-rot fungusPenicillium purpurogenumreveals a high gene dosage for lignocellulolytic enzymes

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

Sexual reproduction and mating-type–mediated strain development in the penicillin-producing fungus Penicillium chrysogenum

Contact Info

Product

Resources

About