Complete Sequencing and Chromosome-Scale Genome Assembly of the Industrial Progenitor Strain P2niaD18 from the Penicillin Producer
            <i>Penicillium chrysogenum</i>

Specht, Thomas; Dahlmann, Tim A.; Zadra, Ivo; Kürnsteiner, Hubert; Kück, Ulrich

doi:10.1128/genomea.00577-14

Cited by 39 publications

(45 citation statements)

References 8 publications

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“…Eighty-two peak regions were, however, positioned within divergent promoters, resulting in a total of 254 genes that may be directly controlled by MAT1-1-1. Comparison to expression data obtained from previous microarray analyses confirmed changes in expression profiles by at least twofold in a ΔMAT1-1-1 strain compared with P2niaD18 for 29.9% (Specht et al, 2014). c. Fraction of tags found in peaks versus genomic background determined by HOMER (Heinz et al, 2010).…”

Section: Resultssupporting

confidence: 63%

“…Sequences corresponding to adaptors were removed from reads, and remaining sequences were subsequently mapped to the latest version of the P. chrysogenum P2niaD18 genome (Specht et al, 2014) using Bowtie version 1.0.1 (Langmead et al, 2009) with the following settings: '-S -qm 1', which only retains unique alignments. Binary Alignment/ Map (BAM) files were sorted and indexed using SAMtools (Li et al, 2009), and visualized using the Integrative Genomics Viewer (IGV) (Thorvaldsdóttir et al, 2012).…”

Section: Data Analysis and Visualizationmentioning

confidence: 99%

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Genome‐wide identification of target genes of a mating‐type α‐domain transcription factor reveals functions beyond sexual development

Becker

Beer

Freitag

et al. 2015

Molecular Microbiology

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SummaryPenicillium chrysogenum is the main industrial producer of the β-lactam antibiotic penicillin, the most commonly used drug in the treatment of bacterial infections. Recently, a functional MAT1-1 locus encoding the α-box transcription factor MAT1-1-1 was discovered to control sexual development in P. chrysogenum. As only little was known from any organism about the regulatory functions mediated by MAT1-1-1, we applied chromatin immunoprecipitation combined with next-generation sequencing (ChIPseq) to gain new insights into the factors that influence MAT1-1-1 functions on a molecular level and its role in genome-wide transcriptional regulatory networks. Most importantly, our data provide evidence for mating-type transcription factor functions that reach far beyond their previously understood role in sexual development. These new roles include regulation of hyphal morphology, asexual development, as well as amino acid, iron, and secondary metabolism. Furthermore, in vitro DNA-protein binding studies and downstream analysis in yeast and P. chrysogenum enabled the identification of a MAT1-1-1 DNAbinding motif, which is highly conserved among euascomycetes. Our studies pave the way to a more general understanding of these master switches for development and metabolism in all fungi, and open up new options for optimization of fungal high production strains.

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Section: Resultssupporting

confidence: 63%

Section: Data Analysis and Visualizationmentioning

confidence: 99%

Genome‐wide identification of target genes of a mating‐type α‐domain transcription factor reveals functions beyond sexual development

Becker

Beer

Freitag

et al. 2015

Molecular Microbiology

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“…Finally, UV mutagenesis resulted in a nitrate reductase-deficient strain, called P2niaD18 (Hoff et al ., 2008 ). The recently published genomic sequence of P2niaD18 (Specht et al ., 2014 ) shows at least two chromosomal rearrangements compared with the previously sequenced Wisconsin 54-1255 strain (van den Berg et al ., 2008 ).…”

Section: Resultsmentioning

confidence: 95%

A MAT1–2 wild‐type strain from Penicillium chrysogenum: functional mating‐type locus characterization, genome sequencing and mating with an industrial penicillin‐producing strain

Böhm

Dahlmann

Gümüşer

et al. 2015

Molecular Microbiology

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In heterothallic ascomycetes, mating is controlled by two nonallelic idiomorphs that determine the ‘sex’ of the corresponding strains. We recently discovered mating-type loci and a sexual life cycle in the penicillin-producing fungus, Penicillium chrysogenum. All industrial penicillin production strains worldwide are derived from a MAT1-1 isolate. No MAT1-2 strain has been investigated in detail until now. Here, we provide the first functional analysis of a MAT1-2 locus from a wild-type strain. Similar to MAT1-1, the MAT1-2 locus has functions beyond sexual development. Unlike MAT1-1, the MAT1-2 locus affects germination and surface properties of conidiospores and controls light-dependent asexual sporulation. Mating of the MAT1-2 wild type with a MAT1-1 high penicillin producer generated sexual spores. We determined the genomic sequences of parental and progeny strains using next-generation sequencing and found evidence for genome-wide recombination. SNP calling showed that derived industrial strains had an uneven distribution of point mutations compared with the wild type. We found evidence for meiotic recombination in all chromosomes. Our results point to a strategy combining the use of mating-type genes, genetics, and next-generation sequencing to optimize conventional strain improvement methods.

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“…In Candida albicans extra copies of a transcriptional activator gene for a transporter was implicated in azole drug resistance (Selmecki et al ., ). Strains of Penicillium chrysogenum that produce very high levels of penicillin contain additional copies of the penicillin biosynthetic gene cluster in tandem repeats (Specht et al ., ). In our study, the duplication of the 1.4 Mb 13:5 ‘translocation’ chromosome was unique to ALP3, and extra copies of genes involved in sugar transport, DNA binding, translation or metabolism present on this chromosome could have improved the efficiency of dothistromin production.…”

Section: Discussionmentioning

confidence: 97%

Global population genomics of the forest pathogen Dothistroma septosporum reveal chromosome duplications in high dothistromin‐producing strains

Bradshaw

Sim

Chettri

et al. 2019

Molecular Plant Pathology

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Summary Dothistroma needle blight is one of the most devastating pine tree diseases worldwide. New and emerging epidemics have been frequent over the last 25 years, particularly in the Northern Hemisphere, where they are in part associated with changing weather patterns. One of the main Dothistroma needle blight pathogens, Dothistroma septosporum, has a global distribution but most molecular plant pathology research has been confined to Southern Hemisphere populations that have limited genetic diversity. Extensive genomic and transcriptomic data are available for a D. septosporum reference strain from New Zealand, where an introduced clonal population of the pathogen predominates. Due to the global importance of this pathogen, we determined whether the genome of this reference strain is representative of the species worldwide by sequencing the genomes of 18 strains sampled globally from different pine hosts. Genomic polymorphism shows substantial variation within the species, clustered into two distinct groups of strains with centres of diversity in Central and South America. A reciprocal chromosome translocation uniquely identifies the New Zealand strains. Globally, strains differ in their production of the virulence factor dothistromin, with extremely high production levels in strain ALP3 from Germany. Comparisons with the New Zealand reference revealed that several strains are aneuploids; for example, ALP3 has duplications of three chromosomes. Increased gene copy numbers therefore appear to contribute to increased production of dothistromin, emphasizing that studies of population structure are a necessary adjunct to functional analyses of genetic polymorphisms to identify the molecular basis of virulence in this important forest pathogen.

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Complete Sequencing and Chromosome-Scale Genome Assembly of the Industrial Progenitor Strain P2niaD18 from the Penicillin Producer Penicillium chrysogenum

Cited by 39 publications

References 8 publications

Genome‐wide identification of target genes of a mating‐type α‐domain transcription factor reveals functions beyond sexual development

Genome‐wide identification of target genes of a mating‐type α‐domain transcription factor reveals functions beyond sexual development

A MAT1–2 wild‐type strain from Penicillium chrysogenum: functional mating‐type locus characterization, genome sequencing and mating with an industrial penicillin‐producing strain

Global population genomics of the forest pathogen Dothistroma septosporum reveal chromosome duplications in high dothistromin‐producing strains

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