Pöggeler, Stefanie

[["dc.bibliographiccitation.artnumber","e1003820"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","PLoS Genetics"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Traeger, Stefanie"],["dc.contributor.author","Altegoer, Florian"],["dc.contributor.author","Freitag, Michael"],["dc.contributor.author","Gabaldon, Toni"],["dc.contributor.author","Kempken, Frank"],["dc.contributor.author","Kumar, Abhishek"],["dc.contributor.author","Marcet-Houben, Marina"],["dc.contributor.author","Poeggeler, Stefanie"],["dc.contributor.author","Stajich, Jason E."],["dc.contributor.author","Nowrousian, Minou"],["dc.date.accessioned","2018-11-07T09:20:30Z"],["dc.date.available","2018-11-07T09:20:30Z"],["dc.date.issued","2013"],["dc.description.abstract","Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely that of the black truffle, Tuber melanosporum, a mycorrhizal species with unusual subterranean fruiting bodies. To help close the sequence gap among basal filamentous ascomycetes, and to allow conclusions about the evolution of fungal development, we sequenced the genome and assayed transcriptomes during development of Pyronema confluens, a saprobic Pezizomycete with a typical apothecium as fruiting body. With a size of 50 Mb and similar to 13,400 protein-coding genes, the genome is more characteristic of higher filamentous ascomycetes than the large, repeat-rich truffle genome; however, some typical features are different in the P. confluens lineage, e.g. the genomic environment of the mating type genes that is conserved in higher filamentous ascomycetes, but only partly conserved in P. confluens. On the other hand, P. confluens has a full complement of fungal photoreceptors, and expression studies indicate that light perception might be similar to distantly related ascomycetes and, thus, represent a basic feature of filamentous ascomycetes. Analysis of spliced RNA-seq sequence reads allowed the detection of natural antisense transcripts for 281 genes. The P. confluens genome contains an unusually high number of predicted orphan genes, many of which are upregulated during sexual development, consistent with the idea of rapid evolution of sex-associated genes. Comparative transcriptomics identified the transcription factor gene pro44 that is upregulated during development in P. confluens and the Sordariomycete Sordaria macrospora. The P. confluens pro44 gene (PCON_06721) was used to complement the S. macrospora pro44 deletion mutant, showing functional conservation of this developmental regulator."],["dc.identifier.doi","10.1371/journal.pgen.1003820"],["dc.identifier.isi","000325076600074"],["dc.identifier.pmid","24068976"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/9290"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/28893"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Public Library Science"],["dc.relation.issn","1553-7404"],["dc.rights","CC BY 2.5"],["dc.rights.uri","https://creativecommons.org/licenses/by/2.5"],["dc.title","The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","Molecular Plant Pathology"],["dc.contributor.author","Harting, Rebekka"],["dc.contributor.author","Starke, Jessica"],["dc.contributor.author","Kusch, Harald"],["dc.contributor.author","Pöggeler, Stefanie"],["dc.contributor.author","Maurus, Isabel"],["dc.contributor.author","Schlüter, Rabea"],["dc.contributor.author","Landesfeind, Manuel"],["dc.contributor.author","Bulla, Ingo"],["dc.contributor.author","Nowrousian, Minou"],["dc.contributor.author","Braus, Gerhard H."],["dc.contributor.author","de Jonge, Ronnie"],["dc.contributor.author","Stahlhut, Gertrud"],["dc.contributor.author","Hoff, Katharina J."],["dc.contributor.author","Aßhauer, Kathrin P."],["dc.contributor.author","Thürmer, Andrea"],["dc.contributor.author","Stanke, Mario"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Morgenstern, Burkhard"],["dc.contributor.author","Thomma, Bart P. H. J."],["dc.contributor.author","Kronstad, James W."],["dc.contributor.author","Braus‐Stromeyer, Susanna A."],["dc.date.accessioned","2021-06-01T09:42:04Z"],["dc.date.available","2021-06-01T09:42:04Z"],["dc.date.issued","2021"],["dc.description.abstract","Abstract Amphidiploid fungal Verticillium longisporum strains Vl43 and Vl32 colonize the plant host Brassica napus but differ in their ability to cause disease symptoms. These strains represent two V. longisporum lineages derived from different hybridization events of haploid parental Verticillium strains. Vl32 and Vl43 carry same‐sex mating‐type genes derived from both parental lineages. Vl32 and Vl43 similarly colonize and penetrate plant roots, but asymptomatic Vl32 proliferation in planta is lower than virulent Vl43. The highly conserved Vl43 and Vl32 genomes include less than 1% unique genes, and the karyotypes of 15 or 16 chromosomes display changed genetic synteny due to substantial genomic reshuffling. A 20 kb Vl43 lineage‐specific (LS) region apparently originating from the Verticillium dahliae‐related ancestor is specific for symptomatic Vl43 and encodes seven genes, including two putative transcription factors. Either partial or complete deletion of this LS region in Vl43 did not reduce virulence but led to induction of even more severe disease symptoms in rapeseed. This suggests that the LS insertion in the genome of symptomatic V. longisporum Vl43 mediates virulence‐reducing functions, limits damage on the host plant, and therefore tames Vl43 from being even more virulent."],["dc.description.abstract","A lineage‐specific region in the Verticillium longisporum Vl43 genome reduces fungal virulence of infected rapeseed host plants. image"],["dc.description.sponsorship","Bundesministerium für Bildung und Forschung: BioFung http://dx.doi.org/10.13039/501100002347"],["dc.description.sponsorship","Natural Sciences and Engineering Research Council of Canada: CREATE http://dx.doi.org/10.13039/501100000038"],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659"],["dc.description.sponsorship","Open-Access-Publikationsfonds 2021"],["dc.identifier.doi","10.1111/mpp.13071"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/85132"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-425"],["dc.relation.eissn","1364-3703"],["dc.relation.issn","1464-6722"],["dc.relation.orgunit","Abteilung Molekulare Mikrobiologie & Genetik"],["dc.rights","CC BY-NC-ND 4.0"],["dc.title","A 20‐kb lineage‐specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","e1000891"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","PLoS Genetics"],["dc.bibliographiccitation.volume","6"],["dc.contributor.author","Nowrousian, Minou"],["dc.contributor.author","Stajich, Jason E."],["dc.contributor.author","Chu, Meiling"],["dc.contributor.author","Engh, Ines"],["dc.contributor.author","Espagne, Eric"],["dc.contributor.author","Halliday, Karen"],["dc.contributor.author","Kamerewerd, Jens"],["dc.contributor.author","Kempken, Frank"],["dc.contributor.author","Knab, Birgit"],["dc.contributor.author","Kuo, Hsiao-Che"],["dc.contributor.author","Osiewacz, Heinz D."],["dc.contributor.author","Poeggeler, Stefanie"],["dc.contributor.author","Read, Nick D."],["dc.contributor.author","Seiler, Stephan"],["dc.contributor.author","Smith, Kristina M."],["dc.contributor.author","Zickler, Denise"],["dc.contributor.author","Kueck, Ulrich"],["dc.contributor.author","Freitag, Michael"],["dc.date.accessioned","2018-11-07T08:44:49Z"],["dc.date.available","2018-11-07T08:44:49Z"],["dc.date.issued","2010"],["dc.description.abstract","Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e. g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30-90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in similar to 4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for comparative studies to address basic questions of fungal biology."],["dc.identifier.doi","10.1371/journal.pgen.1000891"],["dc.identifier.isi","000277354200008"],["dc.identifier.pmid","20386741"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/7264"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/20286"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Public Library Science"],["dc.relation.issn","1553-7390"],["dc.rights","CC BY 2.5"],["dc.rights.uri","https://creativecommons.org/licenses/by/2.5"],["dc.title","De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]