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  • 1
    Publication Date: 2010-03-20
    Description: Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048781/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048781/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ma, Li-Jun -- van der Does, H Charlotte -- Borkovich, Katherine A -- Coleman, Jeffrey J -- Daboussi, Marie-Josee -- Di Pietro, Antonio -- Dufresne, Marie -- Freitag, Michael -- Grabherr, Manfred -- Henrissat, Bernard -- Houterman, Petra M -- Kang, Seogchan -- Shim, Won-Bo -- Woloshuk, Charles -- Xie, Xiaohui -- Xu, Jin-Rong -- Antoniw, John -- Baker, Scott E -- Bluhm, Burton H -- Breakspear, Andrew -- Brown, Daren W -- Butchko, Robert A E -- Chapman, Sinead -- Coulson, Richard -- Coutinho, Pedro M -- Danchin, Etienne G J -- Diener, Andrew -- Gale, Liane R -- Gardiner, Donald M -- Goff, Stephen -- Hammond-Kosack, Kim E -- Hilburn, Karen -- Hua-Van, Aurelie -- Jonkers, Wilfried -- Kazan, Kemal -- Kodira, Chinnappa D -- Koehrsen, Michael -- Kumar, Lokesh -- Lee, Yong-Hwan -- Li, Liande -- Manners, John M -- Miranda-Saavedra, Diego -- Mukherjee, Mala -- Park, Gyungsoon -- Park, Jongsun -- Park, Sook-Young -- Proctor, Robert H -- Regev, Aviv -- Ruiz-Roldan, M Carmen -- Sain, Divya -- Sakthikumar, Sharadha -- Sykes, Sean -- Schwartz, David C -- Turgeon, B Gillian -- Wapinski, Ilan -- Yoder, Olen -- Young, Sarah -- Zeng, Qiandong -- Zhou, Shiguo -- Galagan, James -- Cuomo, Christina A -- Kistler, H Corby -- Rep, Martijn -- BBS/E/C/00004973/Biotechnology and Biological Sciences Research Council/United Kingdom -- DP1 OD003958/OD/NIH HHS/ -- R01 GM086565/GM/NIGMS NIH HHS/ -- R01 GM086565-03/GM/NIGMS NIH HHS/ -- R01 HG000225/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Mar 18;464(7287):367-73. doi: 10.1038/nature08850.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Broad Institute, Cambridge, Massachusetts 02141, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237561" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Fungal/*genetics ; Evolution, Molecular ; Fusarium/classification/*genetics/*pathogenicity ; Genome, Fungal/*genetics ; *Genomics ; Host-Parasite Interactions/genetics ; Multigene Family/genetics ; Phenotype ; Phylogeny ; Proteome/genetics ; Sequence Analysis, DNA ; Synteny/genetics ; Virulence/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2009-05-26
    Description: Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834264/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834264/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Geraldine -- Rasmussen, Matthew D -- Lin, Michael F -- Santos, Manuel A S -- Sakthikumar, Sharadha -- Munro, Carol A -- Rheinbay, Esther -- Grabherr, Manfred -- Forche, Anja -- Reedy, Jennifer L -- Agrafioti, Ino -- Arnaud, Martha B -- Bates, Steven -- Brown, Alistair J P -- Brunke, Sascha -- Costanzo, Maria C -- Fitzpatrick, David A -- de Groot, Piet W J -- Harris, David -- Hoyer, Lois L -- Hube, Bernhard -- Klis, Frans M -- Kodira, Chinnappa -- Lennard, Nicola -- Logue, Mary E -- Martin, Ronny -- Neiman, Aaron M -- Nikolaou, Elissavet -- Quail, Michael A -- Quinn, Janet -- Santos, Maria C -- Schmitzberger, Florian F -- Sherlock, Gavin -- Shah, Prachi -- Silverstein, Kevin A T -- Skrzypek, Marek S -- Soll, David -- Staggs, Rodney -- Stansfield, Ian -- Stumpf, Michael P H -- Sudbery, Peter E -- Srikantha, Thyagarajan -- Zeng, Qiandong -- Berman, Judith -- Berriman, Matthew -- Heitman, Joseph -- Gow, Neil A R -- Lorenz, Michael C -- Birren, Bruce W -- Kellis, Manolis -- Cuomo, Christina A -- BB/F00513X/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F013566/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0400284/Medical Research Council/United Kingdom -- HHSN266200400001C/AO/NIAID NIH HHS/ -- R01 AI050113/AI/NIAID NIH HHS/ -- R01 AI075096/AI/NIAID NIH HHS/ -- R01 DE015873/DE/NIDCR NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01 HG004037-02/HG/NHGRI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-06/HG/NHGRI NIH HHS/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2009 Jun 4;459(7247):657-62. doi: 10.1038/nature08064.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland. geraldine.butler@ucd.ie〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19465905" target="_blank"〉PubMed〈/a〉
    Keywords: Candida/classification/genetics/*pathogenicity/*physiology ; Codon/genetics ; Conserved Sequence ; Diploidy ; *Evolution, Molecular ; Genes, Fungal/genetics ; Genome, Fungal/*genetics ; Meiosis/genetics ; Polymorphism, Genetic ; Reproduction/*genetics ; Saccharomyces/classification/genetics ; Virulence/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 1995-02-24
    Description: Severe combined immunodeficient (SCID) mice are deficient in a recombination process utilized in both DNA double-strand break repair and in V(D)J recombination. The phenotype of these mice involves both cellular hypersensitivity to ionizing radiation and a lack of B and T cell immunity. The catalytic subunit of DNA-dependent protein kinase, p350, was identified as a strong candidate for the murine gene SCID. Both p350 and a gene complementing the SCID defect colocalize to human chromosome 8q11. Chromosomal fragments expressing p350 complement the SCID phenotype, and p350 protein levels are greatly reduced in cells derived from SCID mice compared to cells from wild-type mice.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kirchgessner, C U -- Patil, C K -- Evans, J W -- Cuomo, C A -- Fried, L M -- Carter, T -- Oettinger, M A -- Brown, J M -- CA 15201/CA/NCI NIH HHS/ -- CA 37761/CA/NCI NIH HHS/ -- GM48026/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Feb 24;267(5201):1178-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Radiation Oncology, Stanford University School of Medicine, CA 94305.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7855601" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Cell Line ; Chromosome Mapping ; Chromosomes, Human, Pair 8 ; Cloning, Molecular ; DNA Repair/genetics ; DNA-Activated Protein Kinase ; *DNA-Binding Proteins ; Gamma Rays ; Genetic Complementation Test ; Genetic Markers ; Humans ; In Situ Hybridization, Fluorescence ; Mice ; Mice, SCID ; Molecular Sequence Data ; Nuclear Proteins ; Phenotype ; Protein-Serine-Threonine Kinases/*genetics/metabolism ; Radiation Tolerance ; Recombination, Genetic ; Severe Combined Immunodeficiency/enzymology/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2007-09-08
    Description: We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cuomo, Christina A -- Guldener, Ulrich -- Xu, Jin-Rong -- Trail, Frances -- Turgeon, B Gillian -- Di Pietro, Antonio -- Walton, Jonathan D -- Ma, Li-Jun -- Baker, Scott E -- Rep, Martijn -- Adam, Gerhard -- Antoniw, John -- Baldwin, Thomas -- Calvo, Sarah -- Chang, Yueh-Long -- Decaprio, David -- Gale, Liane R -- Gnerre, Sante -- Goswami, Rubella S -- Hammond-Kosack, Kim -- Harris, Linda J -- Hilburn, Karen -- Kennell, John C -- Kroken, Scott -- Magnuson, Jon K -- Mannhaupt, Gertrud -- Mauceli, Evan -- Mewes, Hans-Werner -- Mitterbauer, Rudolf -- Muehlbauer, Gary -- Munsterkotter, Martin -- Nelson, David -- O'donnell, Kerry -- Ouellet, Therese -- Qi, Weihong -- Quesneville, Hadi -- Roncero, M Isabel G -- Seong, Kye-Yong -- Tetko, Igor V -- Urban, Martin -- Waalwijk, Cees -- Ward, Todd J -- Yao, Jiqiang -- Birren, Bruce W -- Kistler, H Corby -- U54 HG003067/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1400-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17823352" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Fungal ; Evolution, Molecular ; Fusarium/*genetics/physiology ; *Genome, Fungal ; Hordeum/microbiology ; Molecular Sequence Data ; Plant Diseases/microbiology ; Point Mutation ; *Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 1994-06-21
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 6
    Publication Date: 2015-05-12
    Description: Fungi from the genus Candida are common members of the human microbiota; however, they are also important opportunistic pathogens in immunocompromised hosts. Several morphological transitions have been linked to the ability of these fungi to occupy the different ecological niches in the human body. The transcription factor Efg1 from the APSES family plays a central role in the transcription circuits underlying several of these morphological changes. In Candida albicans , for example, Efg1 is a central regulator of filamentation, biofilm formation, and white-opaque switching, processes associated with survival in the human host. Orthologs of Efg1 are present throughout the Candida clade but, surprisingly, the genome sequence of Candida tropicalis failed to uncover a gene coding for Efg1. One possibility was that the paralog of Efg1, Efh1, had assumed the function of Efg1 in C. tropicalis . However, we show that this gene has only a minor role in the morphological transitions mentioned above. Instead, we report here that C. tropicalis does have an ortholog of the EFG1 gene found in other Candida species. The gene is located in a different genomic position than EFG1 in C. albicans , in a region that contains a gap in the current genome assembly of C. tropicalis . We show that the newly identified C. tropicalis EFG1 gene regulates filamentation, biofilm formation, and white-opaque switching. Our results highlight the conserved role of Efg1 in controlling morphogenesis in Candida species and remind us that published genome sequences are drafts that require continuous curation and careful scrutiny.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 7
    Publication Date: 2015-04-01
    Description: Dimorphic mating-type chromosomes in fungi are excellent models for understanding the genomic consequences of recombination suppression. Their suppressed recombination and reduced effective population size are expected to limit the efficacy of natural selection, leading to genomic degeneration. Our aim was to identify the sequences of the mating-type chromosomes (a 1 and a 2 ) of the anther-smut fungi and to investigate degeneration in their nonrecombining regions. We used the haploid a 1 Microbotryum lychnidis-dioicae reference genome sequence. The a 1 and a 2 mating-type chromosomes were both isolated electrophoretically and sequenced. Integration with restriction-digest optical maps identified regions of recombination and nonrecombination in the mating-type chromosomes. Genome sequence data were also obtained for 12 other Microbotryum species. We found strong evidence of degeneration across the genus in the nonrecombining regions of the mating-type chromosomes, with significantly higher rates of nonsynonymous substitution (d N /d S ) than in nonmating-type chromosomes or in recombining regions of the mating-type chromosomes. The nonrecombining regions of the mating-type chromosomes also showed high transposable element content, weak gene expression, and gene losses. The levels of degeneration did not differ between the a 1 and a 2 mating-type chromosomes, consistent with the lack of homogametic/heterogametic asymmetry between them, and contrasting with X/Y or Z/W sex chromosomes.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 8
  • 9
    Publication Date: 2011-06-01
    Description: Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart from their hosts. Their lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101-Mb genome of Melampsora larici-populina, the causal agent of poplar leaf rust, and the 89-Mb genome of Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust. We then compared the 16,399 predicted proteins of M. larici-populina with the 17,773 predicted proteins of P. graminis f. sp tritici. Genomic features related to their obligate biotrophic lifestyle include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins, impaired nitrogen and sulfur assimilation pathways, and expanded families of amino acid and oligopeptide membrane transporters. The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cells.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 2014-04-17
    Description: Black or dark brown (phaeoid) fungi cause cutaneous, subcutaneous, and systemic infections in humans. Black fungi thrive in stressful conditions such as intense light, high radiation, and very low pH. Wangiella ( Exophiala ) dermatitidis is arguably the most studied phaeoid fungal pathogen of humans. Here, we report our comparative analysis of the genome of W. dermatitidis and the transcriptional response to low pH stress. This revealed that W. dermatitidis has lost the ability to synthesize alpha-glucan, a cell wall compound many pathogenic fungi use to evade the host immune system. In contrast, W. dermatitidis contains a similar profile of chitin synthase genes as related fungi and strongly induces genes involved in cell wall synthesis in response to pH stress. The large portfolio of transporters may provide W. dermatitidis with an enhanced ability to remove harmful products as well as to survive on diverse nutrient sources. The genome encodes three independent pathways for producing melanin, an ability linked to pathogenesis; these are active during pH stress, potentially to produce a barrier to accumulated oxidative damage that might occur under stress conditions. In addition, a full set of fungal light-sensing genes is present, including as part of a carotenoid biosynthesis gene cluster. Finally, we identify a two-gene cluster involved in nucleotide sugar metabolism conserved with a subset of fungi and characterize a horizontal transfer event of this cluster between fungi and algal viruses. This work reveals how W. dermatitidis has adapted to stress and survives in diverse environments, including during human infections.
    Electronic ISSN: 2160-1836
    Topics: Biology
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