Kennell JC

References (4)

Title : Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis - Gioti_2013_MBio_4_e00572
Author(s) : Gioti A , Nystedt B , Li W , Xu J , Andersson A , Averette AF , Munch K , Wang X , Kappauf C , Kingsbury JM , Kraak B , Walker LA , Johansson HJ , Holm T , Lehtio J , Stajich JE , Mieczkowski P , Kahmann R , Kennell JC , Cardenas ME , Lundeberg J , Saunders CW , Boekhout T , Dawson TL , Munro CA , de Groot PW , Butler G , Heitman J , Scheynius A
Ref : MBio , 4 :e00572 , 2013
Abstract : Malassezia commensal yeasts are associated with a number of skin disorders, such as atopic eczema/dermatitis and dandruff, and they also can cause systemic infections. Here we describe the 7.67-Mbp genome of Malassezia sympodialis, a species associated with atopic eczema, and contrast its genome repertoire with that of Malassezia globosa, associated with dandruff, as well as those of other closely related fungi. Ninety percent of the predicted M. sympodialis protein coding genes were experimentally verified by mass spectrometry at the protein level. We identified a relatively limited number of genes related to lipid biosynthesis, and both species lack the fatty acid synthase gene, in line with the known requirement of these yeasts to assimilate lipids from the host. Malassezia species do not appear to have many cell wall-localized glycosylphosphatidylinositol (GPI) proteins and lack other cell wall proteins previously identified in other fungi. This is surprising given that in other fungi these proteins have been shown to mediate interactions (e.g., adhesion and biofilm formation) with the host. The genome revealed a complex evolutionary history for an allergen of unknown function, Mala s 7, shown to be encoded by a member of an amplified gene family of secreted proteins. Based on genetic and biochemical studies with the basidiomycete human fungal pathogen Cryptococcus neoformans, we characterized the allergen Mala s 6 as the cytoplasmic cyclophilin A. We further present evidence that M. sympodialis may have the capacity to undergo sexual reproduction and present a model for a pseudobipolar mating system that allows limited recombination between two linked MAT loci. IMPORTANCE: Malassezia commensal yeasts are associated with a number of skin disorders. The previously published genome of M. globosa provided some of the first insights into Malassezia biology and its involvement in dandruff. Here, we present the genome of M. sympodialis, frequently isolated from patients with atopic eczema and healthy individuals. We combined comparative genomics with sequencing and functional characterization of specific genes in a population of clinical isolates and in closely related model systems. Our analyses provide insights into the evolution of allergens related to atopic eczema and the evolutionary trajectory of the machinery for sexual reproduction and meiosis. We hypothesize that M. sympodialis may undergo sexual reproduction, which has important implications for the understanding of the life cycle and virulence potential of this medically important yeast. Our findings provide a foundation for the development of genetic and genomic tools to elucidate host-microbe interactions that occur on the skin and to identify potential therapeutic targets.
ESTHER : Gioti_2013_MBio_4_e00572
PubMedSearch : Gioti_2013_MBio_4_e00572
PubMedID: 23341551
Gene_locus related to this paper: mals4-m5ean5

Title : The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion - Coleman_2009_PLoS.Genet_5_e1000618
Author(s) : Coleman JJ , Rounsley SD , Rodriguez-Carres M , Kuo A , Wasmann CC , Grimwood J , Schmutz J , Taga M , White GJ , Zhou S , Schwartz DC , Freitag M , Ma LJ , Danchin EG , Henrissat B , Coutinho PM , Nelson DR , Straney D , Napoli CA , Barker BM , Gribskov M , Rep M , Kroken S , Molnar I , Rensing C , Kennell JC , Zamora J , Farman ML , Selker EU , Salamov A , Shapiro H , Pangilinan J , Lindquist E , Lamers C , Grigoriev IV , Geiser DM , Covert SF , Temporini E , Vanetten HD
Ref : PLoS Genet , 5 :e1000618 , 2009
Abstract : The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of >50 species known as the "Fusarium solani species complex". Members of this complex have diverse biological properties including the ability to cause disease on >100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6.52 Mb and that the physical size of the genome, 54.43 Mb, and the number of predicted genes, 15,707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin(s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches.
ESTHER : Coleman_2009_PLoS.Genet_5_e1000618
PubMedSearch : Coleman_2009_PLoS.Genet_5_e1000618
PubMedID: 19714214
Gene_locus related to this paper: fusso-cutas , nech7-c7yh18 , nech7-c7yir8 , nech7-c7yiz6 , nech7-c7yjl4 , nech7-c7yjp7 , nech7-c7yjq0 , nech7-c7ymg9 , nech7-c7ymv6 , nech7-c7yna5 , nech7-c7ynt6 , nech7-c7yq59 , nech7-c7yq86 , nech7-c7yqb0 , nech7-c7yqx3 , nech7-c7ysz7 , nech7-c7ysz8 , nech7-c7ytb2 , nech7-c7yum7 , nech7-c7yvb1 , nech7-c7yvb8 , nech7-c7yvf1 , nech7-c7yvq8 , nech7-c7yw21 , nech7-c7yx47 , nech7-c7yx92 , nech7-c7yxe7 , nech7-c7yxq5 , nech7-c7yxz4 , nech7-c7yy47 , nech7-c7yyj7 , nech7-c7yym7 , nech7-c7z0d7 , nech7-c7z0s1 , nech7-c7z1g9 , nech7-c7z1k9 , nech7-c7z2k4 , nech7-c7z2m9 , nech7-c7z2z2 , nech7-c7z3z3 , nech7-c7z4a4 , nech7-c7z5n1 , nech7-c7z5y2 , nech7-c7z6g5 , nech7-c7z7d0 , nech7-c7z7w8 , nech7-c7z8q7 , nech7-c7z9e7 , nech7-c7z073 , nech7-c7z354 , nech7-c7z389 , nech7-c7z688 , nech7-c7z855 , nech7-c7z987 , nech7-c7za94 , nech7-c7zah0 , nech7-c7zb79 , nech7-c7zbr8 , nech7-c7zcd1 , nech7-c7zdx8 , nech7-c7ze42 , nech7-c7ze84 , nech7-c7zed8 , nech7-c7zeh0 , nech7-c7zes2 , nech7-c7zgw2 , nech7-c7zha0 , nech7-c7zhy2 , nech7-c7zi55 , nech7-c7zig4 , nech7-c7zjg0 , nech7-c7zjv2 , nech7-c7zk96 , nech7-c7zkb5 , nech7-c7zkh4 , nech7-c7zla9 , nech7-c7zld2 , nech7-c7zlz1 , nech7-c7zm00 , nech7-c7zmn4 , nech7-c7zmu6 , nech7-c7zp06 , nech7-c7zp78 , nech7-c7zq58 , nech7-c7zq86 , nech7-c7zqb5 , nech7-c7zqk4 , nech7-c7zqp9 , nech7-c7zr59 , nech7-c7zrh2 , nech7-c7zrh3 , nech7-dapb , nech7-kex1 , nech7-c7zgl9 , nech7-c7z935 , nech7-c7znc0 , nech7-c7yiq8 , nech7-c7yiq7 , nech7-c7zhu0 , nech7-c7yw61 , nech7-c7yqd3 , nech7-c7zkb6 , nech7-c7z3b4 , nech7-c7ytr4 , nech7-c7zgf7 , 9hypo-a0a3m2s2j6 , nech7-c7yq54 , fusv7-cbpya

Title : The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization - Cuomo_2007_Science_317_1400
Author(s) : Cuomo CA , Guldener U , Xu JR , Trail F , Turgeon BG , Di Pietro A , Walton JD , Ma LJ , Baker SE , Rep M , Adam G , Antoniw J , Baldwin T , Calvo S , Chang YL , Decaprio D , Gale LR , Gnerre S , Goswami RS , Hammond-Kosack K , Harris LJ , Hilburn K , Kennell JC , Kroken S , Magnuson JK , Mannhaupt G , Mauceli E , Mewes HW , Mitterbauer R , Muehlbauer G , Munsterkotter M , Nelson D , O'Donnell K , Ouellet T , Qi W , Quesneville H , Roncero MI , Seong KY , Tetko IV , Urban M , Waalwijk C , Ward TJ , Yao J , Birren BW , Kistler HC
Ref : Science , 317 :1400 , 2007
Abstract : 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.
ESTHER : Cuomo_2007_Science_317_1400
PubMedSearch : Cuomo_2007_Science_317_1400
PubMedID: 17823352
Gene_locus related to this paper: fusof-f9fxz4 , gibze-a8w610 , gibze-b1pdn0 , gibze-i1r9e6 , gibze-i1rda9 , gibze-i1rdk7 , gibze-i1rec8 , gibze-i1rgs0 , gibze-i1rgy0 , gibze-i1rh52 , gibze-i1rhi8 , gibze-i1rig9 , gibze-i1rip5 , gibze-i1rpg6 , gibze-i1rsg2 , gibze-i1rv36 , gibze-i1rxm5 , gibze-i1rxp8 , gibze-i1rxv5 , gibze-i1s1u3 , gibze-i1s3j9 , gibze-i1s6l7 , gibze-i1s8i8 , gibze-i1s9x4 , gibze-ppme1 , gibze-q4huy1 , gibze-i1rg17 , gibze-i1rb76 , gibze-i1s1m7 , gibze-i1s3z6 , gibze-i1rd78 , gibze-i1rgl9 , gibze-i1rjp7 , gibze-i1s1q6 , gibze-i1ri35 , gibze-i1rf76 , gibze-i1rhp3 , gibza-a0a016pda4 , gibza-a0a016pl96 , gibze-i1rjb5 , gibze-i1rkc4 , gibze-a0a1c3ylb1 , gibze-gra11 , gibze-fsl2

Title : Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis - Kamper_2006_Nature_444_97
Author(s) : Kamper J , Kahmann R , Bolker M , Ma LJ , Brefort T , Saville BJ , Banuett F , Kronstad JW , Gold SE , Muller O , Perlin MH , Wosten HA , de Vries R , Ruiz-Herrera J , Reynaga-Pena CG , Snetselaar K , McCann M , Perez-Martin J , Feldbrugge M , Basse CW , Steinberg G , Ibeas JI , Holloman W , Guzman P , Farman M , Stajich JE , Sentandreu R , Gonzalez-Prieto JM , Kennell JC , Molina L , Schirawski J , Mendoza-Mendoza A , Greilinger D , Munch K , Rossel N , Scherer M , Vranes M , Ladendorf O , Vincon V , Fuchs U , Sandrock B , Meng S , Ho EC , Cahill MJ , Boyce KJ , Klose J , Klosterman SJ , Deelstra HJ , Ortiz-Castellanos L , Li W , Sanchez-Alonso P , Schreier PH , Hauser-Hahn I , Vaupel M , Koopmann E , Friedrich G , Voss H , Schluter T , Margolis J , Platt D , Swimmer C , Gnirke A , Chen F , Vysotskaia V , Mannhaupt G , Guldener U , Munsterkotter M , Haase D , Oesterheld M , Mewes HW , Mauceli EW , Decaprio D , Wade CM , Butler J , Young S , Jaffe DB , Calvo S , Nusbaum C , Galagan J , Birren BW
Ref : Nature , 444 :97 , 2006
Abstract : Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence strategies to kill its host. U. maydis belongs to the group of biotrophic parasites (the smuts) that depend on living tissue for proliferation and development. Here we report the genome sequence for a member of this economically important group of biotrophic fungi. The 20.5-million-base U. maydis genome assembly contains 6,902 predicted protein-encoding genes and lacks pathogenicity signatures found in the genomes of aggressive pathogenic fungi, for example a battery of cell-wall-degrading enzymes. However, we detected unexpected genomic features responsible for the pathogenicity of this organism. Specifically, we found 12 clusters of genes encoding small secreted proteins with unknown function. A significant fraction of these genes exists in small gene families. Expression analysis showed that most of the genes contained in these clusters are regulated together and induced in infected tissue. Deletion of individual clusters altered the virulence of U. maydis in five cases, ranging from a complete lack of symptoms to hypervirulence. Despite years of research into the mechanism of pathogenicity in U. maydis, no 'true' virulence factors had been previously identified. Thus, the discovery of the secreted protein gene clusters and the functional demonstration of their decisive role in the infection process illuminate previously unknown mechanisms of pathogenicity operating in biotrophic fungi. Genomic analysis is, similarly, likely to open up new avenues for the discovery of virulence determinants in other pathogens.
ESTHER : Kamper_2006_Nature_444_97
PubMedSearch : Kamper_2006_Nature_444_97
PubMedID: 17080091
Gene_locus related to this paper: ustma-q4p4j7 , ustma-q4p5d2 , ustma-q4p8h8 , ustma-q4p8x7 , ustma-q4p082 , ustma-q4p194 , ustma-q4pa07 , ustma-q4pas0 , ustma-q4pbb4 , ustma-q4pg48