Guldener U

References (14)

Title : Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria - Sipos_2017_Nat.Ecol.Evol_1_1931
Author(s) : Sipos G , Prasanna AN , Walter MC , O'Connor E , Balint B , Krizsan K , Kiss B , Hess J , Varga T , Slot J , Riley R , Boka B , Rigling D , Barry K , Lee J , Mihaltcheva S , LaButti K , Lipzen A , Waldron R , Moloney NM , Sperisen C , Kredics L , Vagvolgyi C , Patrignani A , Fitzpatrick D , Nagy I , Doyle S , Anderson JB , Grigoriev IV , Guldener U , Munsterkotter M , Nagy LG
Ref : Nat Ecol Evol , 1 :1931 , 2017
Abstract : Armillaria species are both devastating forest pathogens and some of the largest terrestrial organisms on Earth. They forage for hosts and achieve immense colony sizes via rhizomorphs, root-like multicellular structures of clonal dispersal. Here, we sequenced and analysed the genomes of four Armillaria species and performed RNA sequencing and quantitative proteomic analysis on the invasive and reproductive developmental stages of A. ostoyae. Comparison with 22 related fungi revealed a significant genome expansion in Armillaria, affecting several pathogenicity-related genes, lignocellulose-degrading enzymes and lineage-specific genes expressed during rhizomorph development. Rhizomorphs express an evolutionarily young transcriptome that shares features with the transcriptomes of both fruiting bodies and vegetative mycelia. Several genes show concomitant upregulation in rhizomorphs and fruiting bodies and share cis-regulatory signatures in their promoters, providing genetic and regulatory insights into complex multicellularity in fungi. Our results suggest that the evolution of the unique dispersal and pathogenicity mechanisms of Armillaria might have drawn upon ancestral genetic toolkits for wood-decay, morphogenesis and complex multicellularity.
ESTHER : Sipos_2017_Nat.Ecol.Evol_1_1931
PubMedSearch : Sipos_2017_Nat.Ecol.Evol_1_1931
PubMedID: 29085064
Gene_locus related to this paper: armos-armb

Title : Comparative Omics of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis - Niehaus_2016_Genome.Biol.Evol_8_3574
Author(s) : Niehaus EM , Munsterkotter M , Proctor RH , Brown DW , Sharon A , Idan Y , Oren-Young L , Sieber CM , Novak O , Pencik A , Tarkowska D , Hromadova K , Freeman S , Maymon M , Elazar M , Youssef SA , El-Shabrawy ES , Shalaby AB , Houterman P , Brock NL , Burkhardt I , Tsavkelova EA , Dickschat JS , Galuszka P , Guldener U , Tudzynski B
Ref : Genome Biol Evol , 8 :3574 , 2016
Abstract : Species of the Fusarium fujikuroi species complex (FFC) cause a wide spectrum of often devastating diseases on diverse agricultural crops, including coffee, fig, mango, maize, rice, and sugarcane. Although species within the FFC are difficult to distinguish by morphology, and their genes often share 90% sequence similarity, they can differ in host plant specificity and life style. FFC species can also produce structurally diverse secondary metabolites (SMs), including the mycotoxins fumonisins, fusarins, fusaric acid, and beauvericin, and the phytohormones gibberellins, auxins, and cytokinins. The spectrum of SMs produced can differ among closely related species, suggesting that SMs might be determinants of host specificity. To date, genomes of only a limited number of FFC species have been sequenced. Here, we provide draft genome sequences of three more members of the FFC: a single isolate of F. mangiferae, the cause of mango malformation, and two isolates of F. proliferatum, one a pathogen of maize and the other an orchid endophyte. We compared these genomes to publicly available genome sequences of three other FFC species. The comparisons revealed species-specific and isolate-specific differences in the composition and expression (in vitro and in planta) of genes involved in SM production including those for phytohormome biosynthesis. Such differences have the potential to impact host specificity and, as in the case of F. proliferatum, the pathogenic versus endophytic life style.
ESTHER : Niehaus_2016_Genome.Biol.Evol_8_3574
PubMedSearch : Niehaus_2016_Genome.Biol.Evol_8_3574
PubMedID: 28040774
Gene_locus related to this paper: fusma-a0a1l7uhq5 , gibf5-s0ehu3 , fusma-a0a1l7uad3

Title : The genome sequence of the highly acetic acid-tolerant Zygosaccharomyces bailii-derived interspecies hybrid strain ISA1307, isolated from a sparkling wine plant - Mira_2014_DNA.Res_21_299
Author(s) : Mira NP , Munsterkotter M , Dias-Valada F , Santos J , Palma M , Roque FC , Guerreiro JF , Rodrigues F , Sousa MJ , Leao C , Guldener U , Sa-Correia I
Ref : DNA Research , 21 :299 , 2014
Abstract : In this work, it is described the sequencing and annotation of the genome of the yeast strain ISA1307, isolated from a sparkling wine continuous production plant. This strain, formerly considered of the Zygosaccharomyces bailii species, has been used to study Z. bailii physiology, in particular, its extreme tolerance to acetic acid stress at low pH. The analysis of the genome sequence described in this work indicates that strain ISA1307 is an interspecies hybrid between Z. bailii and a closely related species. The genome sequence of ISA1307 is distributed through 154 scaffolds and has a size of around 21.2 Mb, corresponding to 96% of the genome size estimated by flow cytometry. Annotation of ISA1307 genome includes 4385 duplicated genes ( approximately 90% of the total number of predicted genes) and 1155 predicted single-copy genes. The functional categories including a higher number of genes are 'Metabolism and generation of energy', 'Protein folding, modification and targeting' and 'Biogenesis of cellular components'. The knowledge of the genome sequence of the ISA1307 strain is expected to contribute to accelerate systems-level understanding of stress resistance mechanisms in Z. bailii and to inspire and guide novel biotechnological applications of this yeast species/strain in fermentation processes, given its high resilience to acidic stress. The availability of the ISA1307 genome sequence also paves the way to a better understanding of the genetic mechanisms underlying the generation and selection of more robust hybrid yeast strains in the stressful environment of wine fermentations.
ESTHER : Mira_2014_DNA.Res_21_299
PubMedSearch : Mira_2014_DNA.Res_21_299
PubMedID: 24453040
Gene_locus related to this paper: zygba-w0vhg2

Title : Genetic manipulation of the Fusarium fujikuroi fusarin gene cluster yields insight into the complex regulation and fusarin biosynthetic pathway - Niehaus_2013_Chem.Biol_20_1055
Author(s) : Niehaus EM , Kleigrewe K , Wiemann P , Studt L , Sieber CM , Connolly LR , Freitag M , Guldener U , Tudzynski B , Humpf HU
Ref : Chemical Biology , 20 :1055 , 2013
Abstract : In this work, the biosynthesis and regulation of the polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS)-derived mutagenic mycotoxin fusarin C was studied in the fungus Fusarium fujikuroi. The fusarin gene cluster consists of nine genes (fus1-fus9) that are coexpressed under high-nitrogen and acidic pH conditions. Chromatin immunoprecipitation revealed a correlation between high expression and enrichment of activating H3K9-acetylation marks under inducing conditions. We provide evidence that only four genes are sufficient for the biosynthesis. The combination of genetic engineering with nuclear magnetic resonance and mass-spectrometry-based structure elucidation allowed the discovery of the putative fusarin biosynthetic pathway. Surprisingly, we indicate that PKS/NRPS releases its product with an open ring structure, probably as an alcohol. Our data indicate that 2-pyrrolidone ring closure, oxidation at C-20, and, finally, methylation at C-20 are catalyzed by Fus2, Fus8, and Fus9, respectively.
ESTHER : Niehaus_2013_Chem.Biol_20_1055
PubMedSearch : Niehaus_2013_Chem.Biol_20_1055
PubMedID: 23932525
Gene_locus related to this paper: gibf5-fus2 , gibf5-fus5

Title : Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites - Wiemann_2013_PLoS.Pathog_9_e1003475
Author(s) : Wiemann P , Sieber CM , von Bargen KW , Studt L , Niehaus EM , Espino JJ , Huss K , Michielse CB , Albermann S , Wagner D , Bergner SV , Connolly LR , Fischer A , Reuter G , Kleigrewe K , Bald T , Wingfield BD , Ophir R , Freeman S , Hippler M , Smith KM , Brown DW , Proctor RH , Munsterkotter M , Freitag M , Humpf HU , Guldener U , Tudzynski B
Ref : PLoS Pathog , 9 :e1003475 , 2013
Abstract : The fungus Fusarium fujikuroi causes "bakanae" disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary success of F. fujikuroi as a rice pathogen.
ESTHER : Wiemann_2013_PLoS.Pathog_9_e1003475
PubMedSearch : Wiemann_2013_PLoS.Pathog_9_e1003475
PubMedID: 23825955
Gene_locus related to this paper: fusox-a0a1d3s5h0 , fusof-f9f6t8 , fusof-f9f6v2 , fusof-f9f132 , fusof-f9fd90 , fusof-f9fmx2 , fusof-f9fnt4 , fusof-f9g2a2 , fusof-f9g797 , fusof-f9ga50 , fusof-f9gck4 , fusof-f9gd15 , gibf5-s0ea65 , gibf5-s0enx6 , gibf5-s0epd5 , gibf5-s0dwm1 , gibf5-s0egd1 , gibf5-s0duw7 , gibf5-s0ekf7 , gibf5-s0e2n9 , gibf5-s0en31 , gibf5-s0e7t9 , gibf5-s0eim9 , gibf5-s0drv8 , gibf5-s0e9e0 , gibf5-s0e3u9 , gibf5-s0dzu5 , gibf5-s0dqr2 , gibf5-s0ecj3 , gibf5-s0ekc4 , gibf5-s0ejq7 , gibf5-s0eli0 , gibf5-s0dz40 , gibf5-s0ehu3 , gibf5-fuj3 , gibf5-fub5 , gibf5-fus5 , gibf5-bik1

Title : Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci - Schardl_2013_PLoS.Genet_9_e1003323
Author(s) : Schardl CL , Young CA , Hesse U , Amyotte SG , Andreeva K , Calie PJ , Fleetwood DJ , Haws DC , Moore N , Oeser B , Panaccione DG , Schweri KK , Voisey CR , Farman ML , Jaromczyk JW , Roe BA , O'Sullivan DM , Scott B , Tudzynski P , An Z , Arnaoudova EG , Bullock CT , Charlton ND , Chen L , Cox M , Dinkins RD , Florea S , Glenn AE , Gordon A , Guldener U , Harris DR , Hollin W , Jaromczyk J , Johnson RD , Khan AK , Leistner E , Leuchtmann A , Li C , Liu J , Liu M , Mace W , Machado C , Nagabhyru P , Pan J , Schmid J , Sugawara K , Steiner U , Takach JE , Tanaka E , Webb JS , Wilson EV , Wiseman JL , Yoshida R , Zeng Z
Ref : PLoS Genet , 9 :e1003323 , 2013
Abstract : The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloe and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.
ESTHER : Schardl_2013_PLoS.Genet_9_e1003323
PubMedSearch : Schardl_2013_PLoS.Genet_9_e1003323
PubMedID: 23468653
Gene_locus related to this paper: clap2-m1w2a8 , clap2-m1w555 , clap2-m1wa31 , clap2-m1whd2 , clap2-m1weh2 , clap2-m1w5y7 , clap2-m1wh11 , clap2-m1vyn7 , clap2-m1w670

Title : Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of transposable elements - Laurie_2012_Plant.Cell_24_1733
Author(s) : Laurie JD , Ali S , Linning R , Mannhaupt G , Wong P , Guldener U , Munsterkotter M , Moore R , Kahmann R , Bakkeren G , Schirawski J
Ref : Plant Cell , 24 :1733 , 2012
Abstract : Ustilago hordei is a biotrophic parasite of barley (Hordeum vulgare). After seedling infection, the fungus persists in the plant until head emergence when fungal spores develop and are released from sori formed at kernel positions. The 26.1-Mb U. hordei genome contains 7113 protein encoding genes with high synteny to the smaller genomes of the related, maize-infecting smut fungi Ustilago maydis and Sporisorium reilianum but has a larger repeat content that affected genome evolution at important loci, including mating-type and effector loci. The U. hordei genome encodes components involved in RNA interference and heterochromatin formation, normally involved in genome defense, that are lacking in the U. maydis genome due to clean excision events. These excision events were possibly a result of former presence of repetitive DNA and of an efficient homologous recombination system in U. maydis. We found evidence of repeat-induced point mutations in the genome of U. hordei, indicating that smut fungi use different strategies to counteract the deleterious effects of repetitive DNA. The complement of U. hordei effector genes is comparable to the other two smuts but reveals differences in family expansion and clustering. The availability of the genome sequence will facilitate the identification of genes responsible for virulence and evolution of smut fungi on their respective hosts.
ESTHER : Laurie_2012_Plant.Cell_24_1733
PubMedSearch : Laurie_2012_Plant.Cell_24_1733
PubMedID: 22623492
Gene_locus related to this paper: usth4-i2fq24 , usth4-i2fv52 , usth4-i2fz23 , usth4-i2fzu8 , usth4-i2g3y0 , usth4-i2g5f8

Title : Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica - Zuccaro_2011_PLoS.Pathog_7_e1002290
Author(s) : Zuccaro A , Lahrmann U , Guldener U , Langen G , Pfiffi S , Biedenkopf D , Wong P , Samans B , Grimm C , Basiewicz M , Murat C , Martin F , Kogel KH
Ref : PLoS Pathog , 7 :e1002290 , 2011
Abstract : Recent sequencing projects have provided deep insight into fungal lifestyle-associated genomic adaptations. Here we report on the 25 Mb genome of the mutualistic root symbiont Piriformospora indica (Sebacinales, Basidiomycota) and provide a global characterization of fungal transcriptional responses associated with the colonization of living and dead barley roots. Extensive comparative analysis of the P. indica genome with other Basidiomycota and Ascomycota fungi that have diverse lifestyle strategies identified features typically associated with both, biotrophism and saprotrophism. The tightly controlled expression of the lifestyle-associated gene sets during the onset of the symbiosis, revealed by microarray analysis, argues for a biphasic root colonization strategy of P. indica. This is supported by a cytological study that shows an early biotrophic growth followed by a cell death-associated phase. About 10% of the fungal genes induced during the biotrophic colonization encoded putative small secreted proteins (SSP), including several lectin-like proteins and members of a P. indica-specific gene family (DELD) with a conserved novel seven-amino acids motif at the C-terminus. Similar to effectors found in other filamentous organisms, the occurrence of the DELDs correlated with the presence of transposable elements in gene-poor repeat-rich regions of the genome. This is the first in depth genomic study describing a mutualistic symbiont with a biphasic lifestyle. Our findings provide a significant advance in understanding development of biotrophic plant symbionts and suggest a series of incremental shifts along the continuum from saprotrophy towards biotrophy in the evolution of mycorrhizal association from decomposer fungi.
ESTHER : Zuccaro_2011_PLoS.Pathog_7_e1002290
PubMedSearch : Zuccaro_2011_PLoS.Pathog_7_e1002290
PubMedID: 22022265
Gene_locus related to this paper: pirid-g4tjk9 , pirid-g4tkg4 , pirid-g4tn12 , pirid-g4tn25 , pirid-g4tnp6 , pirid-g4tqw0 , pirid-g4tqz1 , pirid-g4trd2 , pirid-g4ts42 , pirid-g4ttw4 , pirid-g4tu99 , pirid-g4txx0 , pirid-g4thl7 , pirid-g4txz4 , pirid-g4tkx2 , pirid-g4u2y4 , serid-g4tly2

Title : Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea - Amselem_2011_PLoS.Genet_7_e1002230
Author(s) : Amselem J , Cuomo CA , van Kan JA , Viaud M , Benito EP , Couloux A , Coutinho PM , de Vries RP , Dyer PS , Fillinger S , Fournier E , Gout L , Hahn M , Kohn L , Lapalu N , Plummer KM , Pradier JM , Quevillon E , Sharon A , Simon A , ten Have A , Tudzynski B , Tudzynski P , Wincker P , Andrew M , Anthouard V , Beever RE , Beffa R , Benoit I , Bouzid O , Brault B , Chen Z , Choquer M , Collemare J , Cotton P , Danchin EG , Da Silva C , Gautier A , Giraud C , Giraud T , Gonzalez C , Grossetete S , Guldener U , Henrissat B , Howlett BJ , Kodira C , Kretschmer M , Lappartient A , Leroch M , Levis C , Mauceli E , Neuveglise C , Oeser B , Pearson M , Poulain J , Poussereau N , Quesneville H , Rascle C , Schumacher J , Segurens B , Sexton A , Silva E , Sirven C , Soanes DM , Talbot NJ , Templeton M , Yandava C , Yarden O , Zeng Q , Rollins JA , Lebrun MH , Dickman M
Ref : PLoS Genet , 7 :e1002230 , 2011
Abstract : Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
ESTHER : Amselem_2011_PLoS.Genet_7_e1002230
PubMedSearch : Amselem_2011_PLoS.Genet_7_e1002230
PubMedID: 21876677
Gene_locus related to this paper: botci-cutas , botci-q6rki2 , botf4-g2y7k8 , botfb-dapb , botfu-g2xyd8 , botfu-g2ynh8 , scls1-a7e814 , scls1-a7edc9 , scls1-a7edh1 , scls1-a7emm0 , scls1-a7eti8 , scls1-a7eu48 , scls1-a7f208 , scls1-dapb , botf4-g2xqp7 , scls1-a7eqq8 , botf4-g2xqc6 , scls1-a7ebs4 , botf4-g2xn51 , scls1-a7f5m9 , botf4-g2xti4 , botf4-g2xtu7 , botf4-g2yfp1 , scls1-a7f534 , botf4-g2yys3 , scls1-a7erz9 , botf4-g2y037 , botf4-g2y0e1 , scls1-a7f706 , scls1-a7ewt6 , botf4-g2yuj6 , botf1-m7u3d1 , botf1-m7u430 , botf1-m7tei8 , botf1-m7u0w9 , botf1-m7tij6 , botf1-m7u819 , botf1-m7u6d8 , botf1-m7tzd4 , botf1-m7tqd7 , botf1-m7tyz9 , botf1-m7unl9 , botf1-m7u429 , botf1-m7u4s5 , botf1-m7ul92 , botf1-m7tx42 , botf1-m7u9h4 , botf1-m7u187 , botf1-m7uz64 , botf1-m7u4q4 , botf1-m7u2f6 , botf1-m7tt59 , botf1-m7v3h2 , botf1-m7u6c9 , botf1-m7tud9 , botf1-m7u309 , scls1-a7et87 , botf4-g2ylt4 , scls1-a7f5a0 , scls1-a7f900 , botf4-g2yib9 , scls1-a7f3m9 , scls1-a7er46 , botf4-g2y3y4 , botf4-g2xyy5 , botf1-m7uct5 , scls1-a7ea78 , scls1-kex1 , scls1-cbpya , botfb-cbpya , scls1-a7ecx1

Title : Pathogenicity determinants in smut fungi revealed by genome comparison - Schirawski_2010_Science_330_1546
Author(s) : Schirawski J , Mannhaupt G , Munch K , Brefort T , Schipper K , Doehlemann G , Di Stasio M , Rossel N , Mendoza-Mendoza A , Pester D , Muller O , Winterberg B , Meyer E , Ghareeb H , Wollenberg T , Munsterkotter M , Wong P , Walter M , Stukenbrock E , Guldener U , Kahmann R
Ref : Science , 330 :1546 , 2010
Abstract : Biotrophic pathogens, such as the related maize pathogenic fungi Ustilago maydis and Sporisorium reilianum, establish an intimate relationship with their hosts by secreting protein effectors. Because secreted effectors interacting with plant proteins should rapidly evolve, we identified variable genomic regions by sequencing the genome of S. reilianum and comparing it with the U. maydis genome. We detected 43 regions of low sequence conservation in otherwise well-conserved syntenic genomes. These regions primarily encode secreted effectors and include previously identified virulence clusters. By deletion analysis in U. maydis, we demonstrate a role in virulence for four previously unknown diversity regions. This highlights the power of comparative genomics of closely related species for identification of virulence determinants.
ESTHER : Schirawski_2010_Science_330_1546
PubMedSearch : Schirawski_2010_Science_330_1546
PubMedID: 21148393
Gene_locus related to this paper: spore-e6zjp7 , spore-e6zjr6 , spore-e6zk43 , spore-e6zlt6 , spore-e6zna3 , spore-e6znp7 , spore-e6zpb0 , spore-e6zs40 , spore-e6zvn2 , spore-e6zw38 , spore-e6zxb1 , spore-e6zz09 , spore-e6zzs9 , spore-e7a0f1 , spore-e7a1t2 , spore-e7a3d1 , spore-e7a031 , spore-e7a048 , spore-e7a199 , ustma-q4p4j7 , ustma-q4p8x7 , ustma-q4pih8 , spore-e7a3b0 , spore-e6zkk3 , spore-e6zvu7 , spore-e6zuc1 , spore-e6zki8 , spore-e6zvu2 , spore-e7a380

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

Title : Functional profiling of the Saccharomyces cerevisiae genome - Giaever_2002_Nature_418_387
Author(s) : Giaever G , Chu AM , Ni L , Connelly C , Riles L , Veronneau S , Dow S , Lucau-Danila A , Anderson K , Andre B , Arkin AP , Astromoff A , El-Bakkoury M , Bangham R , Benito R , Brachat S , Campanaro S , Curtiss M , Davis K , Deutschbauer A , Entian KD , Flaherty P , Foury F , Garfinkel DJ , Gerstein M , Gotte D , Guldener U , Hegemann JH , Hempel S , Herman Z , Jaramillo DF , Kelly DE , Kelly SL , Kotter P , LaBonte D , Lamb DC , Lan N , Liang H , Liao H , Liu L , Luo C , Lussier M , Mao R , Menard P , Ooi SL , Revuelta JL , Roberts CJ , Rose M , Ross-Macdonald P , Scherens B , Schimmack G , Shafer B , Shoemaker DD , Sookhai-Mahadeo S , Storms RK , Strathern JN , Valle G , Voet M , Volckaert G , Wang CY , Ward TR , Wilhelmy J , Winzeler EA , Yang Y , Yen G , Youngman E , Yu K , Bussey H , Boeke JD , Snyder M , Philippsen P , Davis RW , Johnston M
Ref : Nature , 418 :387 , 2002
Abstract : Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.
ESTHER : Giaever_2002_Nature_418_387
PubMedSearch : Giaever_2002_Nature_418_387
PubMedID: 12140549

Title : Functional analysis of 150 deletion mutants in Saccharomyces cerevisiae by a systematic approach - Entian_1999_Mol.Gen.Genet_262_683
Author(s) : Entian KD , Schuster T , Hegemann JH , Becher D , Feldmann H , Guldener U , Gotz R , Hansen M , Hollenberg CP , Jansen G , Kramer W , Klein S , Kotter P , Kricke J , Launhardt H , Mannhaupt G , Maierl A , Meyer P , Mewes W , Munder T , Niedenthal RK , Ramezani Rad M , Rohmer A , Romer A , Rose M , Schafer B , Siegler ML , Vetter J , Wilhelm N , Wolf K , Zimmermann FK , Zollner A , Hinnen A , et al.
Ref : Molecular & General Genetics , 262 :683 , 1999
Abstract : In a systematic approach to the study of Saccharomyces cerevisiae genes of unknown function, 150 deletion mutants were constructed (1 double, 149 single mutants) and phenotypically analysed. Twenty percent of all genes examined were essential. The viable deletion mutants were subjected to 20 different test systems, ranging from high throughput to highly specific test systems. Phenotypes were obtained for two-thirds of the mutants tested. During the course of this investigation, mutants for 26 of the genes were described by others. For 18 of these the reported data were in accordance with our results. Surprisingly, for seven genes, additional, unexpected phenotypes were found in our tests. This suggests that the type of analysis presented here provides a more complete description of gene function.
ESTHER : Entian_1999_Mol.Gen.Genet_262_683
PubMedSearch : Entian_1999_Mol.Gen.Genet_262_683
PubMedID: 10628851
Gene_locus related to this paper: yeast-ict1