Calvo S

References (5)

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 : The genome sequence of the rice blast fungus Magnaporthe grisea - Dean_2005_Nature_434_980
Author(s) : Dean RA , Talbot NJ , Ebbole DJ , Farman ML , Mitchell TK , Orbach MJ , Thon M , Kulkarni R , Xu JR , Pan H , Read ND , Lee YH , Carbone I , Brown D , Oh YY , Donofrio N , Jeong JS , Soanes DM , Djonovic S , Kolomiets E , Rehmeyer C , Li W , Harding M , Kim S , Lebrun MH , Bohnert H , Coughlan S , Butler J , Calvo S , Ma LJ , Nicol R , Purcell S , Nusbaum C , Galagan JE , Birren BW
Ref : Nature , 434 :980 , 2005
Abstract : Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.
ESTHER : Dean_2005_Nature_434_980
PubMedSearch : Dean_2005_Nature_434_980
PubMedID: 15846337
Gene_locus related to this paper: maggr-a4qqu1 , maggr-a4uuq1 , mago7-g4n0f1 , maggr-a4qy60 , maggr-a4qyj3 , maggr-a4r8c0 , maggr-a4r257 , maggr-a4rd24 , maggr-a4ri35 , maggr-a4rlz4 , maggr-a4rme6 , maggr-q0pnd2 , maggr-q0pnd5 , maggr-q2keh4 , maggr-q2khf5 , mago7-a4qsp1 , mago7-a4qt55 , mago7-a4qua7 , mago7-a4qup0 , mago7-a4qvx8 , mago7-a4qwz1 , mago7-a4qx26 , mago7-a4qxi6 , mago7-a4qz39 , mago7-a4qzg2 , mago7-a4r4e9 , mago7-a4r4n4 , mago7-a4r6f4 , mago7-a4r106 , mago7-a4ra37 , mago7-a4rdm3 , mago7-a4rgp8 , mago7-a4rlj9 , mago7-a4rpg7 , mago7-a4uc22 , mago7-dapb , mago7-g4mk92 , mago7-g4mkc6 , mago7-g4mkk9 , mago7-g4mns9 , mago7-g4ms19 , mago7-g4mvm8 , mago7-g4mvw5 , mago7-g4mvw6 , mago7-g4n6j4 , mago7-g4nal1 , mago7-g4naw0 , mago7-g4nba0 , mago7-g4nbs0 , mago7-g4nc41 , mago7-g4ncz9 , mago7-g4nhn9 , mago7-g4nil3 , mago7-g4nky6 , mago7-g5ehg6 , mago7-g5ehv6 , mago7-q2kh83 , mago7-q2khe7 , mago7-a4qxp0 , mago7-g4nih2 , mago7-g4mr24 , mago7-g4nff5 , mago7-g4n8c3 , mago7-g4ni03 , mago7-g4nhm4 , mago7-g4nfb6 , mago7-g4mmn3 , mago7-g4mqv7 , mago7-g4mzv6 , mago7-g4nbz1 , mago7-g4ms46 , mago7-g4n0h2 , mago7-g4nev7 , mago7-g4msm5 , magoy-l7i6m7 , mago7-g4ne75 , magor-a0a4p7n714 , magor-a0a4p7nig7 , mago7-g4mzi2 , mago7-cbpya , mago7-kex1 , mago7-g4n703

Title : The complete genome and proteome of Mycoplasma mobile - Jaffe_2004_Genome.Res_14_1447
Author(s) : Jaffe JD , Stange-Thomann N , Smith C , Decaprio D , Fisher S , Butler J , Calvo S , Elkins T , Fitzgerald MG , Hafez N , Kodira CD , Major J , Wang S , Wilkinson J , Nicol R , Nusbaum C , Birren B , Berg HC , Church GM
Ref : Genome Res , 14 :1447 , 2004
Abstract : Although often considered "minimal" organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete genomic sequence and proteogenomic map for the piscine mycoplasma Mycoplasma mobile, noted for its robust gliding motility. For the first time, proteomic data are used in the primary annotation of a new genome, providing validation of expression for many of the predicted proteins. Several novel features were discovered including a long repeating unit of DNA of approximately 2435 bp present in five complete copies that are shown to code for nearly identical yet uniquely expressed proteins. M. mobile has among the lowest DNA GC contents (24.9%) and most reduced set of tRNAs of any organism yet reported (28). Numerous instances of tandem duplication as well as lateral gene transfer are evident in the genome. The multiple available complete genome sequences for other motile and immotile mycoplasmas enabled us to use comparative genomic and phylogenetic methods to suggest several candidate genes that might be involved in motility. The results of these analyses leave open the possibility that gliding motility might have arisen independently more than once in the mycoplasma lineage.
ESTHER : Jaffe_2004_Genome.Res_14_1447
PubMedSearch : Jaffe_2004_Genome.Res_14_1447
PubMedID: 15289470
Gene_locus related to this paper: mycmo-q6ki90 , mycmo-q6kim4

Title : The genome of M. acetivorans reveals extensive metabolic and physiological diversity - Galagan_2002_Genome.Res_12_532
Author(s) : Galagan JE , Nusbaum C , Roy A , Endrizzi MG , Macdonald P , FitzHugh W , Calvo S , Engels R , Smirnov S , Atnoor D , Brown A , Allen N , Naylor J , Stange-Thomann N , DeArellano K , Johnson R , Linton L , McEwan P , McKernan K , Talamas J , Tirrell A , Ye W , Zimmer A , Barber RD , Cann I , Graham DE , Grahame DA , Guss AM , Hedderich R , Ingram-Smith C , Kuettner HC , Krzycki JA , Leigh JA , Li W , Liu J , Mukhopadhyay B , Reeve JN , Smith K , Springer TA , Umayam LA , White O , White RH , Conway de Macario E , Ferry JG , Jarrell KF , Jing H , Macario AJ , Paulsen I , Pritchett M , Sowers KR , Swanson RV , Zinder SH , Lander E , Metcalf WW , Birren B
Ref : Genome Res , 12 :532 , 2002
Abstract : Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived from acetate. Here we report the complete genome sequence of an acetate-utilizing methanogen, Methanosarcina acetivorans C2A. Methanosarcineae are the most metabolically diverse methanogens, thrive in a broad range of environments, and are unique among the Archaea in forming complex multicellular structures. This diversity is reflected in the genome of M. acetivorans. At 5,751,492 base pairs it is by far the largest known archaeal genome. The 4524 open reading frames code for a strikingly wide and unanticipated variety of metabolic and cellular capabilities. The presence of novel methyltransferases indicates the likelihood of undiscovered natural energy sources for methanogenesis, whereas the presence of single-subunit carbon monoxide dehydrogenases raises the possibility of nonmethanogenic growth. Although motility has not been observed in any Methanosarcineae, a flagellin gene cluster and two complete chemotaxis gene clusters were identified. The availability of genetic methods, coupled with its physiological and metabolic diversity, makes M. acetivorans a powerful model organism for the study of archaeal biology. [Sequence, data, annotations and analyses are available at http://www-genome.wi.mit.edu/.]
ESTHER : Galagan_2002_Genome.Res_12_532
PubMedSearch : Galagan_2002_Genome.Res_12_532
PubMedID: 11932238
Gene_locus related to this paper: metac-MA0077 , metac-MA0362 , metac-MA0419 , metac-MA0736 , metac-MA0993 , metac-MA1571 , metac-MA1856 , metac-MA1857 , metac-MA2002 , metac-MA2343 , metac-MA2629 , metac-MA2691 , metac-MA2743 , metac-MA2933 , metac-MA3611 , metac-MA3635 , metac-MA3920 , metac-META