Author Report for: Ma LJNo contact information in database for Ma LJ
Ma LJ, Hou XD, Qin XY, He RJ, Yu HN, Hu Q, Guan XQ, Jia SN, Hou J and Ge GB <1 more author(s)> Ma LJ, Hou XD, Qin XY, He RJ, Yu HN, Hu Q, Guan XQ, Jia SN, Hou J, Lei T, Ge GB (- 1) Ref: J Pharm Anal, 12:683, 2022 : PubMed ESTHER: Ma_2022_J.Pharm.Anal_12_683 PubMedSearch: Ma 2022 J.Pharm.Anal 12 683 PubMedID: 36105167 Inhibitor(s) related to this paper: Pentagalloylglucose Abstract Although herbal medicines (HMs) are widely used in the prevention and treatment of obesity and obesity-associated disorders, the key constituents exhibiting anti-obesity activity and their molecular mechanisms are poorly understood. Recently, we assessed the inhibitory potentials of several HMs against human pancreatic lipase (hPL, a key therapeutic target for human obesity), among which the root-extract of Rhodiola crenulata (ERC) showed the most potent anti-hPL activity. In this study, we adopted an integrated strategy, involving bioactivity-guided fractionation techniques, chemical profiling, and biochemical assays, to identify the key anti-hPL constituents in ERC. Nine ERC fractions (retention time = 12.5-35 min), obtained using reverse-phase liquid chromatography, showed strong anti-hPL activity, while the major constituents in these bioactive fractions were subsequently identified using liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS/MS). Among the identified ERC constituents, 1,2,3,4,6-penta-O-galloyl-beta-d-glucopyranose (PGG) and catechin gallate (CG) showed the most potent anti-hPL activity, with pIC(50) values of 7.59 +/- 0.03 and 7.68 +/- 0.23, respectively. Further investigations revealed that PGG and CG potently inhibited hPL in a non-competitive manner, with inhibition constant (K (i)) values of 0.012 and 0.082 microM, respectively. Collectively, our integrative analyses enabled us to efficiently identify and characterize the key anti-obesity constituents in ERC, as well as to elucidate their anti-hPL mechanisms. These findings provide convincing evidence in support of the anti-obesity and lipid-lowering properties of ERC. Title: Effector profiles distinguish formae speciales of Fusarium oxysporum van Dam P, Fokkens L, Schmidt SM, Linmans JH, Kistler HC, Ma LJ, Rep M Ref: Environ Microbiol, 18:4087, 2016 : PubMed ESTHER: van Dam_2016_Environ.Microbiol_18_4087 PubMedSearch: van Dam 2016 Environ.Microbiol 18 4087 PubMedID: 27387256 Gene_locus related to this paper: fusox-w9hvf0, fusox-x0d9n6, gibm7-w7n4n0 Abstract Formae speciales (ff.spp.) of the fungus Fusarium oxysporum are often polyphyletic within the species complex, making it impossible to identify them on the basis of conserved genes. However, sequences that determine host-specific pathogenicity may be expected to be similar between strains within the same forma specialis. Whole genome sequencing was performed on strains from five different ff.spp. (cucumerinum, niveum, melonis, radicis-cucumerinum and lycopersici). In each genome, genes for putative effectors were identified based on small size, secretion signal, and vicinity to a "miniature impala" transposable element. The candidate effector genes of all genomes were collected and the presence/absence patterns in each individual genome were clustered. Members of the same forma specialis turned out to group together, with cucurbit-infecting strains forming a supercluster separate from other ff.spp. Moreover, strains from different clonal lineages within the same forma specialis harbour identical effector gene sequences, supporting horizontal transfer of genetic material. These data offer new insight into the genetic basis of host specificity in the F. oxysporum species complex and show that (putative) effectors can be used to predict host specificity in F. oxysporum. Title: Draft Genome Sequence of the Cellulolytic Fungus Chaetomium globosum Cuomo CA, Untereiner WA, Ma LJ, Grabherr M, Birren BW Ref: Genome Announc, 3:, 2015 : PubMed ESTHER: Cuomo_2015_Genome.Announc_3_E00021 PubMedSearch: Cuomo 2015 Genome.Announc 3 E00021 PubMedID: 25720678 Gene_locus related to this paper: chagb-q2h5j0, chagb-q2h6w8, chagb-q2gpq3, chagb-q2gyn8, chagb-q2h2d0 Abstract Chaetomium globosum is a filamentous fungus typically isolated from cellulosic substrates. This species also causes superficial infections of humans and, more rarely, can cause cerebral infections. Here, we report the genome sequence of C. globosum isolate CBS 148.51, which will facilitate the study and comparative analysis of this fungus. Title: Genome Sequence of Fusarium oxysporum f. sp. melonis Strain NRRL 26406, a Fungus Causing Wilt Disease on Melon Ma LJ, Shea T, Young S, Zeng Q, Kistler HC Ref: Genome Announc, 2:, 2014 : PubMed ESTHER: Ma_2014_Genome.Announc_2_e00730 PubMedSearch: Ma 2014 Genome.Announc 2 e00730 PubMedID: 25081257 Gene_locus related to this paper: fusox-a0a1d3s5h0, fusox-w9p5i8, fusox-w9hvf0 Abstract Horizontal chromosome transfer introduces host-specific pathogenicity among members of the Fusarium oxysporum species complex and is responsible for some of the most destructive and intractable plant diseases. This paper reports the genome sequence of F. oxysporum f. sp. melonis (NRRL 26406), a causal agent of Fusarium wilt disease on melon. Title: Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics Zhang Y, Zhang K, Fang A, Han Y, Yang J, Xue M, Bao J, Hu D, Zhou B and Sun W <18 more author(s)> Zhang Y, Zhang K, Fang A, Han Y, Yang J, Xue M, Bao J, Hu D, Zhou B, Sun X, Li S, Wen M, Yao N, Ma LJ, Liu Y, Zhang M, Huang F, Luo C, Zhou L, Li J, Chen Z, Miao J, Wang S, Lai J, Xu JR, Hsiang T, Peng YL, Sun W (- 18) Ref: Nat Commun, 5:3849, 2014 : PubMed ESTHER: Zhang_2014_Nat.Commun_5_3849 PubMedSearch: Zhang 2014 Nat.Commun 5 3849 PubMedID: 24846013 Gene_locus related to this paper: ustvr-a0a063bxn3 Abstract Ustilaginoidea virens (Cooke) Takah is an ascomycetous fungus that causes rice false smut, a devastating emerging disease worldwide. Here we report a 39.4 Mb draft genome sequence of U. virens that encodes 8,426 predicted genes. The genome has ~25% repetitive sequences that have been affected by repeat-induced point mutations. Evolutionarily, U. virens is close to the entomopathogenic Metarhizium spp., suggesting potential host jumping across kingdoms. U. virens possesses reduced gene inventories for polysaccharide degradation, nutrient uptake and secondary metabolism, which may result from adaptations to the specific floret infection and biotrophic lifestyles. Consistent with their potential roles in pathogenicity, genes for secreted proteins and secondary metabolism and the pathogen-host interaction database genes are highly enriched in the transcriptome during early infection. We further show that 18 candidate effectors can suppress plant hypersensitive responses. Together, our analyses offer new insights into molecular mechanisms of evolution, biotrophy and pathogenesis of U. virens. Title: Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK and Ciuffetti LM <16 more author(s)> Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK, Henrissat B, Holman WH, Kodira CD, Martin J, Oliver RP, Robbertse B, Schackwitz W, Schwartz DC, Spatafora JW, Turgeon BG, Yandava C, Young S, Zhou S, Zeng Q, Grigoriev IV, Ma LJ, Ciuffetti LM (- 16) Ref: G3 (Bethesda), 3:41, 2013 : PubMed ESTHER: Manning_2013_G3.(Bethesda)_3_41 PubMedSearch: Manning 2013 G3.(Bethesda) 3 41 PubMedID: 23316438 Gene_locus related to this paper: pyrtr-b2vxe8, pyrtr-b2vvm1, pyrtr-b2vzr5, pyrtr-b2vu22, pyrtr-kex1 Abstract Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes. Title: Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses O'Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, Damm U, Buiate EA, Epstein L and Vaillancourt LJ <57 more author(s)> O'Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, Damm U, Buiate EA, Epstein L, Alkan N, Altmuller J, Alvarado-Balderrama L, Bauser CA, Becker C, Birren BW, Chen Z, Choi J, Crouch JA, Duvick JP, Farman MA, Gan P, Heiman D, Henrissat B, Howard RJ, Kabbage M, Koch C, Kracher B, Kubo Y, Law AD, Lebrun MH, Lee YH, Miyara I, Moore N, Neumann U, Nordstrom K, Panaccione DG, Panstruga R, Place M, Proctor RH, Prusky D, Rech G, Reinhardt R, Rollins JA, Rounsley S, Schardl CL, Schwartz DC, Shenoy N, Shirasu K, Sikhakolli UR, Stuber K, Sukno SA, Sweigard JA, Takano Y, Takahara H, Trail F, van der Does HC, Voll LM, Will I, Young S, Zeng Q, Zhang J, Zhou S, Dickman MB, Schulze-Lefert P, Ver Loren van Themaat E, Ma LJ, Vaillancourt LJ (- 57) Ref: Nat Genet, 44:1060, 2012 : PubMed ESTHER: O'Connell_2012_Nat.Genet_44_1060 PubMedSearch: O'Connell 2012 Nat.Genet 44 1060 PubMedID: 22885923 Gene_locus related to this paper: colgm-kex1, colhi-h1vve5, colhi-h1vkk5, colgm-e3qtg4, colhi-h1vbq5, colgm-e3qyh7, colgm-e3q7u5, colhi-h1vs61, colgm-e3qip4, colgm-e3qv97, colhi-h1v665, colgm-e3qky4, colhi-h1vd91, colhi-h1uvl1, colhi-h1v7k5, colgm-e3qu96, colhi-h1vhh1, colhi-h1v638, colhi-h1vcz3, colgm-e3qwt6, colgm-e3q3z6, colhi-h1vmh6, colgm-e3qqq8, colhi-h1v0e8, colgm-e3qyt9, colgm-e3qby6, colgm-e3qsm5, colgm-e3q6f6, colgm-e3qwt4, colgm-e3qb89, colhi-h1vh96, colgm-e3qwz9, colgm-e3qbd3, colgm-e3qtz0, colhi-h1w5n4, colgm-e3q7y3, colgm-e3qpz1, colhi-h1v2e4, colgm-e3qux5, colgm-e3qx16, colgm-cbpya Abstract Colletotrichum species are fungal pathogens that devastate crop plants worldwide. Host infection involves the differentiation of specialized cell types that are associated with penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). We report here genome and transcriptome analyses of Colletotrichum higginsianum infecting Arabidopsis thaliana and Colletotrichum graminicola infecting maize. Comparative genomics showed that both fungi have large sets of pathogenicity-related genes, but families of genes encoding secreted effectors, pectin-degrading enzymes, secondary metabolism enzymes, transporters and peptidases are expanded in C. higginsianum. Genome-wide expression profiling revealed that these genes are transcribed in successive waves that are linked to pathogenic transitions: effectors and secondary metabolism enzymes are induced before penetration and during biotrophy, whereas most hydrolases and transporters are upregulated later, at the switch to necrotrophy. Our findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types. Title: Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis Desjardins CA, Champion MD, Holder JW, Muszewska A, Goldberg J, Bailao AM, Brigido MM, Ferreira ME, Garcia AM and Cuomo CA <32 more author(s)> Desjardins CA, Champion MD, Holder JW, Muszewska A, Goldberg J, Bailao AM, Brigido MM, Ferreira ME, Garcia AM, Grynberg M, Gujja S, Heiman DI, Henn MR, Kodira CD, Leon-Narvaez H, Longo LV, Ma LJ, Malavazi I, Matsuo AL, Morais FV, Pereira M, Rodriguez-Brito S, Sakthikumar S, Salem-Izacc SM, Sykes SM, Teixeira MM, Vallejo MC, Walter ME, Yandava C, Young S, Zeng Q, Zucker J, Felipe MS, Goldman GH, Haas BJ, McEwen JG, Nino-Vega G, Puccia R, San-Blas G, Soares CMF, Birren BW, Cuomo CA (- 32) Ref: PLoS Genet, 7:e1002345, 2011 : PubMed ESTHER: Desjardins_2011_PLoS.Genet_7_E1002345 PubMedSearch: Desjardins 2011 PLoS.Genet 7 E1002345 PubMedID: 22046142 Gene_locus related to this paper: parbd-c1gc95, parbp-c0s0d7, parbp-c0s257, parbd-c1g8z9, parba-c1grf0, parbp-c0s816, parbp-c0s5g4, parbd-c1g5f5, parbd-c1fzf9, parba-kex1, parbd-kex1, parbp-kex1, parba-cbpya, parbp-cbpya Abstract Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, is coupled with a thermally regulated transition from a soil-dwelling filamentous form to a yeast-like pathogenic form. To better understand the genetic basis of growth and pathogenicity in Paracoccidioides, we sequenced the genomes of two strains of Paracoccidioides brasiliensis (Pb03 and Pb18) and one strain of Paracoccidioides lutzii (Pb01). These genomes range in size from 29.1 Mb to 32.9 Mb and encode 7,610 to 8,130 genes. To enable genetic studies, we mapped 94% of the P. brasiliensis Pb18 assembly onto five chromosomes. We characterized gene family content across Onygenales and related fungi, and within Paracoccidioides we found expansions of the fungal-specific kinase family FunK1. Additionally, the Onygenales have lost many genes involved in carbohydrate metabolism and fewer genes involved in protein metabolism, resulting in a higher ratio of proteases to carbohydrate active enzymes in the Onygenales than their relatives. To determine if gene content correlated with growth on different substrates, we screened the non-pathogenic onygenale Uncinocarpus reesii, which has orthologs for 91% of Paracoccidioides metabolic genes, for growth on 190 carbon sources. U. reesii showed growth on a limited range of carbohydrates, primarily basic plant sugars and cell wall components; this suggests that Onygenales, including dimorphic fungi, can degrade cellulosic plant material in the soil. In addition, U. reesii grew on gelatin and a wide range of dipeptides and amino acids, indicating a preference for proteinaceous growth substrates over carbohydrates, which may enable these fungi to also degrade animal biomass. These capabilities for degrading plant and animal substrates suggest a duality in lifestyle that could enable pathogenic species of Onygenales to transfer from soil to animal hosts. Title: Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum Gao Q, Jin K, Ying SH, Zhang Y, Xiao G, Shang Y, Duan Z, Hu X, Xie XQ and Wang C <14 more author(s)> Gao Q, Jin K, Ying SH, Zhang Y, Xiao G, Shang Y, Duan Z, Hu X, Xie XQ, Zhou G, Peng G, Luo Z, Huang W, Wang B, Fang W, Wang S, Zhong Y, Ma LJ, St Leger RJ, Zhao GP, Pei Y, Feng MG, Xia Y, Wang C (- 14) Ref: PLoS Genet, 7:e1001264, 2011 : PubMed ESTHER: Gao_2011_PLoS.Genet_7_E1001264 PubMedSearch: Gao 2011 PLoS.Genet 7 E1001264 PubMedID: 21253567 Gene_locus related to this paper: metaq-dapb, metaq-e9dr02, metaq-e9dr46, metaq-e9dx32, metaq-e9dy00, metaq-e9e6i5, metaq-e9e332, metaq-e9e873, metaq-e9eaq4, metaq-e9ebs3, metaq-e9ebt3, metaq-e9edi2, metaq-e9edr0, metaq-e9ee29, metaq-e9eej3, metaq-e9ef60, metaq-e9ef98, metaq-e9efc1, metaq-e9eg97, metaq-e9egz7, metaq-kex1, metar-dapb, metar-e9ej81, metar-e9ejw6, metar-e9ek06, metar-e9eka7, metar-e9eku9, metar-e9em68, metar-e9emd0, metar-e9enf9, metar-e9eny8, metar-e9ep20, metar-e9ep60, metar-e9eqh0, metar-e9etb2, metar-e9etp6, metar-e9euh9, metar-e9ey62, metar-e9eyx6, metar-e9ezk2, metar-e9f3f2, metar-e9f3j3, metar-e9f3l3, metar-e9f3z5, metar-e9f6q5, metar-e9f6t6, metar-e9f7y7, metar-e9f9h2, metar-e9f029, metar-e9f205, metar-e9f721, metar-e9fa63, metar-e9fab1, metar-e9fas3, metar-e9fbn5, metar-e9fbt1, metar-e9fd34, metaq-e9eej8, metaq-e9dx35, metar-e9f3e9, metar-e9f0w8, metan-a0a086npb7, 9hypo-a0a014p983, metan-a0a086nhe0, 9hypo-a0a0a1v7e9, metaq-e9e0y0, metan-a0a0d9pev7, metaq-e9edt7, metra-e9ewg3, metra-pks2, metaf-pks1, metaq-pks2 Abstract Metarhizium spp. are being used as environmentally friendly alternatives to chemical insecticides, as model systems for studying insect-fungus interactions, and as a resource of genes for biotechnology. We present a comparative analysis of the genome sequences of the broad-spectrum insect pathogen Metarhizium anisopliae and the acridid-specific M. acridum. Whole-genome analyses indicate that the genome structures of these two species are highly syntenic and suggest that the genus Metarhizium evolved from plant endophytes or pathogens. Both M. anisopliae and M. acridum have a strikingly larger proportion of genes encoding secreted proteins than other fungi, while ~30% of these have no functionally characterized homologs, suggesting hitherto unsuspected interactions between fungal pathogens and insects. The analysis of transposase genes provided evidence of repeat-induced point mutations occurring in M. acridum but not in M. anisopliae. With the help of pathogen-host interaction gene database, ~16% of Metarhizium genes were identified that are similar to experimentally verified genes involved in pathogenicity in other fungi, particularly plant pathogens. However, relative to M. acridum, M. anisopliae has evolved with many expanded gene families of proteases, chitinases, cytochrome P450s, polyketide synthases, and nonribosomal peptide synthetases for cuticle-degradation, detoxification, and toxin biosynthesis that may facilitate its ability to adapt to heterogeneous environments. Transcriptional analysis of both fungi during early infection processes provided further insights into the genes and pathways involved in infectivity and specificity. Of particular note, M. acridum transcribed distinct G-protein coupled receptors on cuticles from locusts (the natural hosts) and cockroaches, whereas M. anisopliae transcribed the same receptor on both hosts. This study will facilitate the identification of virulence genes and the development of improved biocontrol strains with customized properties. Title: Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens Klosterman SJ, Subbarao KV, Kang S, Veronese P, Gold SE, Thomma BP, Chen Z, Henrissat B, Lee YH and Ma LJ <19 more author(s)> Klosterman SJ, Subbarao KV, Kang S, Veronese P, Gold SE, Thomma BP, Chen Z, Henrissat B, Lee YH, Park J, Garcia-Pedrajas MD, Barbara DJ, Anchieta A, de Jonge R, Santhanam P, Maruthachalam K, Atallah Z, Amyotte SG, Paz Z, Inderbitzin P, Hayes RJ, Heiman DI, Young S, Zeng Q, Engels R, Galagan J, Cuomo CA, Dobinson KF, Ma LJ (- 19) Ref: PLoS Pathog, 7:e1002137, 2011 : PubMed ESTHER: Klosterman_2011_PLoS.Pathog_7_E1002137 PubMedSearch: Klosterman 2011 PLoS.Pathog 7 E1002137 PubMedID: 21829347 Gene_locus related to this paper: vera1-c9srn2, vera1-c9sn46, verdv-g2wq49, verdv-g2xca2, vera1-c9sea3, verdv-g2wzn4, vera1-c9sek2, verdv-g2wym5, verdv-g2x5f3, vera1-c9sx20, vera1-c9sw01, verdv-g2x1l1, verdv-g2wuv4, verdv-g2xaw5, verdv-g2wsb2, verdv-g2wty6, vera1-c9si59, verdv-g2xdu9, vera1-c9s818, verdv-g2xdr1, verdv-g2wsw7, verdv-g2wvq8, 9pezi-a0a0g4li73, vera1-kex1, verdv-g2x8m5 Abstract The vascular wilt fungi Verticillium dahliae and V. albo-atrum infect over 200 plant species, causing billions of dollars in annual crop losses. The characteristic wilt symptoms are a result of colonization and proliferation of the pathogens in the xylem vessels, which undergo fluctuations in osmolarity. To gain insights into the mechanisms that confer the organisms' pathogenicity and enable them to proliferate in the unique ecological niche of the plant vascular system, we sequenced the genomes of V. dahliae and V. albo-atrum and compared them to each other, and to the genome of Fusarium oxysporum, another fungal wilt pathogen. Our analyses identified a set of proteins that are shared among all three wilt pathogens, and present in few other fungal species. One of these is a homolog of a bacterial glucosyltransferase that synthesizes virulence-related osmoregulated periplasmic glucans in bacteria. Pathogenicity tests of the corresponding V. dahliae glucosyltransferase gene deletion mutants indicate that the gene is required for full virulence in the Australian tobacco species Nicotiana benthamiana. Compared to other fungi, the two sequenced Verticillium genomes encode more pectin-degrading enzymes and other carbohydrate-active enzymes, suggesting an extraordinary capacity to degrade plant pectin barricades. The high level of synteny between the two Verticillium assemblies highlighted four flexible genomic islands in V. dahliae that are enriched for transposable elements, and contain duplicated genes and genes that are important in signaling/transcriptional regulation and iron/lipid metabolism. Coupled with an enhanced capacity to degrade plant materials, these genomic islands may contribute to the expanded genetic diversity and virulence of V. dahliae, the primary causal agent of Verticillium wilts. Significantly, our study reveals insights into the genetic mechanisms of niche adaptation of fungal wilt pathogens, advances our understanding of the evolution and development of their pathogenesis, and sheds light on potential avenues for the development of novel disease management strategies to combat destructive wilt diseases. Title: Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M and Rep M <53 more author(s)> Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RA, Chapman S, Coulson R, Coutinho PM, Danchin EG, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M (- 53) Ref: Nature, 464:367, 2010 : PubMed ESTHER: Ma_2010_Nature_464_367 PubMedSearch: Ma 2010 Nature 464 367 PubMedID: 20237561 Gene_locus related to this paper: fusox-a0a1d3s5h0, gibf5-fus2, fusof-f9f2k2, fusof-f9f3l6, fusof-f9f6t8, fusof-f9f6v2, fusof-f9f132, fusof-f9f781, fusof-f9fd72, fusof-f9fd90, fusof-f9fem0, fusof-f9fhk2, fusof-f9fj19, fusof-f9fj20, fusof-f9fki8, fusof-f9fmx2, fusof-f9fnt4, fusof-f9fpy4, fusof-f9fvs6, fusof-f9fwu0, fusof-f9fxz4, fusof-f9fzy5, fusof-f9g2a2, fusof-f9g3b1, fusof-f9g5h7, fusof-f9g6e6, fusof-f9g6y7, fusof-f9g7b0, fusof-f9g797, fusof-f9g972, fusof-f9ga50, fusof-f9gck4, fusof-f9gd15, 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-q4huy1, gibze-i1rg17, fuso4-j9mvr9, fuso4-j9ngs6, fuso4-j9niq8, fuso4-j9nqm2, gibze-i1rb76, gibze-i1s1m7, gibze-i1s3z6, gibze-i1rd78, gibze-i1rgl9, gibze-i1rjp7, gibze-i1s1q6, gibze-i1ri35, gibze-i1rf76, gibze-i1rhp3, fusc1-n4uj11, fusc4-n1s9p6, gibf5-s0dqr2, gibm7-w7n1b5, fusof-f9g6q0, gibm7-w7n497, fusox-x0bme4, gibm7-w7mcf8, gibm7-w7mak5, fusox-x0a2c5, gibm7-w7mum7, fusox-w9iyc7, gibm7-w7maw6, gibm7-w7msi0, gibm7-w7luf0, gibm7-w7msa3, gibm7-w7mna8, gibm7-w7n8b7, gibm7-w7n564, fusox-w9jpi0, gibm7-w7ngc3, gibm7-w7m4v6, gibm7-w7m4v2, gibm7-w7lt61, gibm7-w7mly6, gibm7-w7ncn3, fusox-w9ibd7, fusof-f9fnm6, gibm7-w7n526, gibza-a0a016pda4, gibza-a0a016pl96, gibm7-w7muq1, fusof-f9gfd3, gibm7-w7mt52, gibze-i1rjb5, gibf5-s0ehu3, fusox-w9hvf0, gibze-i1rkc4, gibm7-w7mv30, gibze-a0a1c3ylb1, fuso4-a0a0c4diy4, gibm7-w7n4n0, gibze-gra11, gibze-fsl2, gibf5-fub4, gibf5-fub5, gibf5-fus5, gibm7-dlh1 Abstract 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. Title: Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus) Stajich JE, Wilke SK, Ahren D, Au CH, Birren BW, Borodovsky M, Burns C, Canback B, Casselton LA and Pukkila PJ <39 more author(s)> Stajich JE, Wilke SK, Ahren D, Au CH, Birren BW, Borodovsky M, Burns C, Canback B, Casselton LA, Cheng CK, Deng J, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigo R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kues U, Kupfer D, Kwan HS, Lomsadze A, Li W, Lilly WW, Ma LJ, Mackey AJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, Rehmeyer CJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R, Vision TJ, Zeng Q, Zolan ME, Pukkila PJ (- 39) Ref: Proc Natl Acad Sci U S A, 107:11889, 2010 : PubMed ESTHER: Stajich_2010_Proc.Natl.Acad.Sci.U.S.A_107_11889 PubMedSearch: Stajich 2010 Proc.Natl.Acad.Sci.U.S.A 107 11889 PubMedID: 20547848 Gene_locus related to this paper: copc7-a8n2b8, copc7-a8n3e0, copc7-a8n3e1, copc7-a8n6a5, copc7-a8n8h4, copc7-a8n702, copc7-a8n941, copc7-a8nkc7, copc7-a8nll5, copc7-a8nll6, copc7-a8nqf4, copc7-a8nqg3, copc7-a8nqv8, copc7-a8nvb5, copc7-a8nwm2, copc7-a8nz18, copc7-a8p0p4, copc7-d6rlx1, copc7-d6rnh7, copc7-kex1, copci-b9u444, copc7-a8nb05, copc7-a8nha0, copci-b9u443, copc7-a8nq30, copc7-a8nh79, copc7-d6rm78, copc7-a8nzs7, copc7-axe1 Abstract The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi. Title: The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ and Vanetten HD <29 more 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 (- 29) Ref: PLoS Genet, 5:e1000618, 2009 : PubMed 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 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. Title: Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication Ma LJ, Ibrahim AS, Skory C, Grabherr MG, Burger G, Butler M, Elias M, Idnurm A, Lang BF and Wickes BL <22 more author(s)> Ma LJ, Ibrahim AS, Skory C, Grabherr MG, Burger G, Butler M, Elias M, Idnurm A, Lang BF, Sone T, Abe A, Calvo SE, Corrochano LM, Engels R, Fu J, Hansberg W, Kim JM, Kodira CD, Koehrsen MJ, Liu B, Miranda-Saavedra D, O'Leary S, Ortiz-Castellanos L, Poulter R, Rodriguez-Romero J, Ruiz-Herrera J, Shen YQ, Zeng Q, Galagan J, Birren BW, Cuomo CA, Wickes BL (- 22) Ref: PLoS Genet, 5:e1000549, 2009 : PubMed ESTHER: Ma_2009_PLoS.Genet_5_E1000549 PubMedSearch: Ma 2009 PLoS.Genet 5 E1000549 PubMedID: 19578406 Abstract Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid angioinvasive growth with an overall mortality rate that exceeds 50%. As a representative of the paraphyletic basal group of the fungal kingdom called "zygomycetes," R. oryzae is also used as a model to study fungal evolution. Here we report the genome sequence of R. oryzae strain 99-880, isolated from a fatal case of mucormycosis. The highly repetitive 45.3 Mb genome assembly contains abundant transposable elements (TEs), comprising approximately 20% of the genome. We predicted 13,895 protein-coding genes not overlapping TEs, many of which are paralogous gene pairs. The order and genomic arrangement of the duplicated gene pairs and their common phylogenetic origin provide evidence for an ancestral whole-genome duplication (WGD) event. The WGD resulted in the duplication of nearly all subunits of the protein complexes associated with respiratory electron transport chains, the V-ATPase, and the ubiquitin-proteasome systems. The WGD, together with recent gene duplications, resulted in the expansion of multiple gene families related to cell growth and signal transduction, as well as secreted aspartic protease and subtilase protein families, which are known fungal virulence factors. The duplication of the ergosterol biosynthetic pathway, especially the major azole target, lanosterol 14alpha-demethylase (ERG11), could contribute to the variable responses of R. oryzae to different azole drugs, including voriconazole and posaconazole. Expanded families of cell-wall synthesis enzymes, essential for fungal cell integrity but absent in mammalian hosts, reveal potential targets for novel and R. oryzae-specific diagnostic and therapeutic treatments. Title: The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization Cuomo CA, Guldener U, Xu JR, Trail F, Turgeon BG, Di Pietro A, Walton JD, Ma LJ, Baker SE and Kistler HC <35 more 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 (- 35) Ref: Science, 317:1400, 2007 : PubMed 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 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. Title: Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis Kamper J, Kahmann R, Bolker M, Ma LJ, Brefort T, Saville BJ, Banuett F, Kronstad JW, Gold SE and Birren BW <70 more 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 (- 70) Ref: Nature, 444:97, 2006 : PubMed 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 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. Title: The genome sequence of the rice blast fungus Magnaporthe grisea Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ, Thon M, Kulkarni R, Xu JR and Birren BW <25 more 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 (- 25) Ref: Nature, 434:980, 2005 : PubMed 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 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. Title: Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Basturkmen M, Spevak CC and Birren BW <40 more author(s)> Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Basturkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, d'Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Penalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW (- 40) Ref: Nature, 438:1105, 2005 : PubMed ESTHER: Galagan_2005_Nature_438_1105 PubMedSearch: Galagan 2005 Nature 438 1105 PubMedID: 16372000 Gene_locus related to this paper: emeni-axe1, emeni-BST1, emeni-c8vrl3, emeni-CUTI3, emeni-faec, emeni-ppme1, emeni-q5aqv0, emeni-q5ara9, emeni-q5av79, emeni-q5avd3, emeni-q5awc7, emeni-q5awq3, emeni-q5awu9, emeni-q5aww7, emeni-q5ax50, emeni-q5ay37, emeni-q5ay57, emeni-q5ayk9, emeni-q5az32, emeni-q5azl2, emeni-q5azp1, emeni-q5b1v2, emeni-q5b2c1, emeni-q5b3d2, emeni-q5b5j7, emeni-q5b7i6, emeni-q5b8p6, emeni-q5b9e7, emeni-q5b246, emeni-q5b446, emeni-q5b602, emeni-q5b938, emeni-q5ba78, emeni-q5bad3, emeni-q5bar0, emeni-q5bcd1, emeni-q5bcd2, emeni-q5bcf8, emeni-q5bdr0, emeni-q5beh9, emeni-q5bgk7, emeni-q7si80, emeni-q5bdv9, emeni-c8vu15, 9euro-a0a3d8t644, emeni-q5b719, emeni-q5ax97, emeni-tdia, emeni-afoc, emeni-dbae Abstract The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation. Title: The genome sequence of the filamentous fungus Neurospora crassa Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S and Birren B <67 more author(s)> Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B (- 67) Ref: Nature, 422:859, 2003 : PubMed ESTHER: Galagan_2003_Nature_422_859 PubMedSearch: Galagan 2003 Nature 422 859 PubMedID: 12712197 Gene_locus related to this paper: neucr-5E6.090, neucr-64C2.080, neucr-90C4.300, neucr-a7uw78, neucr-a7uwh6, neucr-a7uwy7, neucr-apth1, neucr-ATG15, neucr-B7H23.190, neucr-B11O8.160, neucr-B13B3.090, neucr-B14D6.130, neucr-B18E6.050, neucr-B19A17.360, neucr-B23G1.090, neucr-CBPYA, neucr-MET5, neucr-NCU00292.1, neucr-NCU00350.1, neucr-NCU00536.1, neucr-NCU00825.1, neucr-NCU02148.1, neucr-NCU02679.1, neucr-NCU02904.1, neucr-NCU02924.1, neucr-NCU03158.1, neucr-NCU04930.1, neucr-NCU06332.1, neucr-NCU06573.1, neucr-NCU07081.1, neucr-NCU07415.1, neucr-NCU07909.1, neucr-NCU08752.1, neucr-NCU09575.1, neucr-NCU10022.1, neucr-ppme1, neucr-q6mfs7, neucr-q7rxb4, neucr-q7rxv5, neucr-q7ry06, neucr-q7ryd2, neucr-q7rzk2, neucr-q7s0g7, neucr-q7s1x0, neucr-q7s2b3, neucr-q7s2c5, neucr-q7s2p4, neucr-q7s2u9, neucr-q7s3c6, neucr-q7s3c8, neucr-q7s3m2, neucr-q7s4e3, neucr-q7s4f8, neucr-q7s4j4, neucr-q7s5d6, neucr-q7s5m2, neucr-q7s5v8, neucr-q7s6c5, neucr-q7s8h2, neucr-q7s070, neucr-q7s082, neucr-q7s134, neucr-q7s216, neucr-q7s259, neucr-q7s260, neucr-q7s283, neucr-q7s512, neucr-q7s736, neucr-q7s828, neucr-q7s897, neucr-q7sbf9, neucr-q7sbn0, neucr-q7scr4, neucr-q7sdw5, neucr-q7sdx9, neucr-q7se51, neucr-q7sea3, neucr-q7sez8, neucr-q7sff7, neucr-q7sga3, neucr-q7sgj0, neucr-q7sgp3, neucr-q7sha3, neucr-q7sha5, neucr-q7shu8, neucr-q9p6a7, neucr-q872l1, neucr-f5hbr2, neucr-q7ry64 Abstract Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes--more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes. | |||||||
|
