Author Report for: Birren BWNo contact information in database for Birren BW
Ma L, Chen Z, Huang da W, Kutty G, Ishihara M, Wang H, Abouelleil A, Bishop L, Davey E and Kovacs JA <34 more author(s)> Ma L, Chen Z, Huang da W, Kutty G, Ishihara M, Wang H, Abouelleil A, Bishop L, Davey E, Deng R, Deng X, Fan L, Fantoni G, FitzGerald M, Gogineni E, Goldberg JM, Handley G, Hu X, Huber C, Jiao X, Jones K, Levin JZ, Liu Y, Macdonald P, Melnikov A, Raley C, Sassi M, Sherman BT, Song X, Sykes S, Tran B, Walsh L, Xia Y, Yang J, Young S, Zeng Q, Zheng X, Stephens R, Nusbaum C, Birren BW, Azadi P, Lempicki RA, Cuomo CA, Kovacs JA (- 34) Ref: Nat Commun, 7:10740, 2016 : PubMed ESTHER: Ma_2016_Nat.Commun_7_10740 PubMedSearch: Ma 2016 Nat.Commun 7 10740 PubMedID: 26899007 Gene_locus related to this paper: pnec8-a0a0w4zi95, pnemu-m7nra0, pnej8-l0pgn2, pnemu-m7nsb0 Abstract Pneumocystis jirovecii is a major cause of life-threatening pneumonia in immunosuppressed patients including transplant recipients and those with HIV/AIDS, yet surprisingly little is known about the biology of this fungal pathogen. Here we report near complete genome assemblies for three Pneumocystis species that infect humans, rats and mice. Pneumocystis genomes are highly compact relative to other fungi, with substantial reductions of ribosomal RNA genes, transporters, transcription factors and many metabolic pathways, but contain expansions of surface proteins, especially a unique and complex surface glycoprotein superfamily, as well as proteases and RNA processing proteins. Unexpectedly, the key fungal cell wall components chitin and outer chain N-mannans are absent, based on genome content and experimental validation. Our findings suggest that Pneumocystis has developed unique mechanisms of adaptation to life exclusively in mammalian hosts, including dependence on the lungs for gas and nutrients and highly efficient strategies to escape both host innate and acquired immune defenses. 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 the Pathogenic Fungus Sporothrix schenckii (ATCC 58251) Cuomo CA, Rodriguez-Del Valle N, Perez-Sanchez L, Abouelleil A, Goldberg J, Young S, Zeng Q, Birren BW Ref: Genome Announc, 2:E0044614, 2014 : PubMed ESTHER: Cuomo_2014_Genome.Announc_2_E00446 PubMedSearch: Cuomo 2014 Genome.Announc 2 E00446 PubMedID: 24855299 Gene_locus related to this paper: spos1-u7q5l6, spos1-u7phh2, spos1-u7pxz2, spos1-u7q332, spos1-u7pw92 Abstract Sporothrix schenckii is a pathogenic dimorphic fungus that grows as a yeast and as mycelia. This species is the causative agent of sporotrichosis, typically a skin infection. We report the genome sequence of S. schenckii, which will facilitate the study of this fungus and of the Sporothrix schenckii group. Title: Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011 Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, FitzGerald M, Godfrey P, Haas BJ, Murphy CI and Hanage WP <24 more author(s)> Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, FitzGerald M, Godfrey P, Haas BJ, Murphy CI, Russ C, Sykes S, Walker BJ, Wortman JR, Young S, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, Desmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-Moller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP (- 24) Ref: Proc Natl Acad Sci U S A, 109:3065, 2012 : PubMed ESTHER: Grad_2012_Proc.Natl.Acad.Sci.U.S.A_109_3065 PubMedSearch: Grad 2012 Proc.Natl.Acad.Sci.U.S.A 109 3065 PubMedID: 22315421 Gene_locus related to this paper: ecoli-fes, ecoli-MCMK, ecoli-yaim, ecoli-ycfp, ecoli-YFBB, ecoli-yhet, ecoli-yiel, ecoli-yqia, ecoli-YfhR Abstract The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May-July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak. Title: Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection Martinez DA, Oliver BG, Graser Y, Goldberg JM, Li W, Martinez-Rossi NM, Monod M, Shelest E, Barton RC and White TC <18 more author(s)> Martinez DA, Oliver BG, Graser Y, Goldberg JM, Li W, Martinez-Rossi NM, Monod M, Shelest E, Barton RC, Birch E, Brakhage AA, Chen Z, Gurr SJ, Heiman D, Heitman J, Kosti I, Rossi A, Saif S, Samalova M, Saunders CW, Shea T, Summerbell RC, Xu J, Young S, Zeng Q, Birren BW, Cuomo CA, White TC (- 18) Ref: MBio, 3:e00259, 2012 : PubMed ESTHER: Martinez_2012_MBio_3_e00259 PubMedSearch: Martinez 2012 MBio 3 e00259 PubMedID: 22951933 Gene_locus related to this paper: artgp-e4uup9, artgp-e4v450, artgp-e5qzf5, artgp-e5r1t8, artoc-c5fc55, artoc-c5fds1, artoc-c5fig8, artoc-c5fj58, artoc-c5fme4, artoc-c5fva9, triec-f2ph15, triec-f2plk8, triec-f2pwm2, trirc-f2sf42, trirc-f2sn39, trirc-f2srv5, trirc-f2sy06, triru-q5j6j0, triru-SCPB, triru-SPCA, trit1-f2rna8, trit1-f2s2t8, trivh-d4dbr9, artbc-d4avu9, artoc-c5fsf7, artgp-e4unv7, artoc-c5g0v3, triec-f2pub4, triec-f2pi43, artgp-e4v6t4, trit1-f2s3n3, artoc-c5fnl7, artgp-e4upq1, artgp-e4uzl7, triec-f2pp24, triru-a0a022u299, 9euro-a0a059jk56, artoc-c5fu24, artoc-c5fic4, artgp-e4uza8, triec-f2pqf3, artgp-e4uv28, artoc-c5fiv8, triru-a0a022w2d0, artgp-e4uvk8, triru-a0a178f289, artoc-c5fyj1, artoc-cbpya, artoc-kex1 Abstract The major cause of athlete's foot is Trichophyton rubrum, a dermatophyte or fungal pathogen of human skin. To facilitate molecular analyses of the dermatophytes, we sequenced T. rubrum and four related species, Trichophyton tonsurans, Trichophyton equinum, Microsporum canis, and Microsporum gypseum. These species differ in host range, mating, and disease progression. The dermatophyte genomes are highly colinear yet contain gene family expansions not found in other human-associated fungi. Dermatophyte genomes are enriched for gene families containing the LysM domain, which binds chitin and potentially related carbohydrates. These LysM domains differ in sequence from those in other species in regions of the peptide that could affect substrate binding. The dermatophytes also encode novel sets of fungus-specific kinases with unknown specificity, including nonfunctional pseudokinases, which may inhibit phosphorylation by competing for kinase sites within substrates, acting as allosteric effectors, or acting as scaffolds for signaling. The dermatophytes are also enriched for a large number of enzymes that synthesize secondary metabolites, including dermatophyte-specific genes that could synthesize novel compounds. Finally, dermatophytes are enriched in several classes of proteases that are necessary for fungal growth and nutrient acquisition on keratinized tissues. Despite differences in mating ability, genes involved in mating and meiosis are conserved across species, suggesting the possibility of cryptic mating in species where it has not been previously detected. These genome analyses identify gene families that are important to our understanding of how dermatophytes cause chronic infections, how they interact with epithelial cells, and how they respond to the host immune response. 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, colgm-e3q8b3 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: Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts D'Souza CA, Kronstad JW, Taylor G, Warren R, Yuen M, Hu G, Jung WH, Sham A, Kidd SE and Cuomo CA <31 more author(s)> D'Souza CA, Kronstad JW, Taylor G, Warren R, Yuen M, Hu G, Jung WH, Sham A, Kidd SE, Tangen K, Lee N, Zeilmaker T, Sawkins J, McVicker G, Shah S, Gnerre S, Griggs A, Zeng Q, Bartlett K, Li W, Wang X, Heitman J, Stajich JE, Fraser JA, Meyer W, Carter D, Schein J, Krzywinski M, Kwon-Chung KJ, Varma A, Wang J, Brunham R, Fyfe M, Ouellette BF, Siddiqui A, Marra M, Jones S, Holt R, Birren BW, Galagan JE, Cuomo CA (- 31) Ref: MBio, 2:e00342, 2011 : PubMed ESTHER: D'Souza_2011_MBio_2_e00342 PubMedSearch: D'Souza 2011 MBio 2 e00342 PubMedID: 21304167 Gene_locus related to this paper: crygw-e6qy09, crygw-e6r2n3, crygw-e6r7g6, crygw-e6rbd6, crygw-e6rcm3, crygw-e6rg44, cryne-q5ka03, cryne-q5km63, cryne-q5knq0, cryne-q55va3, crynj-q5kpe0, crygr-a0a095cfy5, crygw-kex1 Abstract Cryptococcus gattii recently emerged as the causative agent of cryptococcosis in healthy individuals in western North America, despite previous characterization of the fungus as a pathogen in tropical or subtropical regions. As a foundation to study the genetics of virulence in this pathogen, we sequenced the genomes of a strain (WM276) representing the predominant global molecular type (VGI) and a clinical strain (R265) of the major genotype (VGIIa) causing disease in North America. We compared these C. gattii genomes with each other and with the genomes of representative strains of the two varieties of Cryptococcus neoformans that generally cause disease in immunocompromised people. Our comparisons included chromosome alignments, analysis of gene content and gene family evolution, and comparative genome hybridization (CGH). These studies revealed that the genomes of the two representative C. gattii strains (genotypes VGI and VGIIa) are colinear for the majority of chromosomes, with some minor rearrangements. However, multiortholog phylogenetic analysis and an evaluation of gene/sequence conservation support the existence of speciation within the C. gattii complex. More extensive chromosome rearrangements were observed upon comparison of the C. gattii and the C. neoformans genomes. Finally, CGH revealed considerable variation in clinical and environmental isolates as well as changes in chromosome copy numbers in C. gattii isolates displaying fluconazole heteroresistance. 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: High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)) Earl AM, Desjardins CA, Fitzgerald MG, Arachchi HM, Zeng Q, Mehta T, Griggs A, Birren BW, Toney NC and Butler WR <2 more author(s)> Earl AM, Desjardins CA, Fitzgerald MG, Arachchi HM, Zeng Q, Mehta T, Griggs A, Birren BW, Toney NC, Carr J, Posey J, Butler WR (- 2) Ref: Stand Genomic Sci, 5:389, 2011 : PubMed ESTHER: Earl_2011_Stand.Genomic.Sci_5_389 PubMedSearch: Earl 2011 Stand.Genomic.Sci 5 389 PubMedID: 22675588 Gene_locus related to this paper: 9acto-e5xtw5, 9acto-e5xpt7, 9acto-e5xpt8, 9acto-e5xue1, 9acto-e5xr49, 9actn-e5xql0 Abstract Segniliparus rugosus represents one of two species in the genus Segniliparus, the sole genus in the family Segniliparaceae. A unique and interesting feature of this family is the presence of extremely long carbon-chain length mycolic acids bound in the cell wall. S. rugosus is also a medically important species because it is an opportunistic pathogen associated with mammalian lung disease. This report represents the second species in the genus to have its genome sequenced. The 3,567,567 bp long genome with 3,516 protein-coding and 49 RNA genes is part of the NIH Roadmap for Medical Research, Human Microbiome Project. Title: Comparative functional genomics of the fission yeasts Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF and Nusbaum C <50 more author(s)> Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, Fitzgerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Muller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C (- 50) Ref: Science, 332:930, 2011 : PubMed ESTHER: Rhind_2011_Science_332_930 PubMedSearch: Rhind 2011 Science 332 930 PubMedID: 21511999 Gene_locus related to this paper: schjy-b6jxl8, schjy-b6k0k9, schjy-b6k7s4, schjy-b6k575, schcr-s9vnl9, schoy-s9q625, schjy-kex1, schpo-ykv6 Abstract The fission yeast clade--comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus--occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade. Title: Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, Whiston E, Hung CY, McMahan C, White J and Rounsley SD <19 more author(s)> Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, Whiston E, Hung CY, McMahan C, White J, Sykes S, Heiman D, Young S, Zeng Q, Abouelleil A, Aftuck L, Bessette D, Brown A, FitzGerald M, Lui A, Macdonald JP, Priest M, Orbach MJ, Galgiani JN, Kirkland TN, Cole GT, Birren BW, Henn MR, Taylor JW, Rounsley SD (- 19) Ref: Genome Res, 20:938, 2010 : PubMed ESTHER: Neafsey_2010_Genome.Res_20_938 PubMedSearch: Neafsey 2010 Genome.Res 20 938 PubMedID: 20516208 Gene_locus related to this paper: cocp7-c5p2u8, cocp7-c5p5s7, cocp7-c5pe69, cocp7-c5pf68, cocp7-c5pgk6, cocim-j3ka92, cocp7-c5phc6, cocps-e9d3i4, cocit-a0a0j8rde7, cocps-e9csw0, cocps-e9dgm8 Abstract We have sequenced the genomes of 18 isolates of the closely related human pathogenic fungi Coccidioides immitis and Coccidioides posadasii to more clearly elucidate population genomic structure, bringing the total number of sequenced genomes for each species to 10. Our data confirm earlier microsatellite-based findings that these species are genetically differentiated, but our population genomics approach reveals that hybridization and genetic introgression have recently occurred between the two species. The directionality of introgression is primarily from C. posadasii to C. immitis, and we find more than 800 genes exhibiting strong evidence of introgression in one or more sequenced isolates. We performed PCR-based sequencing of one region exhibiting introgression in 40 C. immitis isolates to confirm and better define the extent of gene flow between the species. We find more coding sequence than expected by chance in the introgressed regions, suggesting that natural selection may play a role in the observed genetic exchange. We find notable heterogeneity in repetitive sequence composition among the sequenced genomes and present the first detailed genome-wide profile of a repeat-induced point mutation (RIP) process distinctly different from what has been observed in Neurospora. We identify promiscuous HLA-I and HLA-II epitopes in both proteomes and discuss the possible implications of introgression and population genomic data for public health and vaccine candidate prioritization. This study highlights the importance of population genomic data for detecting subtle but potentially important phenomena such as introgression. Title: A catalog of reference genomes from the human microbiome Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E and Zhu D <73 more author(s)> Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, Fitzgerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D (- 73) Ref: Science, 328:994, 2010 : PubMed ESTHER: Nelson_2010_Science_328_994 PubMedSearch: Nelson 2010 Science 328 994 PubMedID: 20489017 Gene_locus related to this paper: strp2-q04l35, strpn-AXE1, strpn-pepx Abstract The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented. 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: Evolution of pathogenicity and sexual reproduction in eight Candida genomes Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A and Cuomo CA <41 more author(s)> Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA (- 41) Ref: Nature, 459:657, 2009 : PubMed ESTHER: Butler_2009_Nature_459_657 PubMedSearch: Butler 2009 Nature 459 657 PubMedID: 19465905 Gene_locus related to this paper: canal-ATG15, canal-bna7, canal-c4yl13, canal-LIP1, canal-LIP2, canal-LIP3, canal-LIP4, canal-LIP5, canal-LIP6, canal-LIP7, canal-LIP8, canal-LIP9, canal-LIP10, canal-ppme1, canal-q5a0c9, canal-q5a2i9, canal-q5a042, canal-q5ad17, canal-q5aeu3, canal-q5afp8, canal-q5ag57, canal-q5ai09, canal-q5ai12, canal-q5ajt3, canal-q5akz5, canal-q5apu4, canal-q59l46, canal-q59m48, canal-q59nw6, canal-q59u61, canal-q59u64, canal-q59vp0, canal-q59y97, canaw-c4ykb1, canaw-c4yrn6, canaw-c4yrn9, canaw-c4yrr3, canaw-c4yrv3, canaw-c4ys26, cantt-c5m3d7, cantt-c5m3y5, cantt-c5m4x0, cantt-c5m5e8, cantt-c5m5w2, cantt-c5m8s7, cantt-c5m9c2, cantt-c5m465, cantt-c5m751, cantt-c5m793, cantt-c5m893, cantt-c5ma78, cantt-c5mag0, cantt-c5mbb8, cantt-c5mc53, cantt-c5md87, cantt-c5mdy3, cantt-c5mey7, cantt-c5mfg0, cantt-c5mfh8, cantt-c5mg56, cantt-c5mgj0, cantt-c5mh75, cantt-c5mh80, cantt-c5mh89, cantt-c5mhh0, cantt-c5mhn5, cantt-c5mij5, cantt-c5min7, clal4-c4xvt8, clal4-c4xwy4, clal4-c4xy03, clal4-c4xyx9, clal4-c4xzz1, clal4-c4y3e1, clal4-c4y4f2, clal4-c4y4w8, clal4-c4y5j4, clal4-c4y5j9, clal4-c4y7z7, clal4-c4y8q1, clal4-c4y035, clal4-c4y481, clal4-c4y538, clal4-c4y898, clal4-c4yas2, clal4-c4yba6, clal4-c4yba7, clal4-c4yc85, lodel-a5drz3, lodel-a5ds97, lodel-a5dsc0, lodel-a5duu4, lodel-a5duy7, lodel-a5dv03, lodel-a5dv46, lodel-a5dw16, lodel-a5dwv7, lodel-a5dww6, lodel-a5dxf3, lodel-a5e0z5, lodel-a5e1c1, lodel-a5e1l4, lodel-a5e1p3, lodel-a5e2s1, lodel-a5e2t8, lodel-a5e2v2, lodel-a5e4u8, lodel-a5e5a9, lodel-a5e5k1, lodel-a5e5z7, lodel-a5e6w1, lodel-a5e028, lodel-atg15, lodel-kex1, picgu-a5d9u2, picgu-a5dav0, picgu-a5dbk0, picgu-a5dc45, picgu-a5dc73, picgu-a5dc74, picgu-a5dc75, picgu-a5ddt8, picgu-a5dev7, picgu-a5dh90, picgu-a5dhe3, picgu-a5di38, picgu-a5dj06, picgu-a5dkd8, picgu-a5dle9, picgu-a5dlj5, picgu-a5dm19, picgu-a5dn92, picgu-a5dnr3, picgu-a5dnt6, picgu-a5dqu5, picgu-a5dr14, picgu-a5drl3, picgu-atg15, picgu-bna7, picgu-a5d9q3, picgu-a5dag9, clal4-c4y5a2, clal4-c4y0l0, cantt-c5mcb1, clal4-c4y8j2, cantt-c5m494, clals-a0a202gac7, canal-hda1, picgu-a5dks8, lodel-a5drs6, canpc-g8bbk1, cantt-kex1, clal4-kex1, picgu-kex1 Abstract Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes. 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: Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE and Taylor JW <14 more author(s)> Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung CY, McMahan C, Muszewska A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, Taylor JW (- 14) Ref: Genome Res, 19:1722, 2009 : PubMed ESTHER: Sharpton_2009_Genome.Res_19_1722 PubMedSearch: Sharpton 2009 Genome.Res 19 1722 PubMedID: 19717792 Gene_locus related to this paper: ajecg-c0nbn5, ajecg-c0nbz4, ajecg-c0ndw0, ajecg-c0nqc6, ajecg-c0nst6, ajecg-c0ntx5, ajecg-c0nu33, ajecg-c0nzh6, ajecg-c0p0h0, ajech-c6h1y9, ajecn-a6qs62, ajecn-a6quy7, ajecn-a6r2c0, ajecn-a6r491, ajecn-a6r635, ajecn-a6rab7, ajecn-a6ram0, ajecn-a6rf08, ajecn-a6rf70, ajecn-atg15, ajecn-dapb, ajeds-c5jqx1, cocim-atg15, cocim-bst1, cocim-j3k8a1, cocp7-c5p0f2, cocp7-c5p0i6, cocp7-c5p1s3, cocp7-c5p1u2, cocp7-c5p2u8, cocp7-c5p4s8, cocp7-c5p4z1, cocp7-c5p5s7, cocp7-c5p129, cocp7-c5p172, cocp7-c5p250, cocps-e9ctz7, cocp7-c5pae0, cocp7-c5pby4, cocp7-c5pdn8, cocp7-c5pdv9, cocp7-c5pe69, cocp7-c5pf68, cocp7-c5pgk6, cocp7-c5pid0, cocp7-dapb, cocps-e9cz73, cocps-e9dbi4, cocps-e9dbu0, cocps-e9dfh7, uncre-c4jf72, uncre-c4jf79, uncre-c4ji27, uncre-c4jj62, uncre-c4jjs9, uncre-c4jk71, uncre-c4jlm9, uncre-c4jlp5, uncre-c4jlr7, uncre-c4jnk2, uncre-c4jnn3, uncre-c4juj6, uncre-c4jve9, uncre-c4jvh5, uncre-c4jw09, uncre-c4jyw9, uncre-c4jzs5, uncre-dapb, ajech-c6h9r4, uncre-c4jds5, cocp7-c5pii3, ajecn-a6r5v8, cocim-j3ka92, cocp7-c5phc6, ajecn-a6qtc4, ajecn-a6r145, cocps-e9d3i4, cocp7-c5p7x1, cocps-e9csw0, ajecg-c0nww6, ajecn-kex1, uncre-kex1, uncre-cbpya, cocps-kex1, ajecn-cbpya Abstract While most Ascomycetes tend to associate principally with plants, the dimorphic fungi Coccidioides immitis and Coccidioides posadasii are primary pathogens of immunocompetent mammals, including humans. Infection results from environmental exposure to Coccidiodies, which is believed to grow as a soil saprophyte in arid deserts. To investigate hypotheses about the life history and evolution of Coccidioides, the genomes of several Onygenales, including C. immitis and C. posadasii; a close, nonpathogenic relative, Uncinocarpus reesii; and a more diverged pathogenic fungus, Histoplasma capsulatum, were sequenced and compared with those of 13 more distantly related Ascomycetes. This analysis identified increases and decreases in gene family size associated with a host/substrate shift from plants to animals in the Onygenales. In addition, comparison among Onygenales genomes revealed evolutionary changes in Coccidioides that may underlie its infectious phenotype, the identification of which may facilitate improved treatment and prevention of coccidioidomycosis. Overall, the results suggest that Coccidioides species are not soil saprophytes, but that they have evolved to remain associated with their dead animal hosts in soil, and that Coccidioides metabolism genes, membrane-related proteins, and putatively antigenic compounds have evolved in response to interaction with an animal host. 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: Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum Hane JK, Lowe RG, Solomon PS, Tan KC, Schoch CL, Spatafora JW, Crous PW, Kodira C, Birren BW and Oliver RP <3 more author(s)> Hane JK, Lowe RG, Solomon PS, Tan KC, Schoch CL, Spatafora JW, Crous PW, Kodira C, Birren BW, Galagan JE, Torriani SF, McDonald BA, Oliver RP (- 3) Ref: Plant Cell, 19:3347, 2007 : PubMed ESTHER: Hane_2007_Plant.Cell_19_3347 PubMedSearch: Hane 2007 Plant.Cell 19 3347 PubMedID: 18024570 Gene_locus related to this paper: phano-at151, phano-bst1, phano-dapb, phano-q0tw42, phano-q0txi3, phano-q0tzh6, phano-q0u0b1, phano-q0u0e9, phano-q0u0t5, phano-q0u1e7, phano-q0u1v1, phano-q0u1x4, phano-q0u2m9, phano-q0u2y5, phano-q0u3i1, phano-q0u5t8, phano-q0u8z8, phano-q0u382, phano-q0u622, phano-q0u753, phano-q0uac8, phano-q0ucn2, phano-q0udp4, phano-q0udr2, phano-q0uem1, phano-q0uet5, phano-q0ufs1, phano-q0ug08, phano-q0ugf2, phano-q0uha0, phano-q0ui22, phano-q0ukj9, phano-q0unt6, phano-q0upq4, phano-q0uq74, phano-q0uq76, phano-q0urz6, phano-q0uua1, phano-q0uuc4, phano-q0uuc6, phano-q0uup2, phano-q0uv86, phano-q0uwb7, phano-q0uyc1, phano-q0uyf1, phano-q0uyi9, phano-q0v0y6, phano-q0v1c5, phano-q0v1s1, phano-q0v2i6, phano-q0v4x4, phano-q0v5x9, phano-q0v6t6, phano-q0v6w1, phano-q0v7e6, phano-q0v615, phano-q0uru8, phano-q0txx8, phano-q0u4u8, phano-q0v3l0, phano-q0ua76, phano-q0ty51, phano-q0twk1, phano-q0v263, phano-q0uh92, phano-q0uxx8, phano-q0v697, phano-q0ug10, phano-q0v5u8, phano-q0u1s8, phano-q0uy34, phano-q0twn7, phano-elca, phano-cbpya, phano-kex1, phano-q0v778 Abstract Stagonospora nodorum is a major necrotrophic fungal pathogen of wheat (Triticum aestivum) and a member of the Dothideomycetes, a large fungal taxon that includes many important plant pathogens affecting all major crop plant families. Here, we report the acquisition and initial analysis of a draft genome sequence for this fungus. The assembly comprises 37,164,227 bp of nuclear DNA contained in 107 scaffolds. The circular mitochondrial genome comprises 49,761 bp encoding 46 genes, including four that are intron encoded. The nuclear genome assembly contains 26 classes of repetitive DNA, comprising 4.5% of the genome. Some of the repeats show evidence of repeat-induced point mutations consistent with a frequent sexual cycle. ESTs and gene prediction models support a minimum of 10,762 nuclear genes. Extensive orthology was found between the polyketide synthase family in S. nodorum and Cochliobolus heterostrophus, suggesting an ancient origin and conserved functions for these genes. A striking feature of the gene catalog was the large number of genes predicted to encode secreted proteins; the majority has no meaningful similarity to any other known genes. It is likely that genes for host-specific toxins, in addition to ToxA, will be found among this group. ESTs obtained from axenic mycelium grown on oleate (chosen to mimic early infection) and late-stage lesions sporulating on wheat leaves were obtained. Statistical analysis shows that transcripts encoding proteins involved in protein synthesis and in the production of extracellular proteases, cellulases, and xylanases predominate in the infection library. This suggests that the fungus is dependant on the degradation of wheat macromolecular constituents to provide the carbon skeletons and energy for the synthesis of proteins and other components destined for the developing pycnidiospores. 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: DNA sequence and analysis of human chromosome 8 Nusbaum C, Mikkelsen TS, Zody MC, Asakawa S, Taudien S, Garber M, Kodira CD, Schueler MG, Shimizu A and Lander ES <66 more author(s)> Nusbaum C, Mikkelsen TS, Zody MC, Asakawa S, Taudien S, Garber M, Kodira CD, Schueler MG, Shimizu A, Whittaker CA, Chang JL, Cuomo CA, Dewar K, Fitzgerald MG, Yang X, Allen NR, Anderson S, Asakawa T, Blechschmidt K, Bloom T, Borowsky ML, Butler J, Cook A, Corum B, DeArellano K, Decaprio D, Dooley KT, Dorris L, 3rd, Engels R, Glockner G, Hafez N, Hagopian DS, Hall JL, Ishikawa SK, Jaffe DB, Kamat A, Kudoh J, Lehmann R, Lokitsang T, Macdonald P, Major JE, Matthews CD, Mauceli E, Menzel U, Mihalev AH, Minoshima S, Murayama Y, Naylor JW, Nicol R, Nguyen C, O'Leary SB, O'Neill K, Parker SC, Polley A, Raymond CK, Reichwald K, Rodriguez J, Sasaki T, Schilhabel M, Siddiqui R, Smith CL, Sneddon TP, Talamas JA, Tenzin P, Topham K, Venkataraman V, Wen G, Yamazaki S, Young SK, Zeng Q, Zimmer AR, Rosenthal A, Birren BW, Platzer M, Shimizu N, Lander ES (- 66) Ref: Nature, 439:331, 2006 : PubMed ESTHER: Nusbaum_2006_Nature_439_331 PubMedSearch: Nusbaum 2006 Nature 439 331 PubMedID: 16421571 Gene_locus related to this paper: human-TG Abstract The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of approximately 15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection--these include the major defensin (DEF) gene cluster and MCPH1, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution. Title: Human chromosome 11 DNA sequence and analysis including novel gene identification Taylor TD, Noguchi H, Totoki Y, Toyoda A, Kuroki Y, Dewar K, Lloyd C, Itoh T, Takeda T and Sakaki Y <24 more author(s)> Taylor TD, Noguchi H, Totoki Y, Toyoda A, Kuroki Y, Dewar K, Lloyd C, Itoh T, Takeda T, Kim DW, She X, Barlow KF, Bloom T, Bruford E, Chang JL, Cuomo CA, Eichler E, Fitzgerald MG, Jaffe DB, LaButti K, Nicol R, Park HS, Seaman C, Sougnez C, Yang X, Zimmer AR, Zody MC, Birren BW, Nusbaum C, Fujiyama A, Hattori M, Rogers J, Lander ES, Sakaki Y (- 24) Ref: Nature, 440:497, 2006 : PubMed ESTHER: Taylor_2006_Nature_440_497 PubMedSearch: Taylor 2006 Nature 440 497 PubMedID: 16554811 Gene_locus related to this paper: human-PRCP Abstract Chromosome 11, although average in size, is one of the most gene- and disease-rich chromosomes in the human genome. Initial gene annotation indicates an average gene density of 11.6 genes per megabase, including 1,524 protein-coding genes, some of which were identified using novel methods, and 765 pseudogenes. One-quarter of the protein-coding genes shows overlap with other genes. Of the 856 olfactory receptor genes in the human genome, more than 40% are located in 28 single- and multi-gene clusters along this chromosome. Out of the 171 disorders currently attributed to the chromosome, 86 remain for which the underlying molecular basis is not yet known, including several mendelian traits, cancer and susceptibility loci. The high-quality data presented here--nearly 134.5 million base pairs representing 99.8% coverage of the euchromatic sequence--provide scientists with a solid foundation for understanding the genetic basis of these disorders and other biological phenomena. Title: DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage Zody MC, Garber M, Adams DJ, Sharpe T, Harrow J, Lupski JR, Nicholson C, Searle SM, Wilming L and Nusbaum C <64 more author(s)> Zody MC, Garber M, Adams DJ, Sharpe T, Harrow J, Lupski JR, Nicholson C, Searle SM, Wilming L, Young SK, Abouelleil A, Allen NR, Bi W, Bloom T, Borowsky ML, Bugalter BE, Butler J, Chang JL, Chen CK, Cook A, Corum B, Cuomo CA, de Jong PJ, Decaprio D, Dewar K, FitzGerald M, Gilbert J, Gibson R, Gnerre S, Goldstein S, Grafham DV, Grocock R, Hafez N, Hagopian DS, Hart E, Norman CH, Humphray S, Jaffe DB, Jones M, Kamal M, Khodiyar VK, LaButti K, Laird G, Lehoczky J, Liu X, Lokyitsang T, Loveland J, Lui A, Macdonald P, Major JE, Matthews L, Mauceli E, McCarroll SA, Mihalev AH, Mudge J, Nguyen C, Nicol R, O'Leary SB, Osoegawa K, Schwartz DC, Shaw-Smith C, Stankiewicz P, Steward C, Swarbreck D, Venkataraman V, Whittaker CA, Yang X, Zimmer AR, Bradley A, Hubbard T, Birren BW, Rogers J, Lander ES, Nusbaum C (- 64) Ref: Nature, 440:1045, 2006 : PubMed ESTHER: Zody_2006_Nature_440_1045 PubMedSearch: Zody 2006 Nature 440 1045 PubMedID: 16625196 Gene_locus related to this paper: human-NLGN2, human-NOTUM Abstract Chromosome 17 is unusual among the human chromosomes in many respects. It is the largest human autosome with orthology to only a single mouse chromosome, mapping entirely to the distal half of mouse chromosome 11. Chromosome 17 is rich in protein-coding genes, having the second highest gene density in the genome. It is also enriched in segmental duplications, ranking third in density among the autosomes. Here we report a finished sequence for human chromosome 17, as well as a structural comparison with the finished sequence for mouse chromosome 11, the first finished mouse chromosome. Comparison of the orthologous regions reveals striking differences. In contrast to the typical pattern seen in mammalian evolution, the human sequence has undergone extensive intrachromosomal rearrangement, whereas the mouse sequence has been remarkably stable. Moreover, although the human sequence has a high density of segmental duplication, the mouse sequence has a very low density. Notably, these segmental duplications correspond closely to the sites of structural rearrangement, demonstrating a link between duplication and rearrangement. Examination of the main classes of duplicated segments provides insight into the dynamics underlying expansion of chromosome-specific, low-copy repeats in the human genome. Title: Analysis of the DNA sequence and duplication history of human chromosome 15 Zody MC, Garber M, Sharpe T, Young SK, Rowen L, O'Neill K, Whittaker CA, Kamal M, Chang JL and Nusbaum C <58 more author(s)> Zody MC, Garber M, Sharpe T, Young SK, Rowen L, O'Neill K, Whittaker CA, Kamal M, Chang JL, Cuomo CA, Dewar K, Fitzgerald MG, Kodira CD, Madan A, Qin S, Yang X, Abbasi N, Abouelleil A, Arachchi HM, Baradarani L, Birditt B, Bloom S, Bloom T, Borowsky ML, Burke J, Butler J, Cook A, DeArellano K, Decaprio D, Dorris L, 3rd, Dors M, Eichler EE, Engels R, Fahey J, Fleetwood P, Friedman C, Gearin G, Hall JL, Hensley G, Johnson E, Jones C, Kamat A, Kaur A, Locke DP, Munson G, Jaffe DB, Lui A, Macdonald P, Mauceli E, Naylor JW, Nesbitt R, Nicol R, O'Leary SB, Ratcliffe A, Rounsley S, She X, Sneddon KM, Stewart S, Sougnez C, Stone SM, Topham K, Vincent D, Wang S, Zimmer AR, Birren BW, Hood L, Lander ES, Nusbaum C (- 58) Ref: Nature, 440:671, 2006 : PubMed ESTHER: Zody_2006_Nature_440_671 PubMedSearch: Zody 2006 Nature 440 671 PubMedID: 16572171 Gene_locus related to this paper: human-DPP8, human-LIPC, human-SPG21 Abstract Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplications in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome. 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, mago7-g4n703 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: DNA sequence and analysis of human chromosome 18 Nusbaum C, Zody MC, Borowsky ML, Kamal M, Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA and Lander ES <45 more author(s)> Nusbaum C, Zody MC, Borowsky ML, Kamal M, Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA, Dewar K, Fitzgerald MG, Yang X, Abouelleil A, Allen NR, Anderson S, Bloom T, Bugalter B, Butler J, Cook A, Decaprio D, Engels R, Garber M, Gnirke A, Hafez N, Hall JL, Norman CH, Itoh T, Jaffe DB, Kuroki Y, Lehoczky J, Lui A, Macdonald P, Mauceli E, Mikkelsen TS, Naylor JW, Nicol R, Nguyen C, Noguchi H, O'Leary SB, O'Neill K, Piqani B, Smith CL, Talamas JA, Topham K, Totoki Y, Toyoda A, Wain HM, Young SK, Zeng Q, Zimmer AR, Fujiyama A, Hattori M, Birren BW, Sakaki Y, Lander ES (- 45) Ref: Nature, 437:551, 2005 : PubMed ESTHER: Nusbaum_2005_Nature_437_551 PubMedSearch: Nusbaum 2005 Nature 437 551 PubMedID: 16177791 Gene_locus related to this paper: human-LIPG Abstract Chromosome 18 appears to have the lowest gene density of any human chromosome and is one of only three chromosomes for which trisomic individuals survive to term. There are also a number of genetic disorders stemming from chromosome 18 trisomy and aneuploidy. Here we report the finished sequence and gene annotation of human chromosome 18, which will allow a better understanding of the normal and disease biology of this chromosome. Despite the low density of protein-coding genes on chromosome 18, we find that the proportion of non-protein-coding sequences evolutionarily conserved among mammals is close to the genome-wide average. Extending this analysis to the entire human genome, we find that the density of conserved non-protein-coding sequences is largely uncorrelated with gene density. This has important implications for the nature and roles of non-protein-coding sequence elements. Title: Mapping of Myxococcus xanthus social motility dsp mutations to the dif genes Lancero H, Brofft JE, Downard J, Birren BW, Nusbaum C, Naylor J, Shi W, Shimkets LJ Ref: Journal of Bacteriology, 184:1462, 2002 : PubMed ESTHER: Lancero_2002_J.Bacteriol_184_1462 PubMedSearch: Lancero 2002 J.Bacteriol 184 1462 PubMedID: 11844780 Gene_locus related to this paper: myxxa-Q8VQX5 Abstract Myxococcus xanthus dsp and dif mutants have similar phenotypes in that they are deficient in social motility and fruiting body development. We compared the two loci by genetic mapping, complementation with a cosmid clone, DNA sequencing, and gene disruption and found that 16 of the 18 dsp alleles map to the dif genes. Another dsp allele contains a mutation in the sglK gene. About 36.6 kb around the dsp-dif locus was sequenced and annotated, and 50% of the genes are novel. | |||||||
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