Author Report for: Nusbaum CNo contact information in database for Nusbaum C
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 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: Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica Jiang RH, de Bruijn I, Haas BJ, Belmonte R, Lobach L, Christie J, Van den Ackerveken G, Bottin A, Bulone V and van West P <31 more author(s)> Jiang RH, de Bruijn I, Haas BJ, Belmonte R, Lobach L, Christie J, Van den Ackerveken G, Bottin A, Bulone V, Diaz-Moreno SM, Dumas B, Fan L, Gaulin E, Govers F, Grenville-Briggs LJ, Horner NR, Levin JZ, Mammella M, Meijer HJ, Morris P, Nusbaum C, Oome S, Phillips AJ, van Rooyen D, Rzeszutek E, Saraiva M, Secombes CJ, Seidl MF, Snel B, Stassen JH, Sykes S, Tripathy S, van den Berg H, Vega-Arreguin JC, Wawra S, Young SK, Zeng Q, Dieguez-Uribeondo J, Russ C, Tyler BM, van West P (- 31) Ref: PLoS Genet, 9:e1003272, 2013 : PubMed ESTHER: Jiang_2013_PLoS.Genet_9_E1003272 PubMedSearch: Jiang 2013 PLoS.Genet 9 E1003272 PubMedID: 23785293 Gene_locus related to this paper: sappc-a0a067bqc9, sappc-a0a067d100, sappc-a0a067cbi1 Abstract Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica. 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: Complete genome sequence of Algoriphagus sp. PR1, bacterial prey of a colony-forming choanoflagellate Alegado RA, Ferriera S, Nusbaum C, Young SK, Zeng Q, Imamovic A, Fairclough SR, King N Ref: Journal of Bacteriology, 193:1485, 2011 : PubMed ESTHER: Alegado_2011_J.Bacteriol_193_1485 PubMedSearch: Alegado 2011 J.Bacteriol 193 1485 PubMedID: 21183675 Gene_locus related to this paper: 9bact-a3hsc2, 9bact-a3hsw0, 9bact-a3ht61, 9bact-a3hta1.1, 9bact-a3hta1.2, 9bact-a3htc8, 9bact-a3htd6, 9bact-a3hti5, 9bact-a3htn1, 9bact-a3htn2, 9bact-a3htn3, 9bact-a3htn9, 9bact-a3htv3, 9bact-a3hu26, 9bact-a3hu92, 9bact-a3hwh7, 9bact-a3hws7, 9bact-a3hws8, 9bact-a3hy22, 9bact-a3hzv9, 9bact-a3i1k2, 9bact-a3i1r2, 9bact-a3i1r3, 9bact-a3i2k7, 9bact-a3i3a8, 9bact-a3i056, 9bact-a3i079, 9bact-a3i222, 9bact-a3hun9 Abstract Bacteria are the primary food source of choanoflagellates, the closest known relatives of animals. Studying signaling interactions between the Gram-negative Bacteroidetes bacterium Algoriphagus sp. PR1 and its predator, the choanoflagellate Salpingoeca rosetta, provides a promising avenue for testing hypotheses regarding the involvement of bacteria in animal evolution. Here we announce the complete genome sequence of Algoriphagus sp. PR1 and initial findings from its annotation. Title: A high-resolution map of human evolutionary constraint using 29 mammals Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G and Kellis M <76 more author(s)> Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alfoldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M (- 76) Ref: Nature, 478:476, 2011 : PubMed ESTHER: Lindblad-Toh_2011_Nature_478_476 PubMedSearch: Lindblad-Toh 2011 Nature 478 476 PubMedID: 21993624 Gene_locus related to this paper: cavpo-1plip, cavpo-2plrp, cavpo-h0v1b7, cavpo-h0v5v8, cavpo-h0vj36, cavpo-lipli, rabit-1hlip, rabit-1plip, rabit-g1t6x7, rabit-LIPH, myolu-l7n1c2, myolu-g1pqd9, cavpo-h0uyz6, cavpo-h0vi56, rabit-g1tbj4, myolu-g1p5c0, rabit-g1sds3, rabit-g1sye0, cavpo-h0v0r2, cavpo-h0v7s5, rabit-g1sp43, myolu-g1p4p3, cavpo-h0vw09, rabit-g1ssu3, myolu-g1pds0, rabit-g1sic4, cavpo-h0v2c4, myolu-g1pg61, myolu-g1pnb1, myolu-g1pu06, myolu-g1qa15, myolu-g1qfu0, rabit-g1sn99, rabit-g1snq9, rabit-g1sns7, rabit-g1tuu8, rabit-g1tzq7, cavpo-h0v2i2, cavpo-h0v2j0, cavpo-h0vsf5, cavpo-a0a286x8d3, cavpo-a0a286xbr3, cavpo-a0a286y0i8, cavpo-a0a286y4p3, myolu-g1q2n9, cavpo-h0v1p4, myolu-g1pan8, myolu-g1paq0, myolu-g1par4, myolu-g1prn3, myolu-g1q3i0, myolu-g1q463, myolu-g1pat6, myolu-g1q859, rabit-g1sul9, rabit-g1sun0, rabit-g1sup0, myolu-l7n125, myolu-g1pan2, rabit-g1sxd0, cavpo-h0v8j4, rabit-d5fit0, rabit-g1tkr5, myolu-g1nty6, myolu-g1p1p3, cavpo-h0vdd5, myolu-g1pdp2, rabit-g1tmm5, cavpo-h0vhq3, myolu-g1nth4, cavpo-h0vqx6, rabit-g1tqr7, myolu-g1p1e9, cavpo-h0v8y6, rabit-g1skt3, myolu-g1nzg3, cavpo-h0v5z0, rabit-g1sgz5, myolu-g1pkg5, rabit-g1tmw5, rabit-g1t134, cavpo-a0a286x9v5, myolu-g1qc57, myolu-g1q061, rabit-g1tnp4, rabit-g1tyf7, cavpo-h0w2w1, rabit-g1ta36, cavpo-h0w342, myolu-g1q4e3, rabit-g1sqa1, cavpo-h0uxk7, myolu-g1p353, cavpo-h0vpm0, rabit-a0a5f9cru6, cavpo-a0a286xtc0 Abstract The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering approximately 4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for approximately 60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease. 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: 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: Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S and Nusbaum C <86 more author(s)> Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, Bozkurt TO, Ah-Fong AM, Alvarado L, Anderson VL, Armstrong MR, Avrova A, Baxter L, Beynon J, Boevink PC, Bollmann SR, Bos JI, Bulone V, Cai G, Cakir C, Carrington JC, Chawner M, Conti L, Costanzo S, Ewan R, Fahlgren N, Fischbach MA, Fugelstad J, Gilroy EM, Gnerre S, Green PJ, Grenville-Briggs LJ, Griffith J, Grunwald NJ, Horn K, Horner NR, Hu CH, Huitema E, Jeong DH, Jones AM, Jones JD, Jones RW, Karlsson EK, Kunjeti SG, Lamour K, Liu Z, Ma L, Maclean D, Chibucos MC, McDonald H, McWalters J, Meijer HJ, Morgan W, Morris PF, Munro CA, O'Neill K, Ospina-Giraldo M, Pinzon A, Pritchard L, Ramsahoye B, Ren Q, Restrepo S, Roy S, Sadanandom A, Savidor A, Schornack S, Schwartz DC, Schumann UD, Schwessinger B, Seyer L, Sharpe T, Silvar C, Song J, Studholme DJ, Sykes S, Thines M, van de Vondervoort PJ, Phuntumart V, Wawra S, Weide R, Win J, Young C, Zhou S, Fry W, Meyers BC, van West P, Ristaino J, Govers F, Birch PR, Whisson SC, Judelson HS, Nusbaum C (- 86) Ref: Nature, 461:393, 2009 : PubMed ESTHER: Haas_2009_Nature_461_393 PubMedSearch: Haas 2009 Nature 461 393 PubMedID: 19741609 Gene_locus related to this paper: phyin-ENDO2, phyin-q2m440, phyin-q58g92, phyit-d0mqp1, phyit-d0mqp2, phyit-d0mt75, phyit-d0muv1, phyit-d0mv34, phyit-d0mv35, phyit-d0mwf9, phyit-d0mxu5, phyit-d0n935, phyit-d0nax9, phyit-d0nfs3, phyit-d0nhj2, phyit-d0nhj4, phyit-d0nhj8, phyit-d0ni28, phyit-d0nj14, phyit-d0nj53, phyit-d0nj54, phyit-d0njf2, phyit-d0nkm4, phyit-d0nr53, phyit-d0nrb1, phyit-d0nrk9, phyit-d0nrl4, phyit-d0ns26, phyit-d0ns42, phyit-d0ns43, phyit-d0nsr8, phyit-d0nu41, phyit-d0nvt3, phyit-d0nwb6, phyit-d0nwm8, phyit-d0nzc0, phyit-d0nzc1, phyit-d0p0z1, phyit-d0p3z2, phyit-kex1, phyit-d0n6q6, phyit-d0n4i8, phyit-d0mqf7, phyit-d0n5g6 Abstract Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $$6.7 billion. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars. Here we report the sequence of the P. infestans genome, which at approximately 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for approximately 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential. Title: Genome sequence of Aedes aegypti, a major arbovirus vector Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K and Severson DW <85 more author(s)> Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, LaButti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'Leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW (- 85) Ref: Science, 316:1718, 2007 : PubMed ESTHER: Nene_2007_Science_316_1718 PubMedSearch: Nene 2007 Science 316 1718 PubMedID: 17510324 Gene_locus related to this paper: aedae-ACHE, aedae-ACHE1, aedae-glita, aedae-q0iea6, aedae-q0iev6, aedae-q0ifn6, aedae-q0ifn8, aedae-q0ifn9, aedae-q0ifp0, aedae-q0ig41, aedae-q1dgl0, aedae-q1dh03, aedae-q1dh19, aedae-q1hqe6, aedae-Q8ITU8, aedae-Q8MMJ6, aedae-Q8T9V6, aedae-q16e91, aedae-q16f04, aedae-q16f25, aedae-q16f26, aedae-q16f28, aedae-q16f29, aedae-q16f30, aedae-q16gq5, aedae-q16iq5, aedae-q16je0, aedae-q16je1, aedae-q16je2, aedae-q16ks8, aedae-q16lf2, aedae-q16lv6, aedae-q16m61, aedae-q16mc1, aedae-q16mc6, aedae-q16mc7, aedae-q16md1, aedae-q16ms7, aedae-q16nk5, aedae-q16rl5, aedae-q16rz9, aedae-q16si8, aedae-q16t49, aedae-q16wf1, aedae-q16x18, aedae-q16xp8, aedae-q16xu6, aedae-q16xw5, aedae-q16xw6, aedae-q16y04, aedae-q16y05, aedae-q16y06, aedae-q16y07, aedae-q16y39, aedae-q16y40, aedae-q16yg4, aedae-q16z03, aedae-q17aa7, aedae-q17av1, aedae-q17av2, aedae-q17av3, aedae-q17av4, aedae-q17b28, aedae-q17b29, aedae-q17b30, aedae-q17b31, aedae-q17b32, aedae-q17bm3, aedae-q17bm4, aedae-q17bv7, aedae-q17c44, aedae-q17cz1, aedae-q17d32, aedae-q17g39, aedae-q17g40, aedae-q17g41, aedae-q17g42, aedae-q17g43, aedae-q17g44, aedae-q17gb8, aedae-q17gr3, aedae-q17if7, aedae-q17if9, aedae-q17ig1, aedae-q17ig2, aedae-q17is4, aedae-q17l09, aedae-q17m26, aedae-q17mg9, aedae-q17mv4, aedae-q17mv5, aedae-q17mv6, aedae-q17mv7, aedae-q17mw8, aedae-q17mw9, aedae-q17nw5, aedae-q17nx5, aedae-q17pa4, aedae-q17q69, aedae-q170k7, aedae-q171y4, aedae-q172e0, aedae-q176i8, aedae-q176j0, aedae-q177k1, aedae-q177k2, aedae-q177l9, aedae-j9hic3, aedae-q179r9, aedae-u483, aedae-j9hj23, aedae-q17d68, aedae-q177c7, aedae-q0ifp1, aedae-a0a1s4fx83, aedae-a0a1s4g2m0, aedae-q1hr49 Abstract We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species. 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 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: 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: The complete genome and proteome of Mycoplasma mobile Jaffe JD, Stange-Thomann N, Smith C, Decaprio D, Fisher S, Butler J, Calvo S, Elkins T, Fitzgerald MG and Church GM <9 more author(s)> Jaffe JD, Stange-Thomann N, Smith C, Decaprio D, Fisher S, Butler J, Calvo S, Elkins T, Fitzgerald MG, Hafez N, Kodira CD, Major J, Wang S, Wilkinson J, Nicol R, Nusbaum C, Birren B, Berg HC, Church GM (- 9) Ref: Genome Res, 14:1447, 2004 : PubMed ESTHER: Jaffe_2004_Genome.Res_14_1447 PubMedSearch: Jaffe 2004 Genome.Res 14 1447 PubMedID: 15289470 Gene_locus related to this paper: mycmo-q6ki90, mycmo-q6kim4 Abstract Although often considered "minimal" organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete genomic sequence and proteogenomic map for the piscine mycoplasma Mycoplasma mobile, noted for its robust gliding motility. For the first time, proteomic data are used in the primary annotation of a new genome, providing validation of expression for many of the predicted proteins. Several novel features were discovered including a long repeating unit of DNA of approximately 2435 bp present in five complete copies that are shown to code for nearly identical yet uniquely expressed proteins. M. mobile has among the lowest DNA GC contents (24.9%) and most reduced set of tRNAs of any organism yet reported (28). Numerous instances of tandem duplication as well as lateral gene transfer are evident in the genome. The multiple available complete genome sequences for other motile and immotile mycoplasmas enabled us to use comparative genomic and phylogenetic methods to suggest several candidate genes that might be involved in motility. The results of these analyses leave open the possibility that gliding motility might have arisen independently more than once in the mycoplasma lineage. Title: Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C and Roest Crollius H <51 more author(s)> Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, de Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H (- 51) Ref: Nature, 431:946, 2004 : PubMed ESTHER: Jaillon_2004_Nature_431_946 PubMedSearch: Jaillon 2004 Nature 431 946 PubMedID: 15496914 Gene_locus related to this paper: tetng-3neur, tetng-4neur, tetng-ACHE, tetng-BCHE, tetng-h3cfz4, tetng-h3ci57, tetng-h3cl30, tetng-h3cnh2, tetng-nlgn2b, tetng-h3czr1, tetng-h3dbr5, tetng-nlgn2a, tetng-nlgn3b, tetng-q4ref8, tetng-q4rjp3, tetng-q4rjy3, tetng-q4rk53, tetng-q4rk63, tetng-q4rk66, tetng-q4rkk3, tetng-q4rli3, tetng-q4rn09, tetng-q4rqj4, tetng-q4rqz6, tetng-q4rr22, tetng-q4rru9, tetng-q4rtq6, tetng-q4rvf8, tetng-q4rwa0, tetng-q4rx90, tetng-q4ryv8, tetng-q4ryz3, tetng-q4s0h8, tetng-q4s5x0, tetng-q4s6r1, tetng-q4s6t6, tetng-q4s7e3, tetng-q4s7x6, tetng-q4s8t5, tetng-q4s9w9, tetng-q4s050, tetng-q4s091, tetng-q4s144, tetng-q4s309, tetng-q4s578, tetng-q4sal4, tetng-q4sbm6, tetng-q4sbp0, tetng-q4sbu0, tetng-q4sd49, tetng-q4ser6, tetng-q4sfm7, tetng-q4sgm5, tetng-q4sgv2, tetng-q4sh74, tetng-q4shl7, tetng-q4si60, tetng-q4sie5, tetng-q4sku6, tetng-q4smu0, tetng-q4smy3, tetng-q4snp0, tetng-q4snq3, tetng-q4spa7, tetng-q4spq0, tetng-q4sqr3, tetng-q4sty0, tetng-q4suu2, tetng-q4suz1, tetng-q4sxh3, tetng-q4syn6, tetng-q4szk0, tetng-q4szy0, tetng-q4t3m9, tetng-q4t4a1, tetng-q4t6m1, tetng-q4t7r6, tetng-q4t173, tetng-q4t826, tetng-q4t920, tetng-q4ta33, tetng-q4tab8, tetng-q4tb62, tetng-q4tbe2, tetng-h3dbw2, tetng-h3cpc8, tetng-h3cjy0, tetng-h3d966, tetng-h3d3e3, tetng-h3d961, tetng-h3ctg6, tetng-h3dde8, tetng-h3dde9, tetng-h3det9, tetng-h3cre8, tetng-h3dfb4, tetng-h3clj8 Abstract Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests approximately 900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype. 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. Title: The genome of M. acetivorans reveals extensive metabolic and physiological diversity Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S and Birren B <45 more author(s)> Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S, Atnoor D, Brown A, Allen N, Naylor J, Stange-Thomann N, DeArellano K, Johnson R, Linton L, McEwan P, McKernan K, Talamas J, Tirrell A, Ye W, Zimmer A, Barber RD, Cann I, Graham DE, Grahame DA, Guss AM, Hedderich R, Ingram-Smith C, Kuettner HC, Krzycki JA, Leigh JA, Li W, Liu J, Mukhopadhyay B, Reeve JN, Smith K, Springer TA, Umayam LA, White O, White RH, Conway de Macario E, Ferry JG, Jarrell KF, Jing H, Macario AJ, Paulsen I, Pritchett M, Sowers KR, Swanson RV, Zinder SH, Lander E, Metcalf WW, Birren B (- 45) Ref: Genome Res, 12:532, 2002 : PubMed ESTHER: Galagan_2002_Genome.Res_12_532 PubMedSearch: Galagan 2002 Genome.Res 12 532 PubMedID: 11932238 Gene_locus related to this paper: metac-MA0077, metac-MA0362, metac-MA0419, metac-MA0736, metac-MA0993, metac-MA1571, metac-MA1856, metac-MA1857, metac-MA2002, metac-MA2343, metac-MA2629, metac-MA2691, metac-MA2743, metac-MA2933, metac-MA3611, metac-MA3635, metac-MA3920, metac-META Abstract Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived from acetate. Here we report the complete genome sequence of an acetate-utilizing methanogen, Methanosarcina acetivorans C2A. Methanosarcineae are the most metabolically diverse methanogens, thrive in a broad range of environments, and are unique among the Archaea in forming complex multicellular structures. This diversity is reflected in the genome of M. acetivorans. At 5,751,492 base pairs it is by far the largest known archaeal genome. The 4524 open reading frames code for a strikingly wide and unanticipated variety of metabolic and cellular capabilities. The presence of novel methyltransferases indicates the likelihood of undiscovered natural energy sources for methanogenesis, whereas the presence of single-subunit carbon monoxide dehydrogenases raises the possibility of nonmethanogenic growth. Although motility has not been observed in any Methanosarcineae, a flagellin gene cluster and two complete chemotaxis gene clusters were identified. The availability of genetic methods, coupled with its physiological and metabolic diversity, makes M. acetivorans a powerful model organism for the study of archaeal biology. [Sequence, data, annotations and analyses are available at http://www-genome.wi.mit.edu/.] 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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