Author Report for: Dietrich FSNo contact information in database for Dietrich FS
Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K and Cherry JM <7 more author(s)> Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (- 7) Ref: G3 (Bethesda), 4:389, 2014 : PubMed ESTHER: Engel_2014_G3.(Bethesda)_4_389 PubMedSearch: Engel 2014 G3.(Bethesda) 4 389 PubMedID: 24374639 Gene_locus related to this paper: yeast-hda1, yeast-ymc0 Abstract The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively studied by geneticists, molecular biologists, and computational scientists all over the world. Maintenance and annotation of the genome sequence have long been provided by the Saccharomyces Genome Database, one of the original model organism databases. To deepen our understanding of the eukaryotic genome, the S. cerevisiae strain S288C reference genome sequence was updated recently in its first major update since 1996. The new version, called "S288C 2010," was determined from a single yeast colony using modern sequencing technologies and serves as the anchor for further innovations in yeast genomic science. Title: Genomes of Ashbya fungi isolated from insects reveal four mating-type loci, numerous translocations, lack of transposons, and distinct gene duplications Dietrich FS, Voegeli S, Kuo S, Philippsen P Ref: G3 (Bethesda), 3:1225, 2013 : PubMed ESTHER: Dietrich_2013_G3.(Bethesda)_3_1225 PubMedSearch: Dietrich 2013 G3.(Bethesda) 3 1225 PubMedID: 23749448 Gene_locus related to this paper: ashgo-q75ay6 Abstract The filamentous fungus Ashbya gossypii is a cotton pathogen transmitted by insects. It is readily grown and manipulated in the laboratory and is commercially exploited as a natural overproducer of vitamin B2. Our previous genome analysis of A. gossypii isolate ATCC10895, collected in Trinidad nearly 100 years ago, revealed extensive synteny with the Saccharomyces cerevisiae genome, leading us to use it as a model organism to understand the evolution of filamentous growth. To further develop Ashbya as a model system, we have investigated the ecological niche of A. gossypii and isolated additional strains and a sibling species, both useful in comparative analysis. We isolated fungi morphologically similar to A. gossypii from different plant-feeding insects of the suborder Heteroptera, generated a phylogenetic tree based on rDNA-ITS sequences, and performed high coverage short read sequencing with one A. gossypii isolate from Florida, a new species, Ashbya aceri, isolated in North Carolina, and a genetically marked derivative of ATCC10895 intensively used for functional studies. In contrast to S. cerevisiae, all strains carry four not three mating type loci, adding a new puzzle in the evolution of Ashbya species. Another surprise was the genome identity of 99.9% between the Florida strain and ATCC10895, isolated in Trinidad. The A. aceri and A. gossypii genomes show conserved gene orders rearranged by eight translocations, 90% overall sequence identity, and fewer tandem duplications in the A. aceri genome. Both species lack transposable elements. Finally, our work identifies plant-feeding insects of the suborder Heteroptera as the most likely natural reservoir of Ashbya, and that infection of cotton and other plants may be incidental to the growth of the fungus in its insect host. 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: Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production Argueso JL, Carazzolle MF, Mieczkowski PA, Duarte FM, Netto OV, Missawa SK, Galzerani F, Costa GG, Vidal RO and Pereira GA <11 more author(s)> Argueso JL, Carazzolle MF, Mieczkowski PA, Duarte FM, Netto OV, Missawa SK, Galzerani F, Costa GG, Vidal RO, Noronha MF, Dominska M, Andrietta MG, Andrietta SR, Cunha AF, Gomes LH, Tavares FC, Alcarde AR, Dietrich FS, McCusker JH, Petes TD, Pereira GA (- 11) Ref: Genome Res, 19:2258, 2009 : PubMed ESTHER: Argueso_2009_Genome.Res_19_2258 PubMedSearch: Argueso 2009 Genome.Res 19 2258 PubMedID: 19812109 Gene_locus related to this paper: yeast-AIM2, yeast-BST1, yeast-cbpy1, yeast-cld1, yeast-dap1, yeast-dap2, yeast-dlhh, yeast-ECM18, yeast-FSH1, yeast-FSH3, yeast-ict1, yeast-kex01, yeast-LDH1, yeast-MCFS1, yeast-MCFS2, yeast-met2, yeast-mgll, yeast-pdat, yeast-ppme1, yeast-ROG1, yeast-SAY1, yeast-tgl1, yeast-tgl2, yeast-yby9, yeast-YDL109C, yeast-YDR428C, yeast-YDR444W, yeast-yg19, yeast-yj77, yeast-yjg8, yeast-YLL012W, yeast-YLR020C, yeast-YLR118c, yeast-ym60, yeast-ynl5, yeast-yo059, yeast-YPR147C, yeast-hda1 Abstract Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (approximately 2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency of viable spores. Hybrid diploids formed by outcrossing with the laboratory strain S288c also displayed good spore viability. Thus, the rearrangements that exist near the ends of chromosomes do not impair meiosis, as they do not span regions that contain essential genes. This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures. We also explored features of the JAY270 and JAY291 genomes that help explain their high adaptation to industrial environments, exhibiting desirable phenotypes such as high ethanol and cell mass production and high temperature and oxidative stress tolerance. The genomic manipulation of such strains could enable the creation of a new generation of industrial organisms, ideally suited for use as delivery vehicles for future bioenergy technologies. Title: Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789 Wei W, McCusker JH, Hyman RW, Jones T, Ning Y, Cao Z, Gu Z, Bruno D, Miranda M and Steinmetz LM <12 more author(s)> Wei W, McCusker JH, Hyman RW, Jones T, Ning Y, Cao Z, Gu Z, Bruno D, Miranda M, Nguyen M, Wilhelmy J, Komp C, Tamse R, Wang X, Jia P, Luedi P, Oefner PJ, David L, Dietrich FS, Li Y, Davis RW, Steinmetz LM (- 12) Ref: Proc Natl Acad Sci U S A, 104:12825, 2007 : PubMed ESTHER: Wei_2007_Proc.Natl.Acad.Sci.U.S.A_104_12825 PubMedSearch: Wei 2007 Proc.Natl.Acad.Sci.U.S.A 104 12825 PubMedID: 17652520 Gene_locus related to this paper: yeast-AIM2, yeast-BST1, yeast-cbpy1, yeast-cld1, yeast-ATG15, yeast-dap1, yeast-dap2, yeast-dlhh, yeast-ECM18, yeast-FSH1, yeast-FSH3, yeast-ict1, yeast-kex01, yeast-LDH1, yeast-MCFS1, yeast-MCFS2, yeast-met2, yeast-mgll, yeast-pdat, yeast-ppme1, yeast-ROG1, yeast-SAY1, yeast-tgl1, yeast-tgl2, yeast-yby9, yeast-YDL109C, yeast-YDR428C, yeast-YDR444W, yeast-yfd4, yeast-yg19, yeast-yj77, yeast-yjg8, yeast-YLL012W, yeast-YLR020C, yeast-YLR118c, yeast-ym60, yeast-ynl5, yeast-yo059, yeast-YPR147C, yeast-hda1 Abstract We sequenced the genome of Saccharomyces cerevisiae strain YJM789, which was derived from a yeast isolated from the lung of an AIDS patient with pneumonia. The strain is used for studies of fungal infections and quantitative genetics because of its extensive phenotypic differences to the laboratory reference strain, including growth at high temperature and deadly virulence in mouse models. Here we show that the approximately 12-Mb genome of YJM789 contains approximately 60,000 SNPs and approximately 6,000 indels with respect to the reference S288c genome, leading to protein polymorphisms with a few known cases of phenotypic changes. Several ORFs are found to be unique to YJM789, some of which might have been acquired through horizontal transfer. Localized regions of high polymorphism density are scattered over the genome, in some cases spanning multiple ORFs and in others concentrated within single genes. The sequence of YJM789 contains clues to pathogenicity and spurs the development of more powerful approaches to dissecting the genetic basis of complex hereditary traits. Title: The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, Mohr C, Pohlmann R, Luedi P and Philippsen P <4 more author(s)> Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, Mohr C, Pohlmann R, Luedi P, Choi S, Wing RA, Flavier A, Gaffney TD, Philippsen P (- 4) Ref: Science, 304:304, 2004 : PubMed ESTHER: Dietrich_2004_Science_304_304 PubMedSearch: Dietrich 2004 Science 304 304 PubMedID: 15001715 Gene_locus related to this paper: ashgo-apth1, ashgo-bna7, ashgo-BST1, ashgo-ppme1, ashgo-q74zz5, ashgo-q75a71, ashgo-q75av7, ashgo-q75b57, ashgo-q75bq1, ashgo-q75bx2, ashgo-q75c14, ashgo-q75c41, ashgo-q75c44, ashgo-q75cn3, ashgo-q75cu9, ashgo-q75d28, ashgo-q75d64, ashgo-q75dn6, ashgo-q75en3, ashgo-q75f98, ashgo-q751m5, ashgo-q751z3, ashgo-q752m5, ashgo-q753d0, ashgo-q753k6, ashgo-q753w6, ashgo-q755k2, ashgo-q755r4, ashgo-q755r5, ashgo-q755r6, ashgo-q756b1, ashgo-q756e3, ashgo-q757j1, ashgo-q757w0, ashgo-q758a8, ashgo-q758x2, ashgo-q759l1, ashgo-q759s1, ashgo-q75ay6 Abstract We have sequenced and annotated the genome of the filamentous ascomycete Ashbya gossypii. With a size of only 9.2 megabases, encoding 4718 protein-coding genes, it is the smallest genome of a free-living eukaryote yet characterized. More than 90% of A. gossypii genes show both homology and a particular pattern of synteny with Saccharomyces cerevisiae. Analysis of this pattern revealed 300 inversions and translocations that have occurred since divergence of these two species. It also provided compelling evidence that the evolution of S. cerevisiae included a whole genome duplication or fusion of two related species and showed, through inferred ancient gene orders, which of the duplicated genes lost one copy and which retained both copies. Title: The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI Bussey H, Storms RK, Ahmed A, Albermann K, Allen E, Ansorge W, Araujo R, Aparicio A, Barrell B and Hani J <79 more author(s)> Bussey H, Storms RK, Ahmed A, Albermann K, Allen E, Ansorge W, Araujo R, Aparicio A, Barrell B, Badcock K, Benes V, Botstein D, Bowman S, Bruckner M, Carpenter J, Cherry JM, Chung E, Churcher C, Coster F, Davis K, Davis RW, Dietrich FS, Delius H, DiPaolo T, Dubois E, Dusterhoft A, Duncan M, Floeth M, Fortin N, Friesen JD, Fritz C, Goffeau A, Hall J, Hebling U, Heumann K, Hilbert H, Hillier L, Hunicke-Smith S, Hyman R, Johnston M, Kalman S, Kleine K, Komp C, Kurdi O, Lashkari D, Lew H, Lin A, Lin D, Louis EJ, Marathe R, Messenguy F, Mewes HW, Mirtipati S, Moestl D, Muller-Auer S, Namath A, Nentwich U, Oefner P, Pearson D, Petel FX, Pohl TM, Purnelle B, Rajandream MA, Rechmann S, Rieger M, Riles L, Roberts D, Schafer M, Scharfe M, Scherens B, Schramm S, Schroder M, Sdicu AM, Tettelin H, Urrestarazu LA, Ushinsky S, Vierendeels F, Vissers S, Voss H, Walsh SV, Wambutt R, Wang Y, Wedler E, Wedler H, Winnett E, Zhong WW, Zollner A, Vo DH, Hani J (- 79) Ref: Nature, 387:103, 1997 : PubMed ESTHER: Bussey_1997_Nature_387_103 PubMedSearch: Bussey 1997 Nature 387 103 PubMedID: 9169875 Gene_locus related to this paper: yeast-MCFS1, yeast-YPR147C Abstract The nucleotide sequence of the 948,061 base pairs of chromosome XVI has been determined, completing the sequence of the yeast genome. Chromosome XVI was the last yeast chromosome identified, and some of the genes mapped early to it, such as GAL4, PEP4 and RAD1 (ref. 2) have played important roles in the development of yeast biology. The architecture of this final chromosome seems to be typical of the large yeast chromosomes, and shows large duplications with other yeast chromosomes. Chromosome XVI contains 487 potential protein-encoding genes, 17 tRNA genes and two small nuclear RNA genes; 27% of the genes have significant similarities to human gene products, and 48% are new and of unknown biological function. Systematic efforts to explore gene function have begun. Title: The nucleotide sequence of Saccharomyces cerevisiae chromosome IV Jacq C, Alt-Morbe J, Andre B, Arnold W, Bahr A, Ballesta JP, Bargues M, Baron L, Becker A and Zaccaria P <126 more author(s)> Jacq C, Alt-Morbe J, Andre B, Arnold W, Bahr A, Ballesta JP, Bargues M, Baron L, Becker A, Biteau N, Blocker H, Blugeon C, Boskovic J, Brandt P, Bruckner M, Buitrago MJ, Coster F, Delaveau T, del Rey F, Dujon B, Eide LG, Garcia-Cantalejo JM, Goffeau A, Gomez-Peris AC, Granotier C, Hanemann V, Hankeln T, Hoheisel JD, Jager W, Jimenez A, Jonniaux JL, Kramer C, Kuster H, Laamanen P, Legros Y, Louis E, Muller-Rieker S, Monnet A, Moro M, Muller-Auer S, Nussbaumer B, Paricio N, Paulin L, Perea J, Perez-Alonso M, Perez-Ortin JE, Pohl TM, Prydz H, Purnelle B, Rasmussen SW, Remacha M, Revuelta JL, Rieger M, Salom D, Saluz HP, Saiz JE, Saren AM, Schafer M, Scharfe M, Schmidt ER, Schneider C, Scholler P, Schwarz S, Soler-Mira A, Urrestarazu LA, Verhasselt P, Vissers S, Voet M, Volckaert G, Wagner G, Wambutt R, Wedler E, Wedler H, Wolfl S, Harris DE, Bowman S, Brown D, Churcher CM, Connor R, Dedman K, Gentles S, Hamlin N, Hunt S, Jones L, McDonald S, Murphy L, Niblett D, Odell C, Oliver K, Rajandream MA, Richards C, Shore L, Walsh SV, Barrell BG, Dietrich FS, Mulligan J, Allen E, Araujo R, Aviles E, Berno A, Carpenter J, Chen E, Cherry JM, Chung E, Duncan M, Hunicke-Smith S, Hyman R, Komp C, Lashkari D, Lew H, Lin D, Mosedale D, Nakahara K, Namath A, Oefner P, Oh C, Petel FX, Roberts D, Schramm S, Schroeder M, Shogren T, Shroff N, Winant A, Yelton M, Botstein D, Davis RW, Johnston M, Hillier L, Riles L, Albermann K, Hani J, Heumann K, Kleine K, Mewes HW, Zollner A, Zaccaria P (- 126) Ref: Nature, 387:75, 1997 : PubMed ESTHER: Jacq_1997_Nature_387_75 PubMedSearch: Jacq 1997 Nature 387 75 PubMedID: 9169867 Gene_locus related to this paper: yeast-dlhh, yeast-ECM18, yeast-YDL109C, yeast-YDR428C, yeast-YDR444W Abstract The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome IV has been determined. Apart from chromosome XII, which contains the 1-2 Mb rDNA cluster, chromosome IV is the longest S. cerevisiae chromosome. It was split into three parts, which were sequenced by a consortium from the European Community, the Sanger Centre, and groups from St Louis and Stanford in the United States. The sequence of 1,531,974 base pairs contains 796 predicted or known genes, 318 (39.9%) of which have been previously identified. Of the 478 new genes, 225 (28.3%) are homologous to previously identified genes and 253 (32%) have unknown functions or correspond to spurious open reading frames (ORFs). On average there is one gene approximately every two kilobases. Superimposed on alternating regional variations in G+C composition, there is a large central domain with a lower G+C content that contains all the yeast transposon (Ty) elements and most of the tRNA genes. Chromosome IV shares with chromosomes II, V, XII, XIII and XV some long clustered duplications which partly explain its origin. | |||||||
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