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4 Genome Data Drives Change at Culture Collections

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Fungal Genomics

Part of the book series: The Mycota ((MYCOTA,volume 13))

Abstract

Collections of living microbes exist in a number of scales and with different degrees of permanence and formality. Many organizations have an interest in the activities and success of these collections. Modern genome data are both dependent on culture collections and transforming the fundamental nature of the collections at the same time. The ability to apply genomic technology to the identical materials as previous studies provides a rapid path to advanced projects on a variety of topics. Genomic analyses of fungi generated from classical genetic or environmental studies are providing an unprecedented level of detail and can differentiate among isolates once considered identical. New approaches to characterize and index living material in microbial collections may enable rapid identification of novel or desirable genetic traits. Resource allocation for living collections is often made without consideration of the intangible benefits provided by collections, and many collections are in peril of being lost.

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References

  • Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31:533–538

    Article  PubMed  CAS  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  PubMed  CAS  Google Scholar 

  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Balter M, Vogel G (2001) Cycling toward Stockholm. Science 294:502–503

    Article  PubMed  CAS  Google Scholar 

  • Boundy-Mills K (2012) Yeast culture collections of the world: meeting the needs of industrial researchers. J Ind Microbiol Biotechnol 39:673–680

    Article  PubMed  CAS  Google Scholar 

  • Campbell L, Betsou F, Garcia D, Giri J, Pitt K, Pugh R, Sexton K, Skubitz A, Somiari S, Astrin J (2012) Best practices for repositories – collection, storage, retrieval and distribution of biological materials for research. Biopreserv Biobank 10:79–161

    Article  Google Scholar 

  • Crous PW, Verkley GJ, Groenewald JZ, Samson R (2009) Fungal biodiversity. Centraalbureau voor Schimmelcultures, Utrecht

    Google Scholar 

  • Daniel HM, Prasad GS (2010) The role of culture collections as an interface between providers and users: the example of yeasts. Res Microbiol 161:488–496

    Article  PubMed  Google Scholar 

  • Diaz-Sanchez V, Estrada AF, Trautmann D, Limon MC, Al-Babili S, Avalos J (2011) Analysis of al-2 mutations in Neurospora. PLoS One 6:e21948

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Dugan FM Jr, Wiest A, McCluskey K (2011) Public germplasm collections and revolutions in biotechnology. J Biosci 36:205–209

    Article  PubMed  Google Scholar 

  • Dunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, Glass NL, McCluskey K, Plamann M, Galagan JE, Birren BW, Weiss RL, Townsend JP, Loros JJ, Nelson MA, Lambreghts R, Colot HV, Park G, Collopy P, Ringelberg C, Crew C, Litvinkova L, DeCaprio D, Hood HM, Curilla S, Shi M, Crawford M, Koerhsen M, Montgomery P, Larson L, Pearson M, Kasuga T, Tian C, Basturkmen M, Altamirano L, Xu J (2007) Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Adv Genet 57:49–96

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Forde BM, O’Toole PW (2013) Next-generation sequencing technologies and their impact on microbial genomics. Brief Funct Genomics 12:440–453

    Article  PubMed  CAS  Google Scholar 

  • Furman JL, Stern S (2011) Climbing atop the shoulders of giants: the impact of institutions on cumulative research. Am Econ Rev 101:1933–1963

    Article  Google Scholar 

  • 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 (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859–868

    Article  PubMed  CAS  Google Scholar 

  • Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG (1996) Life with 6000 genes. Science 274(546):563–567

    Google Scholar 

  • Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA (2012) The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res 40:D26–D32

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • ISO Guide 34:2009 (2009) General requirements for the competence of reference material producers. ISO, Geneva

    Google Scholar 

  • Janssens D, Arahal DR, Bizet C, Garay E (2010) The role of public biological resource centers in providing a basic infrastructure for microbial research. Res Microbiol 161:422–429

    Article  PubMed  Google Scholar 

  • Kitani Y, Olive LS, E-Ani AS (1961) Transreplication and crossing over in Sordaria fimicola. Science 134:668–669

    Article  PubMed  CAS  Google Scholar 

  • Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Doehren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gomez-Rodriguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernandez-Onate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lubeck M, Lubeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV (2011) Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol 12:R40

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Lang JM, Darling AE, Eisen JA (2013) Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS One 8:e62510

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RA, Chapman S, Coulson R, Coutinho PM, Danchin EG, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M (2010) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464:367–373

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Marmeisse R, Nehls U, Öpik M, Selosse MA, Pringle A (2013) Bridging mycorrhizal genomics, metagenomics and forest ecology. New Phytol 198:343–346

    Article  PubMed  Google Scholar 

  • Martin F, Aerts A, Ahren D, Brun A, Danchin E, Duchaussoy F, Gibon J, Kohler A, Lindquist E, Pereda V (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452:88–92

    Article  PubMed  CAS  Google Scholar 

  • McCluskey K (2012) Variation in mitochondrial genome primary sequence among whole-genome-sequenced strains of Neurospora crassa. IMA Fungus 3:93

    Article  PubMed Central  PubMed  Google Scholar 

  • McCluskey K (2013) Biological resource centers provide data and characterized living material for industrial biotechnology. Ind Biotechnol 9:117–122

    Article  Google Scholar 

  • McCluskey K, Wiest A, Plamann M (2010) The Fungal Genetics Stock Center: a repository for 50 years of fungal genetics research. J Biosci 35:119–126

    Article  PubMed  CAS  Google Scholar 

  • McCluskey K, Wiest A, Grigoriev IV, Lipzen A, Martin J, Schackwitz W, Baker SE (2011) Rediscovery by whole genome sequencing: classical mutations and genome polymorphisms in Neurospora crassa. G3 (Bethesda) 1:303–316

    Article  CAS  Google Scholar 

  • McNeill J, Barrie F, Buck W, Demoulin V, Greuter W, Hawksworth D, Herendeen P, Knapp S, Marhold K, Prado J (2012) International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). Koeltz Scientific Books, Koenigstein

    Google Scholar 

  • Ninomiya Y, Suzuki K, Ishii C, Inoue H (2004) Highly efficient gene replacements in Neurospora strains deficient for nonhomologous end-joining. Proc Natl Acad Sci U S A 101:12248–12253

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Nowrousian M, Teichert I, Masloff S, Kuck U (2012) Whole-genome sequencing of Sordaria macrospora mutants identifies developmental genes. G3 (Bethesda) 2:261–270

    Article  CAS  Google Scholar 

  • OECD (2007) OECD best practice guidelines for biological resource centres. The Organisation for Economic Development and Co-operation, Paris

    Google Scholar 

  • Olson LW (1984) Allomyces – a different fungus. Opera Bot 73:1–96

    Google Scholar 

  • Paquin B, Laforest M-J, Forget L, Roewer I, Wang Z, Longcore J, Lang BF (1997) The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression. Curr Genet 31:380–395

    Article  PubMed  CAS  Google Scholar 

  • Perkins DD (1949) Biochemical mutants in the smut fungus Ustilago maydis. Genetics 34:607

    PubMed Central  PubMed  CAS  Google Scholar 

  • Perkins DD, Radford A, Sachs MS (2000) The Neurospora compendium: chromosomal loci. Academic, New York

    Google Scholar 

  • Pomraning KR, Smith KM, Freitag M (2011) Bulk segregant analysis followed by high-throughput sequencing reveals the Neurospora cell cycle gene, ndc-1, to be allelic with the gene for ornithine decarboxylase, spe-1. Eukaryot Cell 10:724–733

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Purnick PE, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10:410–422

    Article  PubMed  CAS  Google Scholar 

  • Rosenblum EB, James TY, Zamudio KR, Poorten TJ, Ilut D, Rodriguez D, Eastman JM, Richards-Hrdlicka K, Joneson S, Jenkinson TS (2013) Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data. Proc Natl Acad Sci U S A 110:9385–9390

    Article  PubMed Central  PubMed  Google Scholar 

  • Rountree MR, Selker EU (2009) Genome defense: the Neurospora paradigm. In: Ferguson-Smith A, Greally J, Martienssen R (eds) Epigenomics. Springer, New York, pp 321–341

    Chapter  Google Scholar 

  • Sentausa E, Fournier PE (2013) Advantages and limitations of genomics in prokaryotic taxonomy. Clin Microbiol Infect 19:790–795

    Article  PubMed  CAS  Google Scholar 

  • Sherman DJ, Martin T, Nikolski M, Cayla C, Souciet JL, Durrens P (2009) Genolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. Nucleic Acids Res 37:D550–D554

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Smith D (2012) Culture collections. Adv Appl Microbiol 79:73–118

    Article  PubMed  Google Scholar 

  • Stackebrandt E (2010) Diversification and focusing: strategies of microbial culture collections. Trends Microbiol 18:283–287

    Article  PubMed  CAS  Google Scholar 

  • Stern S (2004) Biological resource centers: knowledge hubs for the life sciences. Brookings Institution Press, Washington, DC

    Google Scholar 

  • Stratton M (2008) Genome resequencing and genetic variation. Nat Biotechnol 26:65–66

    Article  PubMed  CAS  Google Scholar 

  • Syme RA, Hane JK, Friesen TL, Oliver RP (2013) Resequencing and comparative genomics of Stagonospora nodorum; sectional gene absence and effector discovery. G3 (Bethesda) 3:959–969

    Article  CAS  Google Scholar 

  • Turner BC, Perkins DD, Fairfield A (2001) Neurospora from natural populations: a global study. Fungal Genet Biol 32:67–92

    Article  PubMed  CAS  Google Scholar 

  • Wiest A, McCarthy AJ, Schnittker R, McCluskey K (2012) Molecular analysis of mutants of the Neurospora adenylosuccinate synthetase locus. J Genet 91:199–204

    Article  PubMed  CAS  Google Scholar 

  • Wiest A, Barchers D, Eaton M, Henderson R, Schnittker R, McCluskey K (2013) Molecular analysis of intragenic recombination at the tryptophan synthetase locus in Neurospora crassa. J Genet 92(3):523–528

    Google Scholar 

  • World Intellectual Property Organization (1980) Budapest treaty on the international recognition of the deposit of microorganisms for the purposes of patent procedure done at Budapest on April 28, 1977, and amended on September 26, 1980. World Intellectual Property Organization, Geneva. http://www.wipo.int/treaties/en/text.jsp?file_id=283784

  • Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ (2009) A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature 462:1056–1060

    Article  PubMed Central  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Fungal Genetics Stock Center, University of Missouri–Kansas City, Kansas City, MO, 64110, USA

    Kevin McCluskey & Aric Wiest

  2. Phaff Yeast Culture Collection, University of California, Davis, CA, 95616, USA

    Kyria Boundy-Mills

Authors
  1. Kevin McCluskey
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  2. Aric Wiest
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  3. Kyria Boundy-Mills
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Correspondence to Kevin McCluskey .

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Editors and Affiliations

  1. Department of General and Molecular Bota, Ruhr-University of Bochum, Bochum, Germany

    Minou Nowrousian

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McCluskey, K., Wiest, A., Boundy-Mills, K. (2014). 4 Genome Data Drives Change at Culture Collections. In: Nowrousian, M. (eds) Fungal Genomics. The Mycota, vol 13. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-45218-5_4

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