Fungal genome sequencing and bioenergy

Fungal Biology Reviews

Volumn 22, Issue 1, 2008, Pages 1-5

  Baker, Scott E ^a   Thykaer, Jette ^a,o   Adney, William S ^b   Brettin, Thomas S ^c   Brockman, Fred J ^a   D'haeseleer, Patrik ^d   Martinez, A Diego ^c   Miller, R Michael ^e   Rokhsar, Daniel S ^f   Schadt, Christopher W ^g   Torok, Tamas ^f   Tuskan, Gerald ^f,g   Bennett, Joan ^h   Berka, Randy M ⁱ   Briggs, Steven P ^j   Heitman, Joseph ^k   Taylor, John ^l   Gillian Turgeon, B ^m   Werner Washburne, Margaret ⁿ   Himmel, Michael E ^b  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b NATIONAL RENEWABLE ENERGY LABORATORY   (United States)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^e ARGONNE NATIONAL LABORATORY   (United States)

^f DOE JOINT GENOME INSTITUTE   (United States)

^g OAK RIDGE NATIONAL LABORATORY   (United States)

^h RUTGERS UNIVERSITY   (United States)

ⁱ Novozymes Biotech Inc   (United States)

^j UNIVERSITY OF CALIFORNIA   (United States)

^k DUKE UNIVERSITY   (United States)

^l UNIVERSITY OF CALIFORNIA   (United States)

^m Department of Obstetrics Gynecology   (United States)

ⁿ UNIVERSITY OF NEW MEXICO   (United States)

^o TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

more..

Author keywords

Bioenergy; Biofuel; Bioproduct; Fungal genomics

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); FUNGI;

EID: 44449103796     PISSN: 17494613     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fbr.2008.03.001     Document Type: Review

References (37)

1. Bothast R.J., and Schlicher M.A. Biotechnological processes for conversion of corn into ethanol. Applied Microbiology and Biotechnology 67 (2005) 19-25
2. Coutinho P.M., and Henrissat B. Carbohydrate-active enzymes: an integrated database approach. In: Gilbert H.J., Davies G., Henrissat B., and Svensson B. (Eds). Recent Advances in Carbohydrate Bioengineering (1999), The Royal Society of Chemistry, Cambridge 3-12
3. Cuomo C.A., Guldener U., Xu J.R., Trail F., Turgeon B.G., Di Pietro A., Walton J.D., Ma L.J., Baker S.E., Rep M., Adam G., Antoniw J., Baldwin T., Calvo S., Chang Y.L., Decaprio D., Gale L.R., Gnerre S., Goswami R.S., Hammond-Kosack K., Harris L.J., Hilburn K., Kennell J.C., Kroken S., Magnuson J.K., Mannhaupt G., Mauceli E., Mewes H.W., Mitterbauer R., Muehlbauer G., Munsterkotter M., Nelson D., O'Donnell K., Ouellet T., Qi W., Quesneville H., Roncero M.I., Seong K.Y., Tetko I.V., Urban M., Waalwijk C., Ward T.J., Yao J., Birren B.W., and Kistler H.C. The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317 (2007) 1400-1402
4. Davies G., and Henrissat B. Structures and mechanisms of glycosyl hydrolases. Structure 3 (1995) 853-859
5. Dean R.A., Talbot N.J., Ebbole D.J., Farman M.L., Mitchell T.K., Orbach M.J., Thon M., Kulkarni R., Xu J.R., Pan H., Read N.D., Lee Y.H., Carbone I., Brown D., Oh Y.Y., Donofrio N., Jeong J.S., Soanes D.M., Djonovic S., Kolomiets E., Rehmeyer C., Li W., Harding M., Kim S., Lebrun M.H., Bohnert H., Coughlan S., Butler J., Calvo S., Ma L.J., Nicol R., Purcell S., Nusbaum C., Galagan J.E., and Birren B.W. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434 (2005) 980-986
6. Galagan J.E., Calvo S.E., Borkovich K.A., Selker E.U., Read N.D., Jaffe D., FitzHugh W., Ma L.J., Smirnov S., Purcell S., Rehman B., Elkins T., Engels R., Wang S., Nielsen C.B., Butler J., Endrizzi M., Qui D., Ianakiev P., Bell-Pedersen D., Nelson M.A., Werner-Washburne M., Selitrennikoff C.P., Kinsey J.A., Braun E.L., Zelter A., Schulte U., Kothe G.O., 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 R.L., Perkins D.D., Kroken S., Cogoni C., Macino G., Catcheside D., Li W., Pratt R.J., Osmani S.A., DeSouza C.P., Glass L., Orbach M.J., Berglund J.A., Voelker R., Yarden O., Plamann M., Seiler S., Dunlap J., Radford A., Aramayo R., Natvig D.O., Alex L.A., Mannhaupt G., Ebbole D.J., Freitag M., Paulsen I., Sachs M.S., Lander E.S., Nusbaum C., and Birren B. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422 (2003) 859-868
7. Galagan J.E., Calvo S.E., Cuomo C., Ma L.J., Wortman J.R., Batzoglou S., Lee S.I., Basturkmen M., Spevak C.C., Clutterbuck J., Kapitonov V., Jurka J., Scazzocchio C., Farman M., Butler J., Purcell S., Harris S., Braus G.H., Draht O., Busch S., D'Enfert C., Bouchier C., Goldman G.H., Bell-Pedersen D., Griffiths-Jones S., Doonan J.H., Yu J., Vienken K., Pain A., Freitag M., Selker E.U., Archer D.B., Penalva M.A., Oakley B.R., Momany M., Tanaka T., Kumagai T., Asai K., Machida M., Nierman W.C., Denning D.W., Caddick M., Hynes M., Paoletti M., Fischer R., Miller B., Dyer P., Sachs M.S., Osmani S.A., and Birren B.W. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438 (2005) 1105-1115
8. Galagan J.E., Henn M.R., Ma L.J., Cuomo C.A., and Birren B. Genomics of the fungal kingdom: insights into eukaryotic biology. Genome Research 15 (2005) 1620-1631
9. Goffeau A., Barrell B.G., Bussey H., Davis R.W., Dujon B., Feldmann H., Galibert F., Hoheisel J.D., Jacq C., Johnston M., Louis E.J., Mewes H.W., Murakami Y., Philippsen P., Tettelin H., and Oliver S.G. Life with 6000 genes. Science 274 (1996) 546 563-547
10. van der Heijden M.G.A., Bardgett R.D., and van Straalen N.M. The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecology Letters 11 (2008) 296-310
11. Henrissat B. A classification of glycosyl hydrolases based on amino acid sequence similarities. The Biochemical Journal 280 (1991) 309-316
12. Henrissat B., and Bairoch A. New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. The Biochemical Journal 293 (1993) 781-788
13. Henrissat B., and Bairoch A. Updating the sequence-based classification of glycosyl hydrolases. The Biochemical Journal 316 (1996) 695-696
14. Henrissat B., and Romeu A. Families, superfamilies and subfamilies of glycosyl hydrolases. The Biochemical Journal 311 (1995) 350-351
15. Hibbett D.S., Binder M., Bischoff J.F., Blackwell M., Cannon P.F., Eriksson O.E., Huhndorf S., James T., Kirk P.M., Lucking R., Thorsten Lumbsch H., Lutzoni F., Matheny P.B., McLaughlin D.J., Powell M.J., Redhead S., Schoch C.L., Spatafora J.W., Stalpers J.A., Vilgalys R., Aime M.C., Aptroot A., Bauer R., Begerow D., Benny G.L., Castlebury L.A., Crous P.W., Dai Y.C., Gams W., Geiser D.M., Griffith G.W., Gueidan C., Hawksworth D.L., Hestmark G., Hosaka K., Humber R.A., Hyde K.D., Ironside J.E., Koljalg U., Kurtzman C.P., Larsson K.H., Lichtwardt R., Longcore J., Miadlikowska J., Miller A., Moncalvo J.M., Mozley-Standridge S., Oberwinkler F., Parmasto E., Reeb V., Rogers J.D., Roux C., Ryvarden L., Sampaio J.P., Schussler A., Sugiyama J., Thorn R.G., Tibell L., Untereiner W.A., Walker C., Wang Z., Weir A., Weiss M., White M.M., Winka K., Yao Y.J., and Zhang N. A higher-level phylogenetic classification of the Fungi. Mycological Research 111 (2007) 509-547
16. Himmel M.E., Ding S.Y., Johnson D.K., Adney W.S., Nimlos M.R., Brady J.W., and Foust T.D. Biomass recalcitrance: engineering plants and enzymes for biofuels production. Science 315 (2007) 804-807
17. James T.Y., Kauff F., Schoch C.L., Matheny P.B., Hofstetter V., Cox C.J., Celio G., Gueidan C., Fraker E., Miadlikowska J., Lumbsch H.T., Rauhut A., Reeb V., Arnold A.E., Amtoft A., Stajich J.E., Hosaka K., Sung G.H., Johnson D., O'Rourke B., Crockett M., Binder M., Curtis J.M., Slot J.C., Wang Z., Wilson A.W., Schussler A., Longcore J.E., O'Donnell K., Mozley-Standridge S., Porter D., Letcher P.M., Powell M.J., Taylor J.W., White M.M., Griffith G.W., Davies D.R., Humber R.A., Morton J.B., Sugiyama J., Rossman A.Y., Rogers J.D., Pfister D.H., Hewitt D., Hansen K., Hambleton S., Shoemaker R.A., Kohlmeyer J., Volkmann-Kohlmeyer B., Spotts R.A., Serdani M., Crous P.W., Hughes K.W., Matsuura K., Langer E., Langer G., Untereiner W.A., Lucking R., Budel B., Geiser D.M., Aptroot A., Diederich P., Schmitt I., Schultz M., Yahr R., Hibbett D.S., Lutzoni F., McLaughlin D.J., Spatafora J.W., and Vilgalys R. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443 (2006) 818-822
18. Judelson H.S. The genetics and biology of Phytophthora infestans: modern approaches to a historical challenge. Fungal Genetics and Biology 22 (1997) 65-76
19. Kamper J., Kahmann R., Bolker M., Ma L.J., Brefort T., Saville B.J., Banuett F., Kronstad J.W., Gold S.E., Muller O., Perlin M.H., Wosten H.A., de Vries R., Ruiz-Herrera J., Reynaga-Pena C.G., Snetselaar K., McCann M., Perez-Martin J., Feldbrugge M., Basse C.W., Steinberg G., Ibeas J.I., Holloman W., Guzman P., Farman M., Stajich J.E., Sentandreu R., Gonzalez-Prieto J.M., Kennell J.C., 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 E.C., Cahill M.J., Boyce K.J., Klose J., Klosterman S.J., Deelstra H.J., Ortiz-Castellanos L., Li W., Sanchez-Alonso P., Schreier P.H., 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 H.W., Mauceli E.W., DeCaprio D., Wade C.M., Butler J., Young S., Jaffe D.B., Calvo S., Nusbaum C., Galagan J., and Birren B.W. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444 (2006) 97-101
20. Karaffa L., and Kubicek C.P. Aspergillus niger citric acid accumulation: do we understand this well working black box?. Applied Microbiology and Biotechnology 61 (2003) 189-196
21. Kellis M., Birren B.W., and Lander E.S. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428 (2004) 617-624
22. Kellis M., Patterson N., Birren B., Berger B., and Lander E.S. Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery. Journal of Computational Biology 11 (2004) 319-355
23. Kellis M., Patterson N., Endrizzi M., Birren B., and Lander E.S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423 (2003) 241-254
24. Liolios K., Mavromatis K., Tavernarakis N., and Kyrpides N.C. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Research 36 (2008) D475-D479
25. Levasseur A., Piumi F., Coutinho P.M., Rancurel C., Asther M., Delattre M., Henrissat B., Pontarotti P., Asther M., and Record E. FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds. Fungal Genetics and Biology 45 (2008) 638-645
26. Lutzoni F., Kauff F., Cox C.J., McLaughlin D., Celio G., Dentinger B., Padamsee M., Hibbett D., James T.Y., Baloch E., Grube M., Reeb V., Hofstetter V., Schoch C., Arnold A.E., Miadlikowska J., Spatafora J., Johnson D., Hambleton S., Crockett M., Shoemaker R., Sung G.-H., Luecking R., Lumbsch T., O'Donnell K., Binder M., Diederich P., Ertz D., Gueidan C., Hansen K., Harris R.C., Hosaka K., Lim Y.-W., Matheny B., Nishida H., Pfister D., Rogers J., Rossman A., Schmitt I., Sipman H., Stone J., Sugiyama J., Yahr R., and Vilgalys R. Assembling the fungal tree of life: progress, classification and evolution of subcellular traits. American Journal of Botany 91 (2004) 1446-1480
27. Magnuson J.K., and Lasure L.L. Organic acid production by filamentous fungi. In: Tkacz J.S., and Lange L. (Eds). Advances in Fungal Bio/technology for Industry, Agriculture and Medicine (2004), Kluwer Academic Publishers, Norwell, Mass 307-340
28. Maheshwari R., Bharadwaj G., and Bhat M.K. Thermophilic fungi: their physiology and enzymes. Microbiology and Molecular Biology Reviews 64 (2000) 461-488
29. Reese E.T. Enzymatic hydrolysis of cellulose. Applied and Environmental Microbiology 4 (1956) 39-45
30. Reese E.T., Levinson H.S., Downing M.H., and White W.L. Quartermaster culture collection. Farlowia 4 (1950) 45-86
31. Rosgaard L., Pedersen S., Cherry J.R., Harris P., and Meyer A.S. Efficiency of new fungal cellulase systems in boosting enzymatic degradation of barley straw lignocellulose. Biotechnology Progress 22 (2006) 493-498
32. Teter S.A., Xu F., Nedwin G.E., and Cherry J.R. Enzymes for biorefineries. In: Kamm B., Gruber P.R., and Kamm M. (Eds). Biorefineries - Industrial Processes and Products: Status Quo and Future Directions (2006), John Wiley and Sons, Inc
33. Turgeon B.G., and Baker S.E. Genetic and genomic dissection of the Cochliobolus heterostrophus Tox1 locus controlling biosynthesis of the polyketide virulence factor T-toxin. Advances in Genetics 57 (2007) 219-261
34. Werpy T., Peterson G., Aden A., Bozell J., Holladay J., White J., and Manheim A. Top Value Added Chemicals from Biomass, Volume I: Results of Screening for Potential Candidates from Sugars and Synthesis Gas (2004), U.S. Department of Energy
35. Wolfe K.H. Comparative genomics and genome evolution in yeasts. Philosophical Transactions of the Royal Society of London B Biological Sciences 361 (2006) 403-412
36. Wood V., Gwilliam R., Rajandream M.A., Lyne M., Lyne R., Stewart A., Sgouros J., Peat N., Hayles J., Baker S., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C., Collins M., Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K., Murphy L., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S., Warren T., Whitehead S., Woodward J., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schafer M., Muller-Auer S., Gabel C., Fuchs M., Dusterhoft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., and Nurse P. The genome sequence of Schizosaccharomyces pombe. Nature 415 (2002) 871-880
37. Xu G., and Goodell B. Mechanisms of wood degradation by brown-rot fungi: chelator-mediated cellulose degradation and binding of iron by cellulose. Journal of Biotechnology 87 (2001) 43-57