Fungal genome sequencing: basic biology to biotechnology

References

• Almeida AJ, Matute DR, Carmona JA, et al. (2007). Genome size and ploidy of Paracoccidioides brasiliensis reveals a haploid DNA content: flow cytometry and GP43 sequence analysis. Fungal Genet Biol, 44, 25–31
   PubMed Web of Science ®Google Scholar
• Annaluru N, Muller H, Mitchell LA, et al. (2014). Total synthesis of a functional designer eukaryotic chromosome. Science, 344, 55–8
   PubMed Web of Science ®Google Scholar
• Battaglia E, Benoit I, van den Brink J, et al. (2011). Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level. BMC Genomics, 12, 38
   PubMed Web of Science ®Google Scholar
• Berg MA, Albang R, Albermann K, et al. (2008). Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat Biotechnol, 26, 1161–8
   PubMed Web of Science ®Google Scholar
• Bittinger K, Charlson ES, Loy E, et al. (2014). Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing. Genome Biol, 15, 487
   PubMed Web of Science ®Google Scholar
• Blandin G, Llorente B, Malpertuy A, et al. (2000). Genomic exploration of the hemiascomycetous yeasts: 13. Pichia angusta. FEBS Lett, 487, 76–81
   PubMed Web of Science ®Google Scholar
• Borneman AR, Desany BA, Riches D, et al. (2011). Whole genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae. PLoS Genet, 7, e1001287
   PubMed Web of Science ®Google Scholar
• Brakhage AA. (2013). Regulation of fungal secondary metabolism. Nat Rev Microbiol, 11, 21–32
   PubMed Web of Science ®Google Scholar
• Breitkreutz B-J, Stark C, Reguly T, et al. (2008). The BioGRID Interaction Database: 2008 update. Nucleic Acids Res, 36, D637–40
   PubMed Web of Science ®Google Scholar
• Burmester A, Shelest E, Glöckner G, et al. (2011). Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. Genome Biol, 12, R7
   PubMed Web of Science ®Google Scholar
• Butler G, Rasmussen MD, Lin MF, et al. (2009). Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature, 459, 657–62
   PubMed Web of Science ®Google Scholar
• Cai J, Zhao R, Jiang H, et al. (2008). De Novo origination of a new protein coding gene in Saccharomyces cerevisiae. Genetics, 179, 487–96
   PubMed Web of Science ®Google Scholar
• Cantarel BL, Coutinho PM, Rancurel C, et al. (2009). The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res, 37, D233–8
   PubMed Web of Science ®Google Scholar
• Cantu D, Segovia V, MacLean D, et al. (2013). Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. Tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors. BMC Genomics, 14, 270
   PubMed Web of Science ®Google Scholar
• Cheeseman K, Ropars J, Renault P, et al. (2014). Multiple recent horizontal transfers of a large genomic region in cheese making fungi. Nat Commun, 5, 2876
   PubMed Web of Science ®Google Scholar
• Chen S, Xu J, Liu C, et al. (2012). Genome sequence of the model medicinal mushroom Ganoderma lucidum. Nature Commun, 3, 913
   PubMed Web of Science ®Google Scholar
• Cherry JM, Adler C, Ball C, et al. (1998). SGD: Saccharomyces Genome Database. Nucleic Acids Res, 26, 73–9
   PubMed Web of Science ®Google Scholar
• Cherry JM, Hong EL, Amundsen C, et al. (2012). Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res, 40, D700–5
   PubMed Web of Science ®Google Scholar
• Christie KR, Weng S, Balakrishnan R, et al. (2004). Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res, 32, D311–4
   PubMed Web of Science ®Google Scholar
• Cowen LE, Anderson JB, Kohn LM. (2002). Evolution of drug resistance in Candida albicans. Annu Rev Microbiol, 56, 139–65
   PubMed Web of Science ®Google Scholar
• Crawford JM, Townsend CA. (2010). New insights into the formation of fungal aromatic polyketides. Nat Rev Microbiol, 8, 879–89
   PubMed Web of Science ®Google Scholar
• Cullen D. (2007). The genome of an industrial workhorse. Nat Biotechnol, 25, 189–90
   PubMed Web of Science ®Google Scholar
• Cuomo CA, Güldener U, Xu JR, et al. (2007). The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science, 317, 1400–2
   PubMed Web of Science ®Google Scholar
• Dean R, Van Kan JAL, Pretorius ZA, et al. (2012). The top 10 fungal pathogens in molecular plant pathology. Plant Mol Pathol, 13, 414–30
   PubMed Web of Science ®Google Scholar
• Dean RA, Talbot NJ, Ebbole DJ, et al. (2005). The genome sequence of the rice blast fungus Magnaporthe grisea. Nature, 434, 980–6
   PubMed Web of Science ®Google Scholar
• Denning DW, Ribaud P, Milpied N, et al. (2002). Efficacy and safety of voriconazole in the treatment of acute invasive aspergillosis. Clin Infect Dis, 34, 563–71
   PubMed Web of Science ®Google Scholar
• Dietrich FS, Voegeli S, Brachat S, et al. (2004). The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science, 304, 304–7
   PubMed Web of Science ®Google Scholar
• Dix NJ, Webster J. (1995). Fungal ecology. London: Chapman and Hall
   Google Scholar
• Doddapaneni H, Subramanian V, Fu B, Cullen D. (2013). A comparative genomic analysis of the oxidative enzymes potentially involved in lignin degradation by Agaricus bisporus. Fungal Genet Biol, 55, 22–31
   PubMed Web of Science ®Google Scholar
• Duplessisa S, Cuomob CA, Linc Y-C, et al. (2011). Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc Natl Acad Sci USA, 108, 9166–71
   PubMed Web of Science ®Google Scholar
• Dupree JC, Vanderwalt JP. (1983). Fermentation of xylose to ethanol by a strain of Candida shehatae. Biotech Lett, 5, 357–62
   Web of Science ®Google Scholar
• Eastwood DC, Floudas D, Binder M, et al. (2011). The plant cell wall decomposing machinery underlies the functional diversity of forest fungi. Science, 333, 762
   PubMed Web of Science ®Google Scholar
• Endy D. (2008). Reconstruction of the genomes. Science, 319, 1196–7
   PubMed Web of Science ®Google Scholar
• Engel SR, Balakrishnan R, Binkley G, et al. (2010). Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res, 38, D433–6
   PubMed Web of Science ®Google Scholar
• Engel SR, Cherry JM. (2013). The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces genome database 2013. doi:10.1093/database/bat012
   Google Scholar
• Engelthaler DM, Hicks ND, Gillece JD, et al. (2014). Cryptococcus gattii in North American Pacific Northwest: whole population genome analysis provides insights into species evolution and dispersal. mBio, 5, e01464–14
   PubMed Web of Science ®Google Scholar
• Espagne E, Lespinet O, Malagnac F, et al. (2008). The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol, 9, R77
   PubMed Web of Science ®Google Scholar
• Etienne KA, Chibucos MC, Su Q, et al. (2014). Draft genome sequence of Mortierella alpina isolate CDC-B6842. Genome Announc, 2, e01180–13
   PubMedGoogle Scholar
• Fedorova ND, Khaldi N, Joardar VN, et al. (2008). Genomic Islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet, 4, e1000046
   PubMed Web of Science ®Google Scholar
• Fernández-Fueyo E, Ruiz-Dueñas FJ, Miki Y, et al. (2012). Lignin-degrading peroxidases from genome of selective ligninolytic fungus Ceriporiopsis subvermispora. J Biol Chem, 287, 16903–16
   PubMed Web of Science ®Google Scholar
• Floudas D, Binder M, Riley R, et al. (2012). The paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science, 336, 1715
   PubMed Web of Science ®Google Scholar
• Frazier ME, Johnson GM, Thomassen DG, et al. (2003). Realizing the potential of the genome revolution: the genomes to life program. Science, 300, 290–3
   PubMed Web of Science ®Google Scholar
• Gajendran K, Gonzales MD, Farmer A, et al. (2006). Phytophthora functional genomics database (PFGD): functional genomics of phytophthora–plant interactions. Nucleic Acids Res, 34, D465–70
   PubMed Web of Science ®Google Scholar
• Galagan JE, Calvo SE, Borkovich KA, et al. (2003). The genome sequence of the filamentous fungus Neurospora crassa. Nature, 422, 859–68
   PubMed Web of Science ®Google Scholar
• Galagan JE, Henn MR, Ma L-J, et al. (2005). Genomics of the fungal kingdom: insights into eukaryotic biology. Genome Res, 15, 1620–31
   PubMed Web of Science ®Google Scholar
• Galazka JM, Tian C, Beeson WT, et al. (2010). Cellodextrin transport in yeast for improved biofuel production. Science, 330, 84–6
   PubMed Web of Science ®Google Scholar
• Gao Q, Jin K, Ying S-H, et al. (2011). Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum. PLoS Genet, 7, e1001264
   PubMed Web of Science ®Google Scholar
• Gattiker A, Rischatsch R, Demougin P, et al. (2007). Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists. BMC Genomics, 8, 9
   PubMed Web of Science ®Google Scholar
• Gibson DG, Benders GA, Axelrod KC, et al. (2008). One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc Natl Acad Sci USA, 105, 20404–9
   PubMed Web of Science ®Google Scholar
• Gilsenan JM, Cooley J, Bowyer P. (2012). CADRE: the Central Aspergillus Data Repository. Nucleic Acids Res, 40, D660–6
   PubMed Web of Science ®Google Scholar
• Goffeau A, Barrell BG, Bussey H, et al. (1996). Life with 6000 genes. Science, 274, 563–7
   Web of Science ®Google Scholar
• Goodwin SB, Ben M’Barek S, Dhillon B, et al. (2011). Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis. PLoS Genet, 7, e1002070
   PubMed Web of Science ®Google Scholar
• Grigoriev IV, Cullen D, Goodwin SB, et al. (2011). Fueling the future with fungal genomics. Mycology, 2, 192–209
   Google Scholar
• Grigoriev IV, Nikitin R, Haridas S, et al. (2014). MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res, 42, D699–704
   PubMed Web of Science ®Google Scholar
• Gunde-Cimerman N, Ramos J, Plemenitas A. (2009). Halotolerant and halophilic fungi. Mycol Res, 113, 1231–41
   PubMed Web of Science ®Google Scholar
• Haas BJ, Kamoun S, Zody MC, et al. (2009). Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature, 461, 393–8
   PubMed Web of Science ®Google Scholar
• Haas BJ, Zeng Q, Pearson MD, et al. (2011). Approaches to fungal genome annotation. Mycology, 2, 118–41
   PubMedGoogle Scholar
• Hahn-Hägerdal B, Galbe M, Gorwa-Grauslund M-F, et al. (2006). Bio-ethanol: the fuel of tomorrow from the residues of today. Trends Biotechnol, 24, 549–56
   PubMed Web of Science ®Google Scholar
• Hättenschwiler S, Tiunov AV, Scheu S. (2005). Biodiversity and litter decomposition in terrestrial ecosystems. Annu Rev Ecol Evol Syst, 36, 191–218
   Web of Science ®Google Scholar
• Hector RF, Laniado-Laborin R. (2005). Coccidioidomycosis – a fungal disease of the Americas. PLoS Med, 2, e2
   PubMed Web of Science ®Google Scholar
• Hertz-Fowler C, Pain A. (2007). Specialist fungi, versatile genomes. Nature, 5, 322
   Web of Science ®Google Scholar
• Hohmann S. (2009). Control of high osmolarity signalling in the yeast Saccharomyces cerevisiae. FEBS Lett, 583, 4025–9
   PubMed Web of Science ®Google Scholar
• Hu J, Chen C, Peever T, et al. (2012). Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer. BMC Genomics, 13, 171
   PubMed Web of Science ®Google Scholar
• Jeffries TW. (2006). Engineering yeasts for xylose metabolism. Curr Opin Biotechnol, 17, 320–6
   PubMed Web of Science ®Google Scholar
• Jones T, Federspiel NA, Chibana H, et al. (2004). The diploid genome sequence of Candida albicans. Proc Natl Acad Sci USA, 101, 7329–34
   PubMed Web of Science ®Google Scholar
• Kamoun S. (2003). Molecular genetics of pathogenic oomycetes. Eukar Cell, 2, 191–9
   PubMed Web of Science ®Google Scholar
• Kämper J, Kahmann R, Bölker M, et al. (2006). Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature, 444, 97–101
   PubMed Web of Science ®Google Scholar
• Keller NP, Turner G, Bennet JW. (2005). Fungal secondary metabolism – from biochemistry to genomics. Nat Rev Microbiol, 3, 937–47
   PubMed Web of Science ®Google Scholar
• Kellner H, Vandenbol M. (2010). Fungi unearthed: transcripts encoding lignocellulolytic and chitinolytic enzymes in forest soil. PLoS One, 5, e10971
   PubMed Web of Science ®Google Scholar
• Kersten P, Cullen D. (2007). Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium. Fungal Genet Biol, 44, 77–87
   PubMed Web of Science ®Google Scholar
• Khaldi N, Seifuddin FT, Turner G, et al. (2010). SMURF: genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol, 47, 736–41
   PubMed Web of Science ®Google Scholar
• King BC, Waxman KD, Nenni NV, et al. (2011). Arsenal of plant cell wall degrading enzymes reflects host preference among plant pathogenic fungi. Biotechnol Biofuels, 4, 4
   PubMed Web of Science ®Google Scholar
• Kirk PM, Cannon PF, David JC, Stalpers JA. (2001). Ainsworth and Bisby’s dictionary of the fungi. Wallingford, UK: CAB International
   Google Scholar
• Kis-Papo T, Weig AR, Riley R, et al. (2014). Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum. Nat Commun, 9, 3745
   Web of Science ®Google Scholar
• Kurtzman CP, Robnett CJ. (2010). Systematics of methanol assimilating yeasts and neighboring taxa from multigene sequence analysis and the proposal of Peterozyma gen.nov., a new member of the Saccharomycetales. FEMS Yeast Res, 10, 353–61
   PubMed Web of Science ®Google Scholar
• Lackner G, Misiek M, Braesel J, Hoffmeister D. (2012). Genome mining reveals the evolutionary origin and biosynthetic potential of basidiomycete polyketide synthases. Fungal Genet Biol, 49, 996–1003
   PubMed Web of Science ®Google Scholar
• Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. (2007). The Genome Online Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acid Res, 36, D475–9
   PubMed Web of Science ®Google Scholar
• Loftus BL, Fung E, Roncaglia P, et al. (2005). The genome of the Basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science, 307, 1321–4
   PubMed Web of Science ®Google Scholar
• Lorenz S, Guenther M, Grumaz C, et al. (2014). Genome sequence of the Basidiomycetous Fungus Pseudozyma aphidis DSM70725, an efficient producer of biosurfactant mannosylerythritol lipids. Genome Announc, 2, e00053–14
   PubMedGoogle Scholar
• Ma L-J, Does HC, Borkovich KA, et al. (2010). Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature, 464, 367–73
   PubMed Web of Science ®Google Scholar
• Ma L-J, Shea T, Young S, et al. (2014). Genome sequence of Fusarium oxysporum f. sp. melonis strain NRRL 26406, a fungus causing Wilt disease on melon. Genome Announc, 2, e00730–14
   PubMedGoogle Scholar
• Machida M, Asai K, Sano M, et al. (2005). Genome sequencing and analysis of Aspergillus oryzae. Nature, 2438, 1157–61
   Web of Science ®Google Scholar
• Malthioni SM, Patel N, Riddick B, et al. (2013). Transcriptomics of the rice blast fungus Magnaporthe oryzae in response to the bacterial antagonist Lysobacter enzymogenes reveals candidate fungal defense response genes. PLoS One, 8, e76487
   PubMed Web of Science ®Google Scholar
• Martin F, Aerts A, Ahrén D, et al. (2008). The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature, 452, 88–92
   PubMed Web of Science ®Google Scholar
• Martin F, Kohler A, Murat C. (2010). Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature, 464, 1033–8
   PubMed Web of Science ®Google Scholar
• Martinez D, Berka RM, Henrissat B, et al. (2008). Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol, 26, 553–60
   PubMed Web of Science ®Google Scholar
• Martinez D, Challacombe J, Morgenstern I, et al. (2009). Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci USA, 106, 1954
   PubMed Web of Science ®Google Scholar
• Martinez D, Larrondo LF, Putnam N, et al. (2004). Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol, 22, 695
   PubMed Web of Science ®Google Scholar
• Martinez DA, Oliver BG, Gräser Y, et al. (2012). Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. mBio, 3, e00259–12
   PubMed Web of Science ®Google Scholar
• Medema MH, Blin K, Cimermancic P, et al. (2011). antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res, 39, W339–46
   PubMed Web of Science ®Google Scholar
• Mewes HW, Frishman D, Gruber C, et al. (2000). MIPS: a database for genomes and protein sequences. Nucleic Acids Res, 28, 37–40
   PubMed Web of Science ®Google Scholar
• Mewes HW, Ruepp A, Theis F, et al. (2010). MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res, 39, D220–4
   PubMed Web of Science ®Google Scholar
• Moolhuijzen PM, Manners JM, Wilcox SA, et al. (2013). Genome sequences of six wheat-infecting Fusarium species isolates. Genome Anounc, 1, e00670–13
   PubMedGoogle Scholar
• Moore D, Meškauskas A. (2006). A comprehensive comparative analysis of the occurrence of developmental sequences in fungal, plant and animal genomes. Myco Res, 110, 251–6
   PubMed Web of Science ®Google Scholar
• Morin E, Kohler A, Baker AR, et al. (2012). Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc Natl Acad Sci USA, 109, 17501–6
   PubMed Web of Science ®Google Scholar
• Muller HM, Kenny EE, Sternberg PW. (2004). Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol, 2, e309
   PubMed Web of Science ®Google Scholar
• Nagalakshmi U, Wang Z, Waern K, et al. (2008). The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344–9
   PubMed Web of Science ®Google Scholar
• Nordberg H, Cantor M, Dusheyko S, et al. (2014). The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. Nucleic Acids Res, 42, D26–FD31
   PubMed Web of Science ®Google Scholar
• Ohm RA, Jong JF, Lugones LG, et al. (2010). Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol, 28, 957–65
   PubMed Web of Science ®Google Scholar
• Ormerod KL, Morrow CA, Chow EWL, et al. (2013). Comparative genomics of serial isolates of Cryptococcus neoformans reveals gene associated with carbon utilization and virulence. G3 Genes Genom Genet, 3, 675–86
   Web of Science ®Google Scholar
• Padamsee M, Kumar TKA, Riley R, et al. (2012). The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. Fungal Genet Biol, 49, 217–26
   PubMed Web of Science ®Google Scholar
• Pagani I, Liolios K, Jansson J, et al. (2012). The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res, 40, D571–9
   PubMed Web of Science ®Google Scholar
• Pain A, Hertz-Fowler C. (2008). Genomic adaptation: a fungal perspective. Nat Rev, 6, 572–3
   Google Scholar
• Pain A, Woodward J, Quail MA, et al. (2004). Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster. Fungal Genet Biol, 41, 443–53
   PubMed Web of Science ®Google Scholar
• Park J, Park B, Jung K, et al. (2008). CFGP: a web-based, comparative fungal genomics platform. Nucleic Acids Res, 36, D562
   PubMed Web of Science ®Google Scholar
• Passoth V, Fredlund E, Druvefors UA, Schnürer J. (2006). Biotechnology, physiology and genetics of the yeast Pichia anomala. FEMS Yeast Res, 6, 3–13
   PubMed Web of Science ®Google Scholar
• Pel HJ, de Winde JH, Archer DB, et al. (2007). Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol, 25, 221–31
   PubMed Web of Science ®Google Scholar
• Pitt JI, Hocking AD. (2009). Xerophiles. In: Pitt JI, Hocking AD. Fungi and food spoilage. US: Springer, 339–55
   Google Scholar
• Priebe S, Linde J, Albrecht D, et al. (2011). FungiFun: a web-based application for functional categorization of fungal genes and proteins. Fungal Genet Biol, 48, 353–8
   PubMed Web of Science ®Google Scholar
• Rhind N, Chen Z, Yassour M, et al. (2011). Comparative functional genomics of the fission yeasts. Science, 332, 930–6
   PubMed Web of Science ®Google Scholar
• Rileya R, Salamova AA, Brown DW, et al. (2014). Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci USA, 111, 9923–8
   PubMed Web of Science ®Google Scholar
• Ronning CM, Fedorova ND, Bowyer P, et al. (2005). Genomics of Aspergillus fumigatus. Rev Iberoam Micol, 22, 223–8
   PubMedGoogle Scholar
• Sanodiya BS, Thakur GS, Baghel RK, et al. (2009). Ganoderma lucidum: a potent pharmacological macrofungus. Curr Pharm Biotechnol, 10, 717–42
   PubMed Web of Science ®Google Scholar
• Schneider H, Wang PY, Maleszka CR. (1981). Conversion of d-xylose into ethanol by yeast Pachysolen tannophilus. Biotech Lett, 3, 89–92
   Web of Science ®Google Scholar
• Schneider J, Rupp O, Trost E, et al. (2012). Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities. FEMS Yeast Res, 12, 382–6
   PubMed Web of Science ®Google Scholar
• Schutter KD, Lin Y-C, Tiels P, et al. (2009). Genome sequence of the recombinant protein production host Pichia pastoris. Nat Biotechnol, 27, 561–9
   PubMed Web of Science ®Google Scholar
• Sharma KK, Kuhad RC. (2008). Laccase: enzyme revisited function redefined. Indian J Microbiol, 48, 309–16
   PubMed Web of Science ®Google Scholar
• Sharma KK, Shrivastava B, Sastry VRB, et al. (2013). Middle-redox potential laccase from Ganoderma sp.: its application in improvement of feed for monogastric animals. Sci Rep, 3, 1299
   PubMed Web of Science ®Google Scholar
• Sharpton TJ, Stajich JE, Rounsley SD, et al. (2009). Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res, 19, 1722–31
   PubMed Web of Science ®Google Scholar
• Skrzypek MS, Arnaud MB, Costanzo MC, et al. (2010). New tools at the Candida Genome Database: biochemical pathways and full-text literature search. Nucleic Acids Res, 38, D428–32
   PubMed Web of Science ®Google Scholar
• Smith DR, Quinlan AR, Peckham HE, et al. (2008). Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res, 18, 1638–42
   PubMed Web of Science ®Google Scholar
• Soliai MM, Meyer SE, Udall JA, et al. (2014). De novo genome assembly of the fungal plant pathogen Pyrenophora semeniperda. PLoS One, 9, e87045
   PubMed Web of Science ®Google Scholar
• Stajich JE, Harris T, Brunk BP, et al. (2012). FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res, 40, D675–81
   PubMed Web of Science ®Google Scholar
• Stajich JE, Wilkee SK, Ahrénf D, et al. (2010). Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci USA, 107, 11889–94
   PubMed Web of Science ®Google Scholar
• Steffen KT, Hatakka A, Hofrichter M. (2002). Removal and mineralization of polycyclic aromatic hydrocarbons by litter-decomposing basidiomycetous fungi. Appl Microbiol Biotechnol, 60, 212–17
   PubMed Web of Science ®Google Scholar
• Stein LD, Mungall C, Shu SQ, et al. (2002). The generic genome browser: a building block for a model organism system database. Genome Res, 12, 1599–610
   PubMed Web of Science ®Google Scholar
• Stephanopoulos G. (2007). Challenges in engineering microbes for biofuels production. Science, 315, 801–4
   PubMed Web of Science ®Google Scholar
• Stukenbrock EH, Jørgensen FG, Zala M, et al. (2010). Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola. PLoS Genet, 6, e1001189
   PubMed Web of Science ®Google Scholar
• Takeda I, Tamano K, Yamane N, et al. (2014). Genome sequence of the Mucoromycotina Fungus Umbelopsis isabellina, an effective producer of lipids. Genome Announc, 2, e00071–14
   PubMedGoogle Scholar
• Tavares S, Ramos AP, Pires AS, et al. (2014). Genome size analyses of Pucciniales reveal the largest fungal genomes. Front Plant Sci, 5, 422
   PubMed Web of Science ®Google Scholar
• van der Heijden MGA, Klironomos JN, Ursic M, et al. (1998). Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature, 396, 69–72
   Web of Science ®Google Scholar
• Wainright PO, Hinkle G, Sogin ML, Stickel SK. (1993). Monophyletic origins of the metazoa: an evolutionary link with fungi. Science, 260, 340–2
   PubMed Web of Science ®Google Scholar
• Wang F-Q, Zhong J, Zhao Y, et al. (2014). Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum. BMC Genomics, 15, S11
   PubMed Web of Science ®Google Scholar
• Wang Z, Gerstein M, Snyder M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet, 10, 57–63
   PubMed Web of Science ®Google Scholar
• Ward PP, Lo JY, Duke M, et al. (1992b). Production of biologically active recombinant human lactoferrin in Aspergillus oryzae. Biotechnology, 10, 784–9
   PubMed Web of Science ®Google Scholar
• Wawrzyn GT, Quin MB, Choudhary S, et al. (2012). Draft genome of Omphalotus olearius provides a predictive framework for sesquiterpenoid natural product biosynthesis in Basidiomycota. Chem Biol, 19, 772–83
   PubMed Web of Science ®Google Scholar
• Wilhelm BT, Marguerat S, Watt S, et al. (2008). Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature, 453, 1239–43
   PubMed Web of Science ®Google Scholar
• Wohlbach D, Kuoc A, Satob TK, et al. (2011). Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. Proc Natl Acad Sci USA, 108, 13212–17
   PubMed Web of Science ®Google Scholar
• Wong P, Walter M, Lee W, et al. (2011). FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum. Nucleic Acids Res, 39, D637–9
   PubMed Web of Science ®Google Scholar
• Wood V, Gwilliam R, Rajandream M-A, et al. (2002). The genome sequence of Schizosaccharomyces pombe. Nature, 415, 871–80
   PubMed Web of Science ®Google Scholar
• Xu J, Saunders CW, Hu P, et al. (2007). Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens. Proc Natl Acad Sci USA, 104, 18730–5
   PubMed Web of Science ®Google Scholar
• Zhao Z, Liu H, Wang C, Xu J-R. (2013). Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. BMC Genomics, 14, 274
   PubMed Web of Science ®Google Scholar