References:

1. Samson RA, Visagie CM, Houbraken J, Hong SB, Hubka V, Klaassen CH, et al. Phylogeny, identification and nomenclature of the genus Aspergillus. Stud Mycol. 2014;78:141–73. doi: 10.1016/j.simyco.2014.07.004.

2. Scazzocchio C. Aspergillus, a multifacted genus In: Schaechter M, editor. Encyclopaedia of Microbiology. Amsterdam: Elsevier; 2009. p. 401-420.

3. Geiser DM, Samson RA, Varga J, Rokas A, Witiak SM. A review of molecular phylogenetics in Aspergillus, and prospects for a robust genus-wide phylogeny. In: Varga J, Samson RA, editors. Aspergillusin the genomic era. Wageningen: Wageningen Academic Publishers; 2008. pp. 17–32.

4. Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, et al. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature. 2005;438:1105–15. doi: 10.1038/nature04341.

5. Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, et al. Genome sequencing and analysis of Aspergillus oryzae. Nature. 2005;438:1157–61. doi: 10.1038/nature04300.

6. Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature. 2005;438:1151–6. doi: 10.1038/nature04332.

7. Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, et al. Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res. 2011;21:885–97. doi: 10.1101/gr.112169.110.

8. Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, et al. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet. 2008;4 doi: 10.1371/journal.pgen.1000046.

9. Payne GA, Nierman WC, Wortman JR, Pritchard BL, Brown D, Dean RA, et al. Whole genome comparison of Aspergillus flavus and Aspergillus oryzae. Med Mycol. 2006;44(S1):9–11. doi: 10.1080/13693780600835716.

10. Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, et al. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol. 2007;25:221–31. doi: 10.1038/nbt1282.

11. Benoit I, Malavazi I, Goldman G, Baker SE, de Vries RP. Aspergillus - Genomics of a cosmopolitan fungus. In: Horwitz BA, Mukherjee PK, Mukherjee M, Kubicek CP, editors. Genomics of soil- and plant-associated fungi. Heidelberg: Springer; 2013. pp. 89–126.

12. Rokas A, Payne G, Fedorova ND, Baker SE, Machida M, Yu J, et al. What can comparative genomics tell us about species concepts in the genus Aspergillus? Stud Mycol. 2007;59:11–7. doi: 10.3114/sim.2007.59.02.

13. Mabey Gilsenan J, Cooley J, Bowyer P. CADRE: the Central Aspergillus Data REpository 2012. Nucleic Acids Res. 2012;40:D660–6. doi: 10.1093/nar/gkr971.

14. Arnaud MB, Cerqueira GC, Inglis DO, Skrzypek MS, Binkley J, Chibucos MC, et al. The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. Nucleic Acids Res. 2012;40:D653–9. doi: 10.1093/nar/gkr875

15. Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, et al. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 2014;42:D699–704. doi: 10.1093/nar/gkt1183]

16. Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, et al. The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res. 2012;40:D26–32. doi: 10.1093/nar/gkr947. ]

17. Alker AP, Smith GW, Kim K. Characterization of Aspergillus sydowii (Thom et Church), a fungal pathogen of Caribbean sea fan corals. Hydrobiol. 2001;460:105–11. doi: 10.1023/A:1013145524136.

18. van den Berg MA, Albang R, Albermann K, Badger JH, Daran J-M, Driessen AJM, et al. Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat Biotech. 2008;26:1161–8. doi: 10.1038/nbt.1498.

19. Marcet-Houben M, Ballester AR, de la Fuente B, Harries E, Marcos JF, Gonzalez-Candelas L, et al. Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus. BMC Genomics. 2012;13:646. doi: 10.1186/1471-2164-13-646. ]

20. Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, et al. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res. 2009;19:1722–31. doi: 10.1101/gr.087551.108.

21. Martinez DA, Oliver BG, Graser Y, Goldberg JM, Li W, Martinez-Rossi NM, et al. Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. mBio. 2012;3:e00259–12. doi: 10.1128/mBio.00259-12.

22. Desjardins CA, Champion MD, Holder JW, Muszewska A, Goldberg J, Bailao AM, et al. Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis. PLoS Genet. 2011;7 doi: 10.1371/journal.pgen.1002345.

23. Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, et al. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina) Nat Biotechnol. 2008;26:553–60. doi: 10.1038/nbt1403

24. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, et al. The genome sequence of the filamentous fungus Neurospora crassa. Nature. 2003;422:859–68. doi: 10.1038/nature01554.]

25. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, et al. Life with 6000 genes. Science. 1996;274:546–7. doi: 10.1126/science.274.5287.546.

26. Houbraken J, Samson RA. Phylogeny of Penicillium and the segregation of Trichocomaceae into three families. Stud Mycol. 2011;70:1–51. doi: 10.3114/sim.2011.70.01.

27. Pitt JI, Taylor JW. Aspergillus, its sexual states and the new International Code of Nomenclature. Mycologia. 2014;106:1051–62. doi: 10.3852/14-060.

28. Houbraken J, de Vries RP, Samson RA. Modern taxonomy of biotechnologically important Aspergillusand Penicillium species. Adv Appl Microbiol. 2014;86:199–249. doi: 10.1016/B978-0-12-800262-9.00004-4.

29. Perrone G, Susca A, Cozzi G, Ehrlich K, Varga J, Frisvad JC, et al. Biodiversity of Aspergillus species in some important agricultural products. Stud Mycol. 2007;59:53–66. doi: 10.3114/sim.2007.59.07.

30. Etxebeste O, Garzia A, Espeso EA, Ugalde U. Aspergillus nidulans asexual development: making the most of cellular modules. Trends Microbiol. 2010;18:569–76. doi: 10.1016/j.tim.2010.09.007.

31. Krijgsheld P, Bleichrodt R, van Veluw GJ, Wang F, Muller WH, Dijksterhuis J, et al. Development in Aspergillus. Stud Mycol. 2013;74:1–29. doi: 10.3114/sim0006.

32. Dyer PS, O’Gorman CM. A fungal sexual revolution: Aspergillus and Penicillium show the way. Curr Opin Microbiol. 2011;14:649–54. doi: 10.1016/j.mib.2011.10.001.

33. Dyer PS, O’Gorman CM. Sexual development and cryptic sexuality in fungi: insights from Aspergillusspecies. FEMS Microbiol Rev. 2012;36:165–92. doi: 10.1111/j.1574-6976.2011.00308.x.

34. Scazzocchio C. Aspergillus genomes: secret sex and the secrets of sex. Trends Genet. 2006;22:521–5. doi: 10.1016/j.tig.2006.08.004.

35. Park HS, Yu JH. Genetic control of asexual sporulation in filamentous fungi. Curr Opin Microbiol. 2012;15:669–77. doi: 10.1016/j.mib.2012.09.006.

36. Adams TH, Wieser JK, Yu JH. Asexual sporulation in Aspergillus nidulans. Microbiol Mol Biol Rev. 1998;62:35–54.

37. Lee MK, Kwon NJ, Choi JM, Lee IS, Jung S, Yu JH. NsdD is a key repressor of asexual development in Aspergillus nidulans. Genetics. 2014;197:159–73. doi: 10.1534/genetics.114.161430.

38. Bayram O, Braus GH, Fischer R, Rodriguez-Romero J. Spotlight on Aspergillus nidulans photosensory systems. Fungal Genet Biol. 2010;47:900–8. doi: 10.1016/j.fgb.2010.05.008.

39. Bayram O, Braus GH. Coordination of secondary metabolism and development in fungi: the velvet family of regulatory proteins. FEMS Microbiol Rev. 2012;36:1–24. doi: 10.1111/j.1574-6976.2011.00285.x.

40. Wong HC, Chien CY. Ultrastructural studies of the conidial anamorphs of Monascus. Mycologia. 1986;78:593–9. doi: 10.2307/3807771.

41. Dyer PS, Inderbitzin P, Debuchy R. Mating-type structure, function, regulation and evolution in the Pezizomycotina. In: Wendland J, editor. Growth, differentiation and sexuality. Volume I. The Mycota. 3. Switzerland: Springer International Publishing; 2016. pp. 351–85.

42. Debuchy R, Berteaux-Lecellier V, Silar P. Mating systems and sexual morphogenesis in ascomycetes. In: Borkovich KA, Ebbole DJ, editors. Cellular and molecular biology of filamentous fungi. Washington, DC: ASM Press; 2010. pp. 501–35.

43. Böhm J, Hoff B, O’Gorman CM, Wolfers S, Klix V, Binger D, et al. Sexual reproduction and mating-type-mediated strain development in the penicillin-producing fungus Penicillium chrysogenum. Proc Natl Acad Sci U S A. 2013;110:1476–81. doi: 10.1073/pnas.1217943110.

44. Yun SH, Berbee ML, Yoder OC, Turgeon BG. Evolution of the fungal self-fertile reproductive life style from self-sterile ancestors. Proc Natl Acad Sci U S A. 1999;96:5592–7. doi: 10.1073/pnas.96.10.5592.

45. Geiser DM, Pitt JI, Taylor JW. Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus. Proc Natl Acad Sci U S A. 1998;95:388–93. doi: 10.1073/pnas.95.1.388]

46. Paoletti M, Seymour FA, Alcocer MJ, Kaur N, Calvo AM, Archer DB, et al. Mating type and the genetic basis of self-fertility in the model fungus Aspergillus nidulans. Curr Biol. 2007;17:1384–9. doi: 10.1016/j.cub.2007.07.012.

47. Ramirez-Prado JH, Moore GG, Horn BW, Carbone I. Characterization and population analysis of the mating-type genes in Aspergillus flavus and Aspergillus parasiticus. Fungal Genet Biol. 2008;45:1292–9. doi: 10.1016/j.fgb.2008.06.007.

48. Rydholm C, Dyer PS, Lutzoni F. DNA sequence characterization and molecular evolution of MAT1 and MAT2 mating-type loci of the self-compatible ascomycete mold Neosartorya fischeri. Eukaryot Cell. 2007;6:868–74. doi: 10.1128/EC.00319-06.

49. Flipphi M, Sun J, Robellet X, Karaffa L, Fekete E, Zeng AP, et al. Biodiversity and evolution of primary carbon metabolism in Aspergillus nidulans and other Aspergillus spp. Fungal Genet Biol. 2009;46(Suppl 1):S19–44. doi: 10.1016/j.fgb.2008.07.018.

50. Khosravi C, Benocci T, Battaglia E, Benoit I, de Vries RP. Sugar catabolism in Aspergillus and other fungi related to the utilization of plant biomass. Adv Appl Microbiol. 2014;90:1–28. doi: 10.1016/bs.aambs.2014.09.005.

51. Fekete E, de Vries RP, Seiboth B, vanKuyk PA, Sandor E, Metz B, et al. D-Galactose uptake is nonfunctional in the conidiospores of Aspergillus niger. FEMS Microbiol Lett. 2012;329:198–203. doi: 10.1111/j.1574-6968.2012.02524.x.

52. Hayer K, Stratford M, Archer DB. Structural features of sugars that trigger or support conidial germination in the filamentous fungus Aspergillus niger. Appl Environ Microbiol. 2013;79:6924–31. doi: 10.1128/AEM.02061-13.
53. Hayer K, Stratford M, Archer
DB. Germination of Aspergillus niger conidia is triggered by nitrogen compounds related to L-amino acids. Appl Environ Microbiol. 2014;80:6046–53. doi: 10.1128/AEM.01078-14.

54. Geber A, Williamson PR, Rex JH, Sweeney EC, Bennett JE. Cloning and characterization of a Candida albicans maltase gene involved in sucrose utilization. J Bacteriol. 1992;174:6992–6. doi: 10.1128/jb.174.21.6992-6996.1992.

55. Culleton H, McKie V, de Vries RP. Physiological and molecular aspects of degradation of plant polysaccharides by fungi: What have we learned from Aspergillus? Biotechnol J. 2013;8:884–94. doi: 10.1002/biot.201200382.

56. de Vries RP, Visser J. Aspergillus enzymes involved in degradation of plant cell wall polysaccharides. Microb Mol Biol Rev. 2001;65:497–522. doi: 10.1128/MMBR.65.4.497-522.2001.

57. Benoit I, Culleton H, Zhou M, DiFalco M, Aguilar-Osorio G, Battaglia E, et al. Closely related fungi employ diverse enzymatic strategies to degrade plant biomass. Biotechnol Biofuels. 2015;8:107. doi: 10.1186/s13068-015-0285-0.

58. Coutinho PM, Andersen MR, Kolenova K, vanKuyk PA, Benoit I, Gruben BS, et al. Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. Fungal Genet Biol. 2009;46(Suppl 1):S161–9. doi: 10.1016/j.fgb.2008.07.020.

59. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:D490–5. doi: 10.1093/nar/gkt1178.]

60. Mäkelä MR, Jiménez Barboza LA, de Vries RP, Hildén KS. Production of feruloyl esterases by Aspergillus species. In: de Vries RP, Benoit I, Andersen MR, editors. Aspergillus and Penicillium in the post-genomic era. Norfolk: Caister Academic Press; 2016. pp. 129–44.

61. The fung-growth database. Linking growth to genome. http://www.fung-growth.org/.

62. Klaubauf S, Narang HM, Post H, Zhou M, Brunner K, Mach-Aigner AR, et al. Similar is not the same: Differences in the function of the (hemi-)cellulolytic regulator XlnR (Xlr1/Xyr1) in filamentous fungi. Fungal Genet Biol. 2014;72:73–81. doi: 10.1016/j.fgb.2014.07.007.

63. Brakhage AA. Regulation of fungal secondary metabolism. Nat Rev Microbiol. 2013;11:21–32. doi: 10.1038/nrmicro2916.
64. Wiemann P, Keller NP. Strategies for mining fungal natural products. J Ind Microbiol Biotechnol. 2014;41:301–13. doi: 10.1007/s10295-013-1366-3.

65. Chiang YM, Szewczyk E, Davidson AD, Keller N, Oakley BR, Wang CC. A gene cluster containing two fungal polyketide synthases encodes the biosynthetic pathway for a polyketide, asperfuranone, in Aspergillus nidulans. J Am Chem Soc. 2009;131:2965–70. doi: 10.1021/ja8088185.

66. Bergmann S, Schumann J, Scherlach K, Lange C, Brakhage AA, Hertweck C. Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. Nat Chem Biol. 2007;3:213–7. doi: 10.1038/nchembio869.

67. Sanchez JF, Entwistle R, Hung JH, Yaegashi J, Jain S, Chiang YM, et al. Genome-based deletion analysis reveals the prenyl xanthone biosynthesis pathway in Aspergillus nidulans. J Am Chem Soc. 2011;133:4010–7. doi: 10.1021/ja1096682.

68. Schätzle MA, Husain SM, Ferlaino S, Muller M. Tautomers of anthrahydroquinones: enzymatic reduction and implications for chrysophanol, monodictyphenone, and related xanthone biosyntheses. J Am Chem Soc. 2012;134:14742–5. doi: 10.1021/ja307151x.

69. Simpson TJ. Genetic and biosynthetic studies of the fungal prenylated xanthone shamixanthone and related metabolites in Aspergillus spp. revisited. Chem Bio Chem. 2012;13:1680–8. doi: 10.1002/cbic.201200014.

70. Bromann K, Toivari M, Viljanen K, Vuoristo A, Ruohonen L, Nakari-Setälä T. Identification and characterization of a novel diterpene gene cluster in Aspergillus nidulans. PLoS One. 2012;7 doi: 10.1371/journal.pone.0035450.

71. Bergmann S, Funk AN, Scherlach K, Schroeckh V, Shelest E, Horn U, et al. Activation of a silent fungal polyketide biosynthesis pathway through regulatory cross talk with a cryptic nonribosomal peptide synthetase gene cluster. Appl Environ Microbiol. 2010;76:8143–9. doi: 10.1128/AEM.00683-10

72. Yeh HH, Ahuja M, Chiang YM, Oakley CE, Moore S, Yoon O, et al. Resistance gene-guided genome mining: Serial promoter exchanges in Aspergillus nidulans reveal the biosynthetic pathway for fellutamide B, a proteasome inhibitor. ACS Chem Biol. 2016;11:2275–84. doi: 10.1021/acschembio.6b00213

73. Chiang YM, Szewczyk E, Davidson AD, Entwistle R, Keller NP, Wang CC, et al. Characterization of the Aspergillus nidulans monodictyphenone gene cluster. Appl Environ Microbiol. 2010;76:2067–74. doi: 10.1128/AEM.02187-09.

74. Schroeckh V, Scherlach K, Nutzmann HW, Shelest E, Schmidt-Heck W, Schuemann J, et al. Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans. Proc Natl Acad Sci U S A. 2009;106:14558–63. doi: 10.1073/pnas.0901870106.

75. MacCabe AP, Riach MB, Unkles SE, Kinghorn JR. The Aspergillus nidulans npeA locus consists of three contiguous genes required for penicillin biosynthesis. EMBO J. 1990;9:279–87.

76. Ahuja M, Chiang YM, Chang SL, Praseuth MB, Entwistle R, Sanchez JF, et al. Illuminating the diversity of aromatic polyketide synthases in Aspergillus nidulans. J Am Chem Soc. 2012;134:8212–21. doi: 10.1021/ja3016395.

77. Eisendle M, Oberegger H, Zadra I, Haas H. The siderophore system is essential for viability of Aspergillus nidulans: functional analysis of two genes encoding l-ornithine N 5-monooxygenase (sidA) and a non-ribosomal peptide synthetase (sidC) Mol Microbiol. 2003;49:359–75. doi: 10.1046/j.1365-2958.2003.03586.x.

78. Brown DW, Yu JH, Kelkar HS, Fernandes M, Nesbitt TC, Keller NP, et al. Twenty-five coregulated transcripts define a sterigmatocystin gene cluster in Aspergillus nidulans. Proc Natl Acad Sci U S A. 1996;93:1418–22. doi: 10.1073/pnas.93.4.1418.

79. Bouhired S, Weber M, Kempf-Sontag A, Keller NP, Hoffmeister D. Accurate prediction of the Aspergillus nidulans terrequinone gene cluster boundaries using the transcriptional regulator LaeA. Fungal Genet Biol. 2007;44:1134–45. doi: 10.1016/j.fgb.2006.12.010.

80. Gerke J, Bayram O, Feussner K, Landesfeind M, Shelest E, Feussner I, et al. Breaking the silence: protein stabilization uncovers silenced biosynthetic gene clusters in the fungus Aspergillus nidulans. Appl Environ Microbiol. 2012;78:8234–44. doi: 10.1128/AEM.01808-12.

81. Chiang YM, Ahuja M, Oakley CE, Entwistle R, Asokan A, Zutz C, et al. Development of genetic dereplication strains in Aspergillus nidulans results in the discovery of aspercryptin. Angew Chem Int Ed Engl. 2016;55:1662–5. doi: 10.1002/anie.201507097.

82. Lim FY, Hou Y, Chen Y, Oh JH, Lee I, Bugni TS, et al. Genome-based cluster deletion reveals an endocrocin biosynthetic pathway in Aspergillus fumigatus. Appl Environ Microbiol. 2012;78:4117–25. doi: 10.1128/AEM.07710-11.

83. Lin HC, Chooi YH, Dhingra S, Xu W, Calvo AM, Tang Y. The fumagillin biosynthetic gene cluster in Aspergillus fumigatus encodes a cryptic terpene cyclase involved in the formation of beta-trans-bergamotene. J Am Chem Soc. 2013;135:4616–9. doi: 10.1021/ja312503y.

84. Ames BD, Liu X, Walsh CT. Enzymatic processing of fumiquinazoline F: a tandem oxidative-acylation strategy for the generation of multicyclic scaffolds in fungal indole alkaloid biosynthesis. Biochemistry. 2010;49:8564–76. doi: 10.1021/bi1012029.]

85. O’Hanlon KA, Gallagher L, Schrettl M, Jochl C, Kavanagh K, Larsen TO, et al. Nonribosomal peptide synthetase genes pesL and pes1 are essential for fumigaclavine C production in Aspergillus fumigatus. Appl Environ Microbiol. 2012;78:3166–76. doi: 10.1128/AEM.07249-11.

86. Maiya S, Grundmann A, Li SM, Turner G. The fumitremorgin gene cluster of Aspergillus fumigatus: identification of a gene encoding brevianamide F synthetase. ChemBioChem. 2006;7:1062–9. doi: 10.1002/cbic.200600003.

87. Gardiner DM, Howlett BJ. Bioinformatic and expression analysis of the putative gliotoxin biosynthetic gene cluster of Aspergillus fumigatus. FEMS Microbiol Lett. 2005;248:241–8. doi: 10.1016/j.femsle.2005.05.046.

88. Yin WB, Baccile JA, Bok JW, Chen Y, Keller NP, Schroeder FC. A nonribosomal peptide synthetase-derived iron(III) complex from the pathogenic fungus Aspergillus fumigatus. J Am Chem Soc. 2013;135:2064–7. doi: 10.1021/ja311145n.

89. Chooi YH, Fang J, Liu H, Filler SG, Wang P, Tang Y. Genome mining of a prenylated and immunosuppressive polyketide from pathogenic fungi. Org Lett. 2013;15:780–3. doi: 10.1021/ol303435y.

90. O’Hanlon KA, Cairns T, Stack D, Schrettl M, Bignell EM, Kavanagh K, et al. Targeted disruption of nonribosomal peptide synthetase pes3 augments the virulence of Aspergillus fumigatus. Infect Immun. 2011;79:3978–92. doi: 10.1128/IAI.00192-11.

91. Igarashi Y, Yabuta Y, Sekine A, Fujii K, Harada K, Oikawa T, et al. Directed biosynthesis of fluorinated pseurotin A, synerazol and gliotoxin. J Antibiot (Tokyo) 2004;57:748–54. doi: 10.7164/antibiotics.57.748

92. Maiya S, Grundmann A, Li X, Li SM, Turner G. Identification of a hybrid PKS/NRPS required for pseurotin A biosynthesis in the human pathogen Aspergillus fumigatus. ChemBioChem. 2007;8:1736–43. doi: 10.1002/cbic.200700202.

93. Vödisch M, Scherlach K, Winkler R, Hertweck C, Braun HP, Roth M, et al. Analysis of the Aspergillus fumigatus proteome reveals metabolic changes and the activation of the pseurotin A biosynthesis gene cluster in response to hypoxia. J Proteome Res. 2011;10:2508–24. doi: 10.1021/pr1012812.]

94. Wiemann P, Guo CJ, Palmer JM, Sekonyela R, Wang CC, Keller NP. Prototype of an intertwined secondary-metabolite supercluster. Proc Natl Acad Sci U S A. 2013;110:17065–70. doi: 10.1073/pnas.1313258110.

95. Robinson SL, Panaccione DG. Chemotypic and genotypic diversity in the ergot alkaloid pathway of Aspergillus fumigatus. Mycologia. 2012;104:804–12. doi: 10.3852/11-310.

96. Frisvad JC, Larsen TO, Thrane U, Meijer M, Varga J, Samson RA, et al. Fumonisin and ochratoxin production in industrial Aspergillus niger strains. PLoS One. 2011;6 doi: 10.1371/journal.pone.0023496.

97. Awakawa T, Yang XL, Wakimoto T, Abe I. Pyranonigrin E: a PKS-NRPS hybrid metabolite from Aspergillus niger identified by genome mining. ChemBioChem. 2013;14:2095–9. doi: 10.1002/cbic.201300430.

98. Nakazawa T, Ishiuchi K, Praseuth A, Noguchi H, Hotta K, Watanabe K. Overexpressing transcriptional regulator in Aspergillus oryzae activates a silent biosynthetic pathway to produce a novel polyketide. ChemBioChem. 2012;13:855–61. doi: 10.1002/cbic.201200107.

99. Imamura K, Tsuyama Y, Hirata T, Shiraishi S, Sakamoto K, Yamada O, et al. Identification of a gene involved in the synthesis of a dipeptidyl peptidase IV inhibitor in Aspergillus oryzae. Appl Environ Microbiol. 2012;78:6996–7002. doi: 10.1128/AEM.01770-12.

100. Yu J, Chang PK, Ehrlich KC, Cary JW, Bhatnagar D, Cleveland TE, et al. Clustered pathway genes in aflatoxin biosynthesis. Appl Environ Microbiol. 2004;70:1253–62. doi: 10.1128/AEM.70.3.1253-1262.2004.

101. Chang PK, Horn BW, Dorner JW. Clustered genes involved in cyclopiazonic acid production are next to the aflatoxin biosynthesis gene cluster in Aspergillus flavus. Fungal Genet Biol. 2009;46:176–82. doi: 10.1016/j.fgb.2008.11.002.

102. Zhang S, Monahan BJ, Tkacz JS, Scott B. Indole-diterpene gene cluster from Aspergillus flavus. Appl Environ Microbiol. 2004;70:6875–83. doi: 10.1128/AEM.70.11.6875-6883.2004.

103. Nielsen MT, Nielsen JB, Anyaogu DC, Holm DK, Nielsen KF, Larsen TO, et al. Heterologous reconstitution of the intact geodin gene cluster in Aspergillus nidulans through a simple and versatile PCR based approach. PLoS One. 2013;8 doi: 10.1371/journal.pone.0072871.

104. Qiao K, Chooi YH, Tang Y. Identification and engineering of the cytochalasin gene cluster from Aspergillus clavatus NRRL 1. Metab Eng. 2011;13:723–32. doi: 10.1016/j.ymben.2011.09.008.

105. Yin WB, Grundmann A, Cheng J, Li SM. Acetylaszonalenin biosynthesis in Neosartorya fischeri. Identification of the biosynthetic gene cluster by genomic mining and functional proof of the genes by biochemical investigation. J Biol Chem. 2009;284:100–9. doi: 10.1074/jbc.M807606200.

106. Guo CJ, Yeh HH, Chiang YM, Sanchez JF, Chang SL, Bruno KS, et al. Biosynthetic pathway for the epipolythiodioxopiperazine acetylaranotin in Aspergillus terreus revealed by genome-based deletion analysis. J Am Chem Soc. 2013;135:7205–13. doi: 10.1021/ja3123653.

107. Lo HC, Entwistle R, Guo CJ, Ahuja M, Szewczyk E, Hung JH, et al. Two separate gene clusters encode the biosynthetic pathway for the meroterpenoids austinol and dehydroaustinol in Aspergillus nidulans. J Am Chem Soc. 2012;134:4709–20. doi: 10.1021/ja209809t.

108. Inglis DO, Binkley J, Skrzypek MS, Arnaud MB, Cerqueira GC, Shah P, et al. Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae. BMC Microbiol. 2013;13:91. doi: 10.1186/1471-2180-13-91.]

109. Seshime Y, Juvvadi PR, Kitamoto K, Ebizuka Y, Fujii I. Identification of csypyrone B1 as the novel product of Aspergillus oryzae type III polyketide synthase CsyB. Bioorg Med Chem. 2010;18:4542–6. doi: 10.1016/j.bmc.2010.04.058. ]

110. Chiang YM, Szewczyk E, Nayak T, Davidson AD, Sanchez JF, Lo HC, et al. Molecular genetic mining of the Aspergillus secondary metabolome: discovery of the emericellamide biosynthetic pathway. Chem Biol. 2008;15:527–32. doi: 10.1016/j.chembiol.2008.05.010.

111. Birse CE, Clutterbuck AJ. Isolation and developmentally regulated expression of an Aspergillus nidulans phenol oxidase-encoding gene, ivoB. Gene. 1991;98:69–76. doi: 10.1016/0378-1119(91)90105-K.

112. Andersen MR, Nielsen JB, Klitgaard A, Petersen LM, Zachariasen M, Hansen TJ, et al. Accurate prediction of secondary metabolite gene clusters in filamentous fungi. Proc Natl Acad Sci U S A. 2013;110:E99–107. doi: 10.1073/pnas.1205532110.

113. Zaehle C, Gressler M, Shelest E, Geib E, Hertweck C, Brock M. Terrein biosynthesis in Aspergillus terreus and its impact on phytotoxicity. Chem Biol. 2014;21:719–31. doi: 10.1016/j.chembiol.2014.03.010.]

114. Botha CJ, Legg MJ, Truter M, Sulyok M. Multitoxin analysis of Aspergillus clavatus-infected feed samples implicated in two outbreaks of neuromycotoxicosis in cattle in South Africa. Onderstepoort J Vet Res. 2014;81. Art. #848, 6 pages.

115. Zutz C, Gacek A, Sulyok M, Wagner M, Strauss J, Rychli K. Small chemical chromatin effectors alter secondary metabolite production in Aspergillus clavatus. Toxins (Basel) 2013;5:1723–41. doi: 10.3390/toxins5101723.

116. Shaaban M, El-Metwally MM, Nasr H. A new diketopiperazine alkaloid from Aspergillus oryzae. Nat Prod Res. 2014;28:86–94. doi: 10.1080/14786419.2013.841687.

117. Frisvad JC, Samson RA. Neopetromyces gen. nov. and an overview of teleomorphs of Aspergillussubg. Circumdati. Stud Mycol. 2000;45:201–7.

118. Marui J, Ohashi-Kunihiro S, Ando T, Nishimura M, Koike H, Machida M. Penicillin biosynthesis in Aspergillus oryzae and its overproduction by genetic engineering. J Biosci Bioeng. 2010;110:8–11. doi: 10.1016/j.jbiosc.2010.01.001.

119. Tamiya H, Ochiai E, Kikuchi K, Yahiro M, Toyotome T, Watanabe A, et al. Secondary metabolite profiles and antifungal drug susceptibility of Aspergillus fumigatus and closely related species, Aspergillus lentulus, Aspergillus udagawae, and Aspergillus viridinutans. J Infect Chemother. 2015;21:385–91. doi: 10.1016/j.jiac.2015.01.005.

120. Fremlin LJ, Piggott AM, Lacey E, Capon RJ. Cottoquinazoline A and cotteslosins A and B, metabolites from an Australian marine-derived strain of Aspergillus versicolor. J Nat Prod. 2009;72:666–70. doi: 10.1021/np800777f.

121. Clardy J, Springer JP, Buchi G, Matsuo K, Wightman R. Letter: Tryptoquivaline and tryptoquivalone, two tremorgenic metabolites of Aspergillus clavatus. J Am Chem Soc. 1975;97:663–5. doi: 10.1021/ja00836a045.

122. Jurjevic Z, Peterson SW, Solfrizzo M, Peraica M. Sterigmatocystin production by nine newly described Aspergillus species in section Versicolores grown on two different media. Mycotoxin Res. 2013;29:141–5. doi: 10.1007/s12550-013-0160-4.

123. Nielsen KF, Mogensen JM, Johansen M, Larsen TO, Frisvad JC. Review of secondary metabolites and mycotoxins from the Aspergillus niger group. Anal Bioanal Chem. 2009;395:1225–42. doi: 10.1007/s00216-009-3081-5.

124. Kelly DE, Krasevec N, Mullins J, Nelson DR. The CYPome (Cytochrome P450 complement) of Aspergillus nidulans. Fungal Genet Biol. 2009;46(Suppl 1):S53–61. doi: 10.1016/j.fgb.2008.08.010.

125. Yoshida Y, Aoyama Y, Noshiro M, Gotoh O. Sterol 14-demethylase P450 (CYP51) provides a breakthrough for the discussion on the evolution of cytochrome P450 gene superfamily. Biochem Biophys Res Commun. 2000;273:799–804. doi: 10.1006/bbrc.2000.3030.

126. Kelly SL, Lamb DC, Corran AJ, Baldwin BC, Parks LW, Kelly DE. Purification and reconstitution of activity of Saccharomyces cerevisiae P450 61, a sterol delta 22-desaturase. FEBS Lett. 1995;377:217–20. doi: 10.1016/0014-5793(95)01342-3.

127. Briza P, Kalchhauser H, Pittenauer E, Allmaier G, Breitenbach M. N, N’-Bisformyl dityrosine is an in vivo precursor of the yeast ascospore wall. Eur J Biochem. 1996;239:124–31. doi: 10.1111/j.1432-1033.1996.0124u.x.

128. Jawallapersand P, Mashele SS, Kovacic L, Stojan J, Komel R, Pakala SB, et al. Cytochrome P450 monooxygenase CYP53 family in fungi: comparative structural and evolutionary analysis and its role as a common alternative anti-fungal drug target. PLoS One. 2014;9 doi: 10.1371/journal.pone.0107209.

129. Novak M, Lah L, Sala M, Stojan J, Bohlmann J, Komel R. Oleic acid metabolism via a conserved cytochrome P450 system-mediated omega-hydroxylation in the bark beetle-associated fungus Grosmannia clavigera. PLoS One. 2015;10 doi: 10.1371/journal.pone.0120119.

130. Brodhun F, Feussner I. Oxylipins in fungi. FEBS J. 2011;278:1047–63. doi: 10.1111/j.1742-4658.2011.08027.x.

131. Podobnik B, Stojan J, Lah L, Krasevec N, Seliskar M, Rizner TL, et al. CYP53A15 of Cochliobolus lunatus, a target for natural antifungal compounds. J Med Chem. 2008;51:3480–6. doi: 10.1021/jm800030e.

132. Miskei M, Karányi Z, Pócsi I. Annotation of stress-response proteins in the aspergilli. Fungal Genet Biol. 2009;46 Suppl 1:S105–20

133. Fungal Stress Database. http://www.fung-stress.org/.

134. Goetz KE, Coyle CM, Cheng JZ, O’Connor SE, Panaccione DG. Ergot cluster-encoded catalase is required for synthesis of chanoclavine-I in Aspergillus fumigatus. Curr Genet. 2011;57:201–11. doi: 10.1007/s00294-011-0336-4.

135. Fillinger S, Ruijter G, Tamas MJ, Visser J, Thevelein JM, d’Enfert C. Molecular and physiological characterization of the NAD- dependent glycerol 3-phosphate dehydrogenase in the filamentous fungus Aspergillus nidulans. Mol Microbiol. 2001;39:145–57. doi: 10.1046/j.1365-2958.2001.02223.x.

136. Ouedraogo JP, Hagen S, Spielvogel A, Engelhardt S, Meyer V. Survival strategies of yeast and filamentous fungi against the antifungal protein AFP. J Biol Chem. 2011;286:13859–68. doi: 10.1074/jbc.M110.203588.

137. Horák J. Regulations of sugar transporters: insights from yeast. Curr Genet. 2013;59:1–31. doi: 10.1007/s00294-013-0388-8.

138. Yan N. Structural biology of the major facilitator superfamily transporters. Annu Rev Biophys. 2015;44:257–83. doi:10.1146/annurev-biophys-060414-033901.

139. Chen LQ, Cheung LS, Feng L, Tanner W, Frommer WB. Transport of sugars. Annu Rev Biochem. 2015;84:865–94. doi: 10.1146/annurev-biochem-060614-033904.

140. Saier MH, Jr, Reddy VS, Tamang DG, Vastermark A. The transporter classification database. Nucleic Acids Res. 2014;42:D251–8. doi: 10.1093/nar/gkt1097.

141. Saier MHJ, Beatty JT, Goffeau A, Harley KT, Heijne WH, Huang SC, et al. The major facilitator superfamily. J Mol Microbiol Biotechnol. 1999;1:257–79.

142. Dos Reis TF, Menino JF, Bom VL, Brown NA, Colabardini AC, Savoldi M, et al. Identification of glucose transporters in Aspergillus nidulans. PLoS One. 2013;8 doi: 10.1371/journal.pone.0081412.

143. Forment JV, Flipphi M, Ramon D, Ventura L, Maccabe AP. Identification of the mstE gene encoding a glucose-inducible, low affinity glucose transporter in Aspergillus nidulans. J Biol Chem. 2006;281:8339–46. doi: 10.1074/jbc.M508198200.

144. Forment JV, Flipphi M, Ventura L, Gonzalez R, Ramon D, et al. High-affinity glucose transport in Aspergillus nidulans is mediated by the products of two related but differentially expressed genes. PLoS One. 2014;9 doi: 10.1371/journal.pone.0094662.

145. Li J, Lin L, Li H, Tian C, Ma Y. Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose. Biotechnol Biofuels. 2014;7:31. doi: 10.1186/1754-6834-7-31.

146. vanKuyk PA, Diderich JA, MacCabe AP, Hererro O, Ruijter GJG, Visser J. Aspergillus niger mstAencodes a high-affinity sugar/H+ symporter which is regulated in response to extracellular pH. Biochem J. 2004;379:375–83. doi: 10.1042/bj20030624.

147. Xie X, Wilkinson HH, Correa A, Lewis ZA, Bell-Pedersen D, Ebbole DJ. Transcriptional response to glucose starvation and functional analysis of a glucose transporter of Neurospora crassa. Fungal Genet Biol. 2004;41:1104–19. doi: 10.1016/j.fgb.2004.08.009.

148. Li J, Xu J, Cai P, Wang B, Ma Y, Benz JP, et al. Functional analysis of two L-arabinose transporters from filamentous fungi reveals promising characteristics for improved pentose utilization in Saccharomyces cerevisiae. Appl Environ Microbiol. 2015;81:4062–70. doi: 10.1128/AEM.00165-15.

149. Wei H, Vienken K, Weber R, Bunting S, Requena N, Fischer R. A putative high affinity hexose transporter, hxtA, of Aspergillus nidulans is induced in vegetative hyphae upon starvation and in ascogenous hyphae during cleistothecium formation. Fungal Genet Biol. 2004;41:148–56. doi: 10.1016/j.fgb.2003.10.006.

150. Colabardini AC, Ries LN, Brown NA, Dos Reis TF, Savoldi M, Goldman MH, et al. Functional characterization of a xylose transporter in Aspergillus nidulans. Biotechnol Biofuels. 2014;7:46. doi: 10.1186/1754-6834-7-46.

151. Du J, Li S, Zhao H. Discovery and characterization of novel d-xylose-specific transporters from Neurospora crassa and Pichia stipitis. Mol Biosyst. 2010;6:2150–6. doi: 10.1039/c0mb00007h.

152. Giles NH, Case ME, Baum J, Geever R, Huiet L, Patel V, et al. Gene organization and regulation in the qa (quinic acid) gene cluster of Neurospora crassa. Microbiol Rev. 1985;49:338–58.

153. Whittington HA, Grant S, Roberts CF, Lamb H, Hawkins AR.
Identification and isolation of a putative permease gene in the quinic acid utilization (QUT) gene cluster of Aspergillus nidulans. Curr Genet. 1987;12:135–9. doi: 10.1007/BF00434668.

154. Benz JP, Protzko RJ, Andrich JM, Bauer S, Dueber JE, Somerville CR. Identification and characterization of a galacturonic acid transporter from Neurospora crassa and its application for Saccharomyces cerevisiae fermentation processes. Biotechnol Biofuels. 2014;7:20. doi: 10.1186/1754-6834-7-20.

155. Sloothaak J, Schilders M, Schaap PJ, de Graaff LH. Overexpression of the Aspergillus niger GatA transporter leads to preferential use of D-galacturonic acid over D-xylose. AMB Express. 2014;4:66. doi: 10.1186/s13568-014-0066-3.

156. Nikawa J, Tsukagoshi Y, Yamashita S. Isolation and characterization of two distinct myo-inositol transporter genes of Saccharomyces cerevisiae. J Biol Chem. 1991;266:11184–91.

157. Xue C, Liu T, Chen L, Li W, Liu I, Kronstad JW, et al. Role of an expanded inositol transporter repertoire in Cryptococcus neoformans sexual reproduction and virulence. mBio. 2010;1:e00084–10. doi: 10.1128/mBio.00084-10.

158. Doehlemann G, Molitor F, Hahn M. Molecular and functional characterization of a fructose specific transporter from the gray mold fungus Botrytis cinerea. Fungal Genet Biol. 2005;42:601–10. doi: 10.1016/j.fgb.2005.03.001.

159. Goncalves AM, Silva CS, Madeira TI, Coelho R, de Sanctis D, San Romao MV, et al. Endo-beta-D-1,4-mannanase from Chrysonilia sitophila displays a novel loop arrangement for substrate selectivity. Acta Crystallogr D Biol Crystallogr. 2012;68:1468–78. doi: 10.1107/S0907444912034646.

160. Fan J, Chaturvedi V, Shen SH. Identification and phylogenetic analysis of a glucose transporter gene family from the human pathogenic yeast Candida albicans. J Mol Evol. 2002;55:336–46. doi: 10.1007/s00239-002-2330-4.

161. Hasegawa S, Takizawa M, Suyama H, Shintani T, Gomi K. Characterization and expression analysis of a maltose-utilizing (MAL) cluster in Aspergillus oryzae. Fungal Genet Biol. 2010;47:1–9. doi: 10.1016/j.fgb.2009.10.005.

162. Lingner U, Munch S, Sode B, Deising HB, Sauer N. Functional characterization of a eukaryotic melibiose transporter. Plant Physiol. 2011;156:1565–76. doi: 10.1104/pp.111.178624.

163. Fang W, St Leger RJ. Mrt, a gene unique to fungi, encodes an oligosaccharide transporter and facilitates rhizosphere competency in Metarhizium robertsii. Plant Physiol. 2010;154:1549–57. doi: 10.1104/pp.110.163014.

164. Bun-Ya M, Nishimura M, Harashima S, Oshima Y. The PHO84 gene of Saccharomyces cerevisiaeencodes an inorganic phosphate transporter. Mol Cell Biol. 1991;11:3229–38. doi: 10.1128/MCB.11.6.3229.

165. Dick CF, Dos-Santos AL, Meyer-Fernandes JR. Inorganic phosphate uptake in unicellular eukaryotes. Biochim Biophys Acta. 2014;1840:2123–7. doi: 10.1016/j.bbagen.2014.03.014.

166. Yadav V, Kumar M, Deep DK, Kumar H, Sharma R, Tripathi T, et al. A phosphate transporter from the root endophytic fungus Piriformospora indica plays a role in phosphate transport to the host plant. J Biol Chem. 2010;285:26532–44. doi: 10.1074/jbc.M110.111021.

167. Patton-Vogt JL, Henry SA. GIT1, a gene encoding a novel transporter for glycerophosphoinositol in Saccharomyces cerevisiae. Genetics. 1998;149:1707–15.

168. McDermott JR, Rosen BP, Liu Z. Jen1p: a high affinity selenite transporter in yeast. Mol Biol Cell. 2010;21:3934–41. doi: 10.1091/mbc.E10-06-0513.

169. Ferreira C, van Voorst F, Martins A, Neves L, Oliveira R, Kielland-Brandt MC, et al. A member of the sugar transporter family, Stl1p is the glycerol/H+ symporter in Saccharomyces cerevisiae. Mol Biol Cell. 2005;16:2068–76. doi: 10.1091/mbc.E04-10-0884.

170. Fekete E, Karaffa L, Seiboth B, Fekete E, Kubicek CP, Flipphi M. Identification of a permease gene involved in lactose utilisation in Aspergillus nidulans. Fungal Genet Biol. 2012;49:415–25. doi: 10.1016/j.fgb.2012.03.001.

171. Fekete E, Orosz A, Kulcsar L, Kavalecz N, Flipphi M, Karaffa L. Characterization of a second physiologically relevant lactose permease gene (lacpB) in Aspergillus nidulans. Microbiology. 2016;162:837–47. doi: 10.1099/mic.0.000267

172. Cai P, Wang B, Ji J, Jiang Y, Wan L, Tian C, et al. The putative cellodextrin transporter-like protein CLP1 is involved in cellulase induction in Neurospora crassa. J Biol Chem. 2015;290:788–96. doi: 10.1074/jbc.M114.609875.

173. Galazka JM, Tian C, Beeson WT, Martinez B, Glass NL, Cate JH. Cellodextrin transport in yeast for improved biofuel production. Science. 2010;330:84–6. doi: 10.1126/science.1192838.

174. Margolis-Clark E, Hunt I, Espinosa S, Bowman BJ. Identification of the gene at the pmg locus, encoding system II, the general amino acid transporter in Neurospora crassa. Fungal Genet Biol. 2001;33:127–35. doi: 10.1006/fgbi.2001.1273.

175. Vasseur V, Van Montagu M, Goldman GH. Trichoderma harzianum genes induced during growth on Rhizoctonia solani cell walls. Microbiology. 1995;141(Pt 4):767–74. doi: 10.1099/13500872-141-4-767.

176. Omura F, Hatanaka H, Nakao Y. Characterization of a novel tyrosine permease of lager brewing yeast shared by Saccharomyces cerevisiae strain RM11-1a. FEMS Yeast Res. 2007;7:1350–61. doi: 10.1111/j.1567-1364.2007.00310.x.

177. Yadav AK, Bachhawat AK. CgCYN1, a plasma membrane cystine-specific transporter of Candida glabrata with orthologues prevalent among pathogenic yeast and fungi. J Biol Chem. 2011;286:19714–23. doi: 10.1074/jbc.M111.240648.

178. Gournas C, Evangelidis T, Athanasopoulos A, Mikros E, Sophianopoulou V. The Aspergillus nidulansproline permease as a model for understanding the factors determining substrate binding and specificity of fungal amino acid transporters. J Biol Chem. 2015;290:6141–55. doi: 10.1074/jbc.M114.612069.

179. Apostolaki A, Erpapazoglou Z, Harispe L, Billini M, Kafasla P, Kizis D, et al. AgtA, the dicarboxylic amino acid transporter of Aspergillus nidulans, is concertedly down-regulated by exquisite sensitivity to nitrogen metabolite repression and ammonium-elicited endocytosis. Eukaryot Cell. 2009;8:339–52. doi: 10.1128/EC.00270-08.

180. Ghaddar K, Krammer EM, Mihajlovic N, Brohee S, Andre B, Prevost M. Converting the yeast arginine can1 permease to a lysine permease. J Biol Chem. 2014;289:7232–46. doi: 10.1074/jbc.M113.525915.

181. Gournas C, Prevost M, Krammer EM, Andre B. Function and regulation of fungal amino acid transporters: Insights from predicted structure. Adv Exp Med Biol. 2016;892:69–106. doi: 10.1007/978-3-319-25304-6_4.

182. Russnak R, Konczal D, McIntire SL. A family of yeast proteins mediating bidirectional vacuolar amino acid transport. J Biol Chem. 2001;276:23849–57. doi: 10.1074/jbc.M008028200.

183. Abreu C, Sanguinetti M, Amillis S, Ramon A. UreA, the major urea/H+ symporter in Aspergillus nidulans. Fungal Genet Biol. 2010;47:1023–33. doi: 10.1016/j.fgb.2010.07.004.

184. Pateman JA, Dunn E, Mackay EM. Urea and thiourea transport in Aspergillus nidulans. Biochem Genet. 1982;20:777–90. doi: 10.1007/BF00483973.

185. Sanguinetti M, Amillis S, Pantano S, Scazzocchio C, Ramon A. Modelling and mutational analysis of Aspergillus nidulans UreA, a member of the subfamily of urea/H(+) transporters in fungi and plants. Open Biol. 2014;4:140070. doi: 10.1098/rsob.140070.

186. Unkles SE, Karabika E, Symington VF, Cecile JL, Rouch DA, Akhtar N, et al. Alanine scanning mutagenesis of a high-affinity nitrate transporter highlights the requirement for glycine and asparagine residues in the two nitrate signature motifs. Biochem J. 2012;447:35–42. doi: 10.1042/BJ20120631.

187. Unkles SE, Rouch DA, Wang Y, Siddiqi MY, Glass AD, Kinghorn JR. Two perfectly conserved arginine residues are required for substrate binding in a high-affinity nitrate transporter. Proc Natl Acad Sci U S A. 2004;101:17549–54. doi: 10.1073/pnas.0405054101.
188. Zheng H, Wisedchaisri G, G
onen T. Crystal structure of a nitrate/nitrite exchanger. Nature. 2013;497:647–51. doi: 10.1038/nature12139.

189. Unkles SE, Zhou D, Siddiqi MY, Kinghorn JR, Glass AD. Apparent genetic redundancy facilitates ecological plasticity for nitrate transport. EMBO J. 2001;20:6246–55. doi: 10.1093/emboj/20.22.6246

190. Wang Y, Li W, Siddiqi Y, Symington VF, Kinghorn JR, Unkles SE, et al. Nitrite transport is mediated by the nitrite-specific high-affinity NitA transporter and by nitrate transporters NrtA, NrtB in Aspergillus nidulans. Fungal Genet Biol. 2008;45:94–102. doi: 10.1016/j.fgb.2007.10.001

191. Unkles SE, Symington VF, Kotur Z, Wang Y, Siddiqi MY, Kinghorn JR, et al. Physiological and biochemical characterization of AnNitA, the Aspergillus nidulans high-affinity nitrite transporter. Eukaryot Cell. 2011;10:1724–32. doi: 10.1128/EC.05199-11.

192. Parker JL, Newstead S. Molecular basis of nitrate uptake by the plant nitrate transporter NRT1.1. Nature. 2014;507:68–72. doi: 10.1038/nature13116.

193. Sun J, Bankston JR, Payandeh J, Hinds TR, Zagotta WN, Zheng N. Crystal structure of the plant dual-affinity nitrate transporter NRT1.1. Nature. 2014;507:73–7. doi: 10.1038/nature13074.

194. Monahan BJ, Askin MC, Hynes MJ, Davis MA. Differential expression of Aspergillus nidulansammonium permease genes is regulated by GATA transcription factor AreA. Eukaryot Cell. 2006;5:226–37. doi: 10.1128/EC.5.2.226-237.2006.

195. Hamari Z, Amillis S, Drevet C, Apostolaki A, Vagvolgyi C, Diallinas G, et al. Convergent evolution and orphan genes in the Fur4p-like family and characterization of a general nucleoside transporter in Aspergillus nidulans. Mol Microbiol. 2009;73:43–57. doi: 10.1111/j.1365-2958.2009.06738.x.

196. Lougiakis N, Gavriil ES, Kairis M, Sioupouli G, Lambrinidis G, Benaki D, et al. Design and synthesis of purine analogues as highly specific ligands for FcyB, a ubiquitous fungal nucleobase transporter. Bioorg Med Chem. 2016;24:5941–52. doi: 10.1016/j.bmc.2016.09.055.

197. Diallinas G. Understanding transporter specificity and the discrete appearance of channel-like gating domains in transporters. Front Pharmacol. 2014;5:207. doi: 10.3389/fphar.2014.00207.

198. Diallinas G, Gournas C. Structure-function relationships in the nucleobase-ascorbate transporter (NAT) family: lessons from model microbial genetic systems. Channels (Austin) 2008;2:363–72. doi: 10.4161/chan.2.5.6902.

199. Gournas C, Papageorgiou I, Diallinas G. The nucleobase-ascorbate transporter (NAT) family: genomics, evolution, structure-function relationships and physiological role. Mol Biosyst. 2008;4:404–16. doi: 10.1039/b719777b.

200. Alguel Y, Amillis S, Leung J, Lambrinidis G, Capaldi S, Scull NJ, et al. Structure of eukaryotic purine/H(+) symporter UapA suggests a role for homodimerization in transport activity. Nat Commun. 2016;7:11336. doi: 10.1038/ncomms11336.

201. Koukaki M, Vlanti A, Goudela S, Pantazopoulou A, Gioule H, Tournaviti S, et al. The nucleobase-ascorbate transporter (NAT) signature motif in UapA defines the function of the purine translocation pathway. J Mol Biol. 2005;350:499–513. doi: 10.1016/j.jmb.2005.04.076.

202. Pantazopoulou A, Diallinas G. The first transmembrane segment (TMS1) of UapA contains determinants necessary for expression in the plasma membrane and purine transport. Mol Membr Biol. 2006;23:337–48. doi: 10.1080/09687860600738239.

203. Goudela S, Karatza P, Koukaki M, Frillingos S, Diallinas G. Comparative substrate recognition by bacterial and fungal purine transporters of the NAT/NCS2 family. Mol Membr Biol. 2005;22:263–75. doi: 10.1080/09687860500093016.

204. Goudela S, Reichard U, Amillis S, Diallinas G. Characterization and kinetics of the major purine transporters in Aspergillus fumigatus. Fungal Genet Biol. 2008;45:459–72. doi: 10.1016/j.fgb.2007.08.001.

205. Krypotou E, Scazzocchio C, Diallinas G. Functional characterization of NAT/NCS2 proteins of Aspergillus brasiliensis reveals a genuine xanthine-uric acid transporter and an intrinsically misfolded polypeptide. Fungal Genet Biol. 2015;75:56–63. doi: 10.1016/j.fgb.2015.01.009.

206. Krypotou E, Diallinas G. Transport assays in filamentous fungi: kinetic characterization of the UapC purine transporter of Aspergillus nidulans. Fungal Genet Biol. 2014;63:1–8. doi: 10.1016/j.fgb.2013.12.004.

207. Krypotou E, Evangelidis T, Bobonis J, Pittis AA, Gabaldon T, Scazzocchio C, et al. Origin, diversification and substrate specificity in the family of NCS1/FUR transporters. Mol Microbiol. 2015;96:927–50. doi: 10.1111/mmi.12982.

208. Cecchetto G, Amillis S, Diallinas G, Scazzocchio C, Drevet C. The AzgA purine transporter of Aspergillus nidulans. Characterization of a protein belonging to a new phylogenetic cluster. J Biol Chem. 2004;279:3132–41. doi: 10.1074/jbc.M308826200.

209. Krypotou E, Lambrinidis G, Evangelidis T, Mikros E, Diallinas G. Modelling, substrate docking and mutational analysis identify residues essential for function and specificity of the major fungal purine transporter AzgA. Mol Microbiol. 2014;93:129–45. doi: 10.1111/mmi.12646.

210. Krypotou E, Kosti V, Amillis S, Myrianthopoulos V, Mikros E, Diallinas G. Modeling, substrate docking, and mutational analysis identify residues essential for the function and specificity of a eukaryotic purine-cytosine NCS1 transporter. J Biol Chem. 2012;287:36792–803. doi: 10.1074/jbc.M112.400382.

211. Vlanti A, Diallinas G. The Aspergillus nidulans FcyB cytosine-purine scavenger is highly expressed during germination and in reproductive compartments and is downregulated by endocytosis. Mol Microbiol. 2008;68:959–77. doi: 10.1111/j.1365-2958.2008.06198.x.

212. Sioupouli G, Lambrinidis G, Mikros E, Amillis S, Diallinas G. Cryptic purine transporters in Aspergillus nidulans reveal the role of specific residues in the evolution of specificity in the NCS1 family. Mol Microbiol. 2016; in press.

213. Loewen SK, Ng AM, Mohabir NN, Baldwin SA, Cass CE, Young JD. Functional characterization of a H+/nucleoside co-transporter (CaCNT) from Candida albicans, a fungal member of the concentrative nucleoside transporter (CNT) family of membrane proteins. Yeast. 2003;20:661–75. doi: 10.1002/yea.1000.

214. Canovas D, Marcos JF, Marcos AT, Strauss J. Nitric oxide in fungi: is there NO light at the end of the tunnel? Curr Genet. 2016;62:513–8. doi: 10.1007/s00294-016-0574-6.

215. Gardner PR, Gardner AM, Martin LA, Salzman AL. Nitric oxide dioxygenase: an enzymic function for flavohemoglobin. Proc Natl Acad Sci U S A. 1998;95:10378–83. doi: 10.1073/pnas.95.18.10378.

216. Schinko T, Berger H, Lee W, Gallmetzer A, Pirker K, Pachlinger R, et al. Transcriptome analysis of nitrate assimilation in Aspergillus nidulans reveals connections to nitric oxide metabolism. Mol Microbiol. 2010;78:720–38. doi: 10.1111/j.1365-2958.2010.07363.x.

217. te Biesebeke R, Levasseur A, Boussier A, Record E, van den Hondel CA, Punt PJ. Phylogeny of fungal hemoglobins and expression analysis of the Aspergillus oryzae flavohemoglobin gene fhbA during hyphal growth. Fungal Biol. 2010;114:135–43. doi: 10.1016/j.mycres.2009.08.007.

218. Zhou S, Fushinobu S, Kim SW, Nakanishi Y, Maruyama J, Kitamoto K, et al. Functional analysis and subcellular location of two flavohemoglobins from Aspergillus oryzae. Fungal Genet Biol. 2011;48:200–7. doi: 10.1016/j.fgb.2010.08.011.

219. Marcos AT, Ramos MS, Marcos JF, Carmona L, Strauss J, Canovas D. Nitric oxide synthesis by nitrate reductase is regulated during development in Aspergillus. Mol Microbiol. 2016;99:15–33. doi: 10.1111/mmi.13211.

220. Nakahara K, Tanimoto T, Hatano K, Usuda K, Shoun H. Cytochrome P-450 55A1 (P-450dNIR) acts as nitric oxide reductase employing NADH as the direct electron donor. J Biol Chem. 1993;268:8350–5.

221. de Jesus-Berrios M, Liu L, Nussbaum JC, Cox GM, Stamler JS, Heitman J. Enzymes that counteract nitrosative stress promote fungal virulence. Curr Biol. 2003;13:1963–8. doi: 10.1016/j.cub.2003.10.029.

222. Zhang Z, Wang J, Chai R, Qiu H, Jiang H, Mao X, et al. An S-(hydroxymethyl)glutathione dehydrogenase is involved in conidiation and full virulence in the rice blast fungus Magnaporthe oryzae. PLoS One. 2015;10 doi: 10.1371/journal.pone.0120627.

223. Lapp K, Vodisch M, Kroll K, Strassburger M, Kniemeyer O, Heinekamp T, et al. Characterization of the Aspergillus fumigatus detoxification systems for reactive nitrogen intermediates and their impact on virulence. Front Microbiol. 2014;5:469. doi: 10.3389/fmicb.2014.00469.

224. Philippe B, Ibrahim-Granet O, Prevost MC, Gougerot-Pocidalo MA, Sanchez Perez M, Van der Meeren A, et al. Killing of Aspergillus fumigatus by alveolar macrophages is mediated by reactive oxidant intermediates. Infect Immun. 2003;71:3034–42. doi: 10.1128/IAI.71.6.3034-3042.2003.

225. Han KH, Prade RA. Osmotic stress-coupled maintenance of polar growth in Aspergillus nidulans. Mol Microbiol. 2002;43:1065–78. doi: 10.1046/j.1365-2958.2002.02774.x.

226. Lafon A, Han KH, Seo JA, Yu JH, d’Enfert C. G-protein and cAMP-mediated signaling in aspergilli: a genomic perspective. Fungal Genet Biol. 2006;43:490–502. doi: 10.1016/j.fgb.2006.02.001.

227. Li L, Wright SJ, Krystofova S, Park G, Borkovich KA. Heterotrimeric G protein signaling in filamentous fungi. Annu Rev Microbiol. 2007;61:423–52. doi: 10.1146/annurev.micro.61.080706.093432.

228. Chang MH, Chae KS, Han DM, Jahng KY. The GanB Galpha-protein negatively regulates asexual sporulation and plays a positive role in conidial germination in Aspergillus nidulans. Genetics. 2004;167:1305–15. doi: 10.1534/genetics.103.025379.

229. Lafon A, Seo JA, Han KH, Yu JH, d’Enfert C. The heterotrimeric G-protein GanB(a)-SfaD(b)-GpgA(g) is a carbon source sensor involved in early cAMP-dependent germination in Aspergillus nidulans. Genetics. 2005;171:71–80. doi: 10.1534/genetics.105.040584.

230. Rosen S, Yu JH, Adams TH. The Aspergillus nidulans sfaD gene encodes a G protein beta subunit that is required for normal growth and repression of sporulation. EMBO J. 1999;18:5592–600. doi: 10.1093/emboj/18.20.5592.

231. Downes GB, Gautam N. The G protein subunit gene families. Genomics. 1999;62:544–52. doi: 10.1006/geno.1999.5992.

232. Giannakouros T, Nikolakaki E, Mylonis I, Georgatsou E.
Serine-arginine protein kinases: a small protein kinase family with a large cellular presence. FEBS J. 2011;278:570–86. doi: 10.1111/j.1742-4658.2010.07987.x.

233. De Souza CP, Hashmi SB, Osmani AH, Andrews P, Ringelberg CS, Dunlap JC, et al. Functional analysis of the Aspergillus nidulans kinome. PLoS One. 2013;8 doi: 10.1371/journal.pone.0058008.

234. Widmann C, Gibson S, Jarpe MB, Johnson GL. Mitogen-activated protein kinase: conservation of a three-kinase module from yeast to human. Physiol Rev. 1999;79:143–80.

235. Moorhead GB, Trinkle-Mulcahy L, Ulke-Lemee A. Emerging roles of nuclear protein phosphatases. Nat Rev Mol Cell Biol. 2007;8:234–44. doi: 10.1038/nrm2126.

236. Son S, Osmani SA. Analysis of all protein phosphatase genes in Aspergillus nidulans identifies a new mitotic regulator, fcp1. Eukaryot Cell. 2009;8:573–85. doi: 10.1128/EC.00346-08.

237. Lyon MA, Ducruet AP, Wipf P, Lazo JS. Dual-specificity phosphatases as targets for antineoplastic agents. Nat Rev Drug Discov. 2002;1:961–76. doi: 10.1038/nrd963.

238. Scazzocchio C, Ramón A. Chromatin in the genus Aspergillus. In: Osmani S, Goldman G, editors. The Aspergilli: Genomics, medical applications, biotechnology, and research methods. Boca Raton, FL: CRC Press; 2008. pp. 321–42.

239. Ehinger A, Denison SH, May GS. Sequence, organization and expression of the core histone genes of Aspergillus nidulans. Mol Gen Genet. 1990;222:416–24. doi: 10.1007/BF00633848.

240. Hays SM, Swanson J, Selker EU. Identification and characterization of the genes encoding the core histones and histone variants of Neurospora crassa. Genetics. 2002;160:961–73.

241. Santisteban MS, Kalashnikova T, Smith MM. Histone H2A.Z regulats transcription and is partially redundant with nucleosome remodeling complexes. Cell. 2000;103:411–22. doi: 10.1016/S0092-8674(00)00133-1.

242. Ahmed S, Dul B, Qiu X, Walworth NC. Msc1 acts through histone H2A.Z to promote chromosome stability in Schizosaccharomyces pombe. Genetics. 2007;177:1487–97. doi: 10.1534/genetics.107.078691.

243. Linz JE, Wee J, Roze LV. Aspergillus parasiticus SU-1 genome sequence, predicted chromosome structure, and comparative gene expression under aflatoxin-inducing conditions: evidence that differential expression contributes to species phenotype. Eukaryot Cell. 2014;13:1113–23. doi: 10.1128/EC.00108-14.

244. Nikkuni S, Nakajima H, Hoshina SI, Ohno M, Suzuki C, Kashiwagi Y, et al. Evolutionary relationships among Aspergillus oryzae and related species based on the sequences of 18S rRNA genes and internal transcribed spacers. J Gen Appl Microbiol. 1998;44:225–30. doi: 10.2323/jgam.44.225.

245. Sato A, Oshima K, Noguchi H, Ogawa M, Takahashi T, Oguma T, et al. Draft genome sequencing and comparative analysis of Aspergillus sojae NBRC4239. DNA Res. 2011;18:165–76. doi: 10.1093/dnares/dsr009.

246. Faustinelli PC, Wang XM, Palencia ER, Arias RS. Genome sequences of eight Aspergillus flavus spp. and one A. parasiticus sp., isolated from peanut seeds in Georgia. Genome Announc. 2016;4:e00278–16. doi: 10.1128/genomeA.00278-16.

247. Malik HS, Vermaak D, Henikoff S. Recurrent evolution of DNA-binding motifs in the Drosophilacentromeric histone. Proc Natl Acad Sci U S A. 2002;99:1449–54. doi: 10.1073/pnas.032664299.

248. Freitag M, Williams RL, Kothe GO, Selker EU. A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa. Proc Natl Acad Sci U S A. 2002;99:8802–7. doi: 10.1073/pnas.132212899.

249. Malagnac F, Wendel B, Goyon C, Faugeron G, Zickler D, Rossignol JL, et al. A gene essential for de novo methylation and development in Ascobolus reveals a novel type of eukaryotic DNA methyltransferase structure. Cell. 1997;91:281–90. doi: 10.1016/S0092-8674(00)80410-9.
250. Kouzminova E, Selker EU. dim-2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora. EMBO J. 2001;20:4309–23. doi: 10.1093/emboj/20.15.4309
.
251. Lee DW, Freitag M, Selker EU, Aramayo R. A cytosine methyltransferase homologue is essential for sexual development in Aspergillus nidulans. PLoS One. 2008;3 doi: 10.1371/journal.pone.0002531

252. Li Destri Nicosia MG, Brocard-Masson C, Demais S, Hua Van A, Daboussi MJ, Scazzocchio C. Heterologous transposition in Aspergillus nidulans. Mol Microbiol. 2001;39:1330–44. doi: 10.1111/j.1365-2958.2001.02323.x.

253. Liu SY, Lin JQ, Wu HL, Wang CC, Huang SJ, Luo YF, et al. Bisulfite sequencing reveals that Aspergillus flavus holds a hollow in DNA methylation. PLoS One. 2012;7 doi: 10.1371/journal.pone.0030349.

254. Malagnac F, Gregoire A, Goyon C, Rossignol JL, Faugeron G. Masc2, a gene from Ascobolusencoding a protein with a DNA-methyltransferase activity in vitro, is dispensable for in vivo methylation. Mol Microbiol. 1999;31:331–8. doi: 10.1046/j.1365-2958.1999.01177.x

255. Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A. 2011;108:1513–8. doi: 10.1073/pnas.1017351108.

256. Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, et al. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics. 2010;11:663. doi: 10.1186/1471-2164-11-663.

257. Smit AFA, Hubley R, Geen P. RepeatMasker Open-3.0. 1996-2010. http://www.repeatmasker.org.

258. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110:462–7. doi: 10.1159/000084979.

259. Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. Bioinformatics. 2005;21(Suppl 1):i351–8. doi: 10.1093/bioinformatics/bti1018.

260. Salamov AA, Solovyev VV. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 2000;10:516–22. doi: 10.1101/gr.10.4.516.

261. Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 2008;18:1979–90. doi: 10.1101/gr.081612.108.

262. Birney E, Durbin R. Using GeneWise in the Drosophila annotation experiment. Genome Res. 2000;10:547–8. doi: 10.1101/gr.10.4.547.

263. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10. doi: 10.1016/S0022-2836(05)80360-2.

264. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955–64. doi: 10.1093/nar/25.5.0955.

265. Nielsen H, Engelbrecht J, Brunak S, von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 1997;10:1–6. doi: 10.1093/protein/10.1.1.

266. Melen K, Fagerlund R, Franke J, Kohler M, Kinnunen L, Julkunen I. Importin alpha nuclear localization signal binding sites for STAT1, STAT2, and influenza A virus nucleoprotein. J Biol Chem. 2003;78:28193–200. doi: 10.1074/jbc.M303571200.

267. Zdobnov EM, Apweiler R. InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001;17:847–8. doi: 10.1093/bioinformatics/17.9.847.

268. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36:D480–4. doi: 10.1093/nar/gkm882

269. Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 2004;5:R7. doi: 10.1186/gb-2004-5-2-r7.

270. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–9. doi: 10.1038/75556

271. Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002;30:1575–84. doi: 10.1093/nar/30.7.1575.

272. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222–30. doi: 10.1093/nar/gkt1223

273. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80. doi: 10.1093/molbev/mst010.

274. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17:540–52. doi: 10.1093/oxfordjournals.molbev.a026334.

275. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3. doi: 10.1093/bioinformatics/btu033.

276. Li L, Stoeckert CJ, Jr, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13:2178–89. doi: 10.1101/gr.1224503.

277. NCBI BLAST tool 2.4.0. http://blast.ncbi.nlm.nih.gov/Blast.cgi.

278. Klitgaard A, Iversen A, Andersen MR, Larsen TO, Frisvad JC, Nielsen KF. Aggressive dereplication using UHPLC-DAD-QTOF: screening extracts for up to 3000 fungal secondary metabolites. Anal Bioanal Chem. 2014;406:1933–43. doi: 10.1007/s00216-013-7582-x.

279. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–9. doi: 10.1093/molbev/msr121.

280. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992;8:275–82.

281. PFAM Domain PF00083. http://pfam.xfam.org/family/PF00083/alignment/seed/jalview.

282. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, et al. The Pfam protein families database. Nucleic Acids Res. 2012;40:D290–301. doi: 10.1093/nar/gkr1065.

283. DTU. TMHMM Server v. 2.0. 2015. http://www.cbs.dtu.dk/services/TMHMM/.

284. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013;30:2725–9. doi: 10.1093/molbev/mst197.

285. Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics. 2011;12:124. doi: 10.1186/1471-2105-12-124

286. Isnard AD, Thomas D, Surdin-Kerjan Y. The study of methionine uptake in Saccharomyces cerevisiaereveals a new family of amino acid permeases. J Mol Biol. 1996;262:473–84. doi: 10.1006/jmbi.1996.0529.

287. Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, et al. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiaeand related sequences from other organisms. Nucleic Acids Res. 2004;32:D311–4. doi: 10.1093/nar/gkh033.

288. Vangelatos I, Vlachakis D, Sophianopoulou V, Diallinas G. Modelling and mutational evidence identify the substrate binding site and functional elements in APC amino acid transporters. Mol Membr Biol. 2009;26:356–70. doi: 10.1080/09687680903170546.

289. Katoh K, Kuma K-i, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005;33:511–8. doi: 10.1093/nar/gki198.

290. Criscuolo A, Gribaldo S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol. 2010;10:210. doi: 10.1186/1471-2148-10-210.

291. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21. doi: 10.1093/sysbio/syq010.

292. FigTree v1.4.2. http://tree.bio.ed.ac.uk/software/figtree/.

293. Pérez-Rodriguez P, Riaño-Pachón DM, Corrêa LG, Rensing SA, Kersten B, Mueller-Roeber B. PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res. 2010;38:D822–7. doi: 10.1093/nar/gkp805.

294. Bitbucket PlnTFDB. https://bitbucket.org/diriano/plntfdb.

295. de Vries RP, Burgers K, van de Vondervoort PJI, Frisvad JC, Samson RA, Visser J. A new black Aspergillus species, A. vadensis, is a promising host for homologous and heterologous protein production. Appl Environ Microbiol. 2004;70:3954–9. doi: 10.1128/AEM.70.7.3954-3959.2004.

296. Barratt RW, Johnson GB, Ogata WN. Wild-type and mutant stocks of Aspergillus nidulans. Genetics. 1965;52:233–46.

297. Yin WB, Reinke AW, Szilágyi M, Emri T, Chiang YM, Keating AE, et al. bZIP transcription factors affecting secondary metabolism, sexual development and stress responses in Aspergillus nidulans. Microbiology. 2013;159:77–88.

298. Karányi Z, Holb I, Hornok L, Pócsi I, Miskei M. FSRD: fungal stress response database. Database (Oxford). 2013;2013:bat037.

299. Sigoillot JC, H