[1] | Jiang DW, Zhu W, Wang YC, Sun C, Zhang KQ, Yang JK. Molecular tools for functional genomics in filamentous fungi: recent advances and new strategies. Biotechnol Adv, 2013, 31(8): 1562-1574. | [2] | Osiewacz HD. Genes, mitochondria and aging in filamentous fungi. Ageing Res Rev, 2002, 1(3): 425-442. | [3] | Long LK, Wang YL, Yang J, Xu XX, Liu G. A septation related gene AcsepH in Acremonium chrysogenum is involved in the cellular differentiation and cephalosporin production. Fungal Genet Biol, 2013, 50: 11-20. | [4] | Liu L, Long LK, An Y, Yang J, Xu XX, Hu CH, Liu G. The thioredoxin reductase-encoding gene ActrxR1 is involved in the cephalosporin C production of Acremonium chrysogenum in methionine-supplemented medium. Appl Microbiol Biotechnol, 2013, 97(6): 2551-2562. | [5] | Li JY, Pan YY, Liu G. Disruption of the nitrogen regulatory gene AcareA in Acremonium chrysogenum leads to reduction of cephalosporin production and repression of nitrogen metabolism. Fungal Genet Biol, 2013, 61: 69-79. | [6] | Wang HT, Pan YY, Hu PJ, Zhu YX, Li JY, Jiang XJ, Liu G. The autophagy-related gene Acatg1 is involved in conidiation and cephalosporin production in Acremonium chrysogenum. Fungal Genet Biol, 2014, 69: 65-74. | [7] | Hu PJ, Wang Y, Zhou J, Pan YY, Liu G. AcstuA, which encodes an APSES transcription regulator, is involved in conidiation, cephalosporin biosynthesis and cell wall integrity of Acremonium chrysogenum. Fungal Genet Biol, 2015, 83: 26-40. | [8] | Li J, Zhang Y, Chen KL, Shan QW, Wang YP, Liang Z, Gao CX. CRISPR/Cas: a novel way of RNA-guided genome editing. Hereditas (Beijing), 2013, 35(11): 1265-1273. | [8] | 李君, 张毅, 陈坤玲, 单奇伟, 王延鹏, 梁振, 高彩霞. CRISPR/Cas系统: RNA靶向的基因组定向编辑新技术. 遗传, 2013, 35(11): 1265-1273. | [9] | Wei CX, Liu JY, Yu ZS, Zhang B, Gao GJ, Jiao RJ. TALEN or Cas9-rapid, efficient and specific choices for genome modifications. J Genet Genomics, 2013, 40(6): 281-289. | [10] | da Silva Ferreira ME, Kress MRVZ, Savoldi M, Goldman MHS, H?rtl A, Heinekamp T, Brakhage AA, Goldman GH. The akuB KU80 mutant deficient for nonhomologous end joining is a powerful tool for analyzing pathogenicity in Aspergillus fumigatus. Eukaryot Cell, 2006, 5(1): 207-211. | [11] | Mouyna I, Henry C, Doering TL, Latgé JP. Gene silencing with RNA interference in the human pathogenic fungus Aspergillus fumigatus. FEMS Microbiol Lett, 2004, 237(2): 317-324. | [12] | Henry C, Mouyna I, Latgé JP. Testing the efficacy of RNA interference constructs in Aspergillus fumigatus. Curr Genet, 2007, 51(4): 277-284. | [13] | Shan QW, Gao CX. Research progress of genome editing and derivative technologies in plants. Hereditas (Beijing), 2015, 37(10): 953-973. | [13] | 单奇伟, 高彩霞. 植物基因组编辑及衍生技术最新研究进展. 遗传, 2015, 37(10): 953-973. | [14] | Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res, 2014, 42(W1): W401-W407. | [15] | Sakurai T, Watanabe S, Kamiyoshi A, Sato M, Shindo T. A single blastocyst assay optimized for detecting CRISPR/Cas9 system-induced indel mutations in mice. BMC Biotechnol, 2014, 14: 69. | [16] | Shen B, Brown KM, Lee TD, Sibley LD. Efficient gene disruption in diverse strains of Toxoplasma gondii using CRISPR/CAS9. mBio, 2014, 5(3): e01114. | [17] | Jinek M, East A, Cheng A, Lin S, Ma EB, Doudna J. RNA-programmed genome editing in human cells. eLife, 2013, 2: e00471. | [18] | Hwang WY, Fu YF, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol, 2013, 31(3): 227-229. | [19] | Cong L, Ran FA, Cox D, Lin SL, Barretto R, Habib N, Hsu PD, Wu XB, Jiang WY, Marraffini LA, Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science, 2013, 339(6121): 819-823. | [20] | Mali P, Yang LH, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science, 2013, 339(6121): 823-826. | [21] | Cho SW, Kim S, Kim JM, Kim JS. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol, 2013, 31(3): 230-232. | [22] | Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell, 2014, 157(6): 1262-1278. | [23] | Gratz SJ, Wildonger J, Harrison MM, O'Connor-Giles KM. CRISPR/Cas9-mediated genome engineering and the promise of designer flies on demand. Fly, 2013, 7(4): 249-255. | [24] | Arazoe T, Miyoshi K, Yamato T, Ogawa T, Ohsato S, Arie T, Kuwata S. Tailor-made CRISPR/Cas system for highly efficient targeted gene replacement in the rice blast fungus. Biotechnol Bioeng, 2015, 112(12): 2543-2549. | [25] | Matsu-Ura T, Baek M, Kwon J, Hong C. Efficient gene editing in Neurospora crassa with CRISPR technology. Fungal Biol Biotechnol, 2015, 2: 4. | [26] | Katayama T, Tanaka Y, Okabe T, Nakamura H, Fujii W, Kitamoto K, Maruyama JI. Development of a genome editing technique using the CRISPR/Cas9 system in the industrial filamentous fungus Aspergillus oryzae. Biotechnol Lett, 2016, 38(4): 637-642. | [27] | Fuller KK, Chen S, Loros JJ, Dunlap JC. Development of the CRISPR/Cas9 system for targeted gene disruption in Aspergillus fumigatus. Eukaryot Cell, 2015, 14(11): 1073-1080. | [28] | N?dvig CS, Nielsen JB, Kogle ME, Mortensen UH. A CRISPR-Cas9 system for genetic engineering of filamentous fungi. PLoS One, 2015, 10(7): e0133085. | [29] | Schuster M, Schweizer G, Reissmann S, Kahmann R. Genome editing in Ustilago maydis using the CRISPR-Cas system. Fungal Genet Biol, 2016, 89: 3-9. | [30] | Liu R, Chen L, Jiang YP, Zhou ZH, Zou G. Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system. Cell Discov, 2015, 1: 15007. | [31] | Pohl C, Kiel JAKW, Driessen AJM, Bovenberg RAL, Nyg?rd Y. CRISPR/Cas9 based genome editing of Penicillium chrysogenum. ACS Synth Biol, 2016, 5(7): 754-764. | [32] | Liu Q, Gao RR, Li JG, Lin L, Zhao JQ, Sun WL, Tian CG. Development of a genome-editing CRISPR/Cas9 system in thermophilic fungal Myceliophthora species and its application to hyper-cellulase production strain engineering. Biotechnol Biofuels, 2017, 10: 1. | [33] | Nielsen ML, Isbrandt T, Rasmussen KB, Thrane U, Hoof JB, Larsen TO, Mortensen UH. Genes linked to production of secondary metabolites in Talaromyces atroroseus revealed using CRISPR-Cas9. PLoS One, 2017, 12(1): e0169712. | [34] | Wenderoth M, Pinecker C, Vo? B, Fischer R. Establishment of CRISPR/Cas9 in Alternaria alternata. Fungal Genet Biol, 2017, 101: 55-60. | [35] | Jia HG, Wang N. Targeted genome editing of sweet orange using Cas9/sgRNA. PLoS One, 2014, 9(4): e93806. | [36] | Upadhyay SK, Kumar J, Alok A, Tuli R. RNA-guided genome editing for target gene mutations in wheat. G3 (Bethesda), 2013, 3(12): 2233-2238. | [37] | Roche CM, Loros JJ, McCluskey K, Glass NL. Neurospora crassa: looking back and looking forward at a model microbe. Am J Bot, 2014, 101(12): 2022-2035. | [38] | Ninomiya Y, Suzuki K, Ishii C, Inoue H. Highly efficient gene replacements in Neurospora strains deficient for nonhomologous end-joining. Proc Natl Acad Sci USA, 2004, 101(33): 12248-12253. | [39] | Coradetti ST, Craig JP, Xiong Y, Shock T, Tian C, Glass NL. Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi. Proc Natl Acad Sci USA, 2012, 109(19): 7397-7402. | [40] | Gooch VD, Mehra A, Larrondo LF, Fox J, Touroutoutoudis M, Loros JJ, Dunlap JC. Fully codon-optimized luciferase uncovers novel temperature characteristics of the Neurospora clock. Eukaryot Cell, 2008, 7(1): 28-37. | [41] | Zhang C, Meng XH, Wei XL, Lu L. Highly efficient CRISPR mutagenesis by microhomology-mediated end joining in Aspergillus fumigatus. Fungal Genet Biol, 2015, 86: 47-57. | [42] | K?mper J, Kahmann R, B?lker M, Ma LJ, Brefort T, Saville BJ, Banuett F, Kronstad JW, Gold SE, Müller O, Perlin MH, W?sten HAB, de Vries R, Ruiz-Herrera J, Reynaga-Pe?a CG, Snetselaar K, McCann M, Pérez- Martín J, Feldbrügge M, Basse CW, Steinberg G, Ibeas JI, Holloman W, Guzman P, Farman M, Stajich JE, Sentandreu R, González-Prieto JM, Kennell JC, Molina L, Schirawski J, Mendoza-Mendoza A, Greilinger D, Münch K, R?ssel N, Scherer M, Vranes M, Ladendorf O, Vincon V, Fuchs U, Sandrock B, Meng SW, Ho ECH, Cahill MJ, Boyce KJ, Klose J, Klosterman SJ, Deelstra HJ, Ortiz-Castellanos L, Li WX, Sanchez-Alonso P, Schreier PH, H?user-Hahn I, Vaupel M, Koopmann E, Friedrich G, Voss H, Schlüter T, Margolis J, Platt D, Swimmer C, Gnirke A, Chen F, Vysotskaia V, Mannhaupt G, Güldener U, Münsterk?tter M, Haase D, Oesterheld M, Mewes HW, Mauceli EW, DeCaprio D, Wade CM, Butler J, Young S, Jaffe DB, Calvo S, Nusbaum C, Galagan J, Birren BW. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature, 2006, 444(7115): 97-101. | [43] | Schilling L, Matei A, Redkar A, Walbot V, Doehlemann G. Virulence of the maize smut Ustilago maydis is shaped by organ-specific effectors. Mol Plant Pathol, 2014, 15(8): 780-789. | [44] | Schirawski J, Mannhaupt G, Münch K, Brefort T, Schipper K, Doehlemann G, Di Stasio M, R?ssel N, Mendoza-Mendoza A, Pester D, Müller O, Winterberg B, Meyer E, Ghareeb H, Wollenberg T, Münsterk?tter M, Wong P, Walter M, Stukenbrock E, Güldener U, Kahmann R. Pathogenicity determinants in smut fungi revealed by genome comparison. Science, 2010, 330(6010): 1546-1548. | [45] | Punt PJ, van Biezen N, Conesa A, Albers A, Mangnus J, van den Hondel C. Filamentous fungi as cell factories for heterologous protein production. Trends Biotechnol, 2002, 20(5): 200-206. | [46] | McLean KJ, Hans M, Meijrink B, van Scheppingen WB, Vollebregt A, Tee KL, van der Laan JM, Leys D, Munro AW, van den Berg MA. Single-step fermentative production of the cholesterol-lowering drug pravastatin via reprogramming of Penicillium chrysogenum. Proc Natl Acad Sci USA, 2015, 112(9): 2847-2852. | [47] | Visser H, Joosten V, Punt PJ, Gusakov AV, Olson PT, Joosten R, Bartels J, Visser J, Sinitsyn AP, Emalfarb MA. Development of a mature fungal technology and production platform for industrial enzymes based on a Myceliophthora thermophila isolate, previously known as Chrysosporium lucknowense C1. Ind Biotechnol, 2011, 7(3): 214-223. | [48] | Nielsen ML, Isbrandt T, Petersen LM, Mortensen UH, Andersen MR, Hoof JB, Larsen TO. Linker flexibility facilitates module exchange in fungal hybrid PKS-NRPS engineering. PLoS One, 2016, 11(8): e0161199. | [49] | West RR, Van Ness J, Varming AM, Rassing B, Biggs S, Gasper S, Mckernan PA, Piggott J. ZG-1494α, a novel platelet-activating factor acetyltransferase inhibitor from Penicilium rubrum, isolation, structure elucidation and biological activity. J Antibiot (Tokyo), 1996, 49(10): 967-973. | [50] | Suzuki S, Hosoe T, Nozawa K, Kawai KI, Yaguchi T, Udagawa SI. Antifungal substances against pathogenic fungi, talaroconvolutins, from Talaromyces convolutus. J Nat Prod, 2000, 63(6): 768-772. | [51] | Krappmann S. CRISPR-Cas9, the new kid on the block of fungal molecular biology. Med Mycol, 2017, 55(1): 16-23. | [52] | Bi YW, Sun L, Gao DD, Ding C, Li ZH, Li YD, Cun W, Li QH. High-efficiency targeted editing of large viral genomes by RNA-guided nucleases. PLoS Pathog, 2014, 10(5): e1004090. | [53] | Gagnon JA, Valen E, Thyme SB, Huang P, Ahkmetova L, Pauli A, Montague TG, Zimmerman S, Richter C, Schier AF. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One, 2014, 9(5): e98186. | [54] | DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res, 2013, 41(7): 4336-4343. | [55] | Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li YQ, Fine EJ, Wu XB, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol, 2013, 31(9): 827-832. | [56] | Dianov G L, Hübscher U. Mammalian base excision repair: the forgotten archangel. Nucleic Acids Res, 2013, 41(6): 3483-3490. | [57] | O'Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature, 2014, 516(7530): 263-266. | [58] | Jiang WZ, Yang B, Weeks DP. Efficient CRISPR/ Cas9-mediated gene editing in Arabidopsis thaliana and inheritance of modified genes in the T2 and T3 generations. PLoS One, 2014, 9(6): e99225. | [59] | Chen CC, Fenk LA, de Bono M. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Res, 2013, 41(20): e193. | [60] | Duan JZ, Lu GQ, Xie Z, Lou ML, Luo J, Guo L, Zhang Y. Genome-wide identification of CRISPR/Cas9 off-targets in human genome. Cell Res, 2014, 24(8): 1009-1012. | [61] | Hisano Y, Ota S, Kawahara A. Genome editing using artificial site-specific nucleases in zebrafish. Dev Growth Differ, 2014, 56(1): 26-33. |
|