Genome Sequence, Comparative Analysis, and Evolutionary Insights into Chitinases of Entomopathogenic Fungus Hirsutella thompsonii
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Alsmark, 2013, Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes, Genome Biol., 14, R19, 10.1186/gb-2013-14-2-r19
Altschul, 1990, Basic local alignment search tool, J Mol Biol., 215, 403, 10.1016/S0022-2836(05)80360-2
Arruda, 1992, Selective expression of a major allergen and cytotoxin, Asp f I, in Aspergillus fumigatus. Implications for the immunopathogenesis of Aspergillus-related diseases, J Immunol., 149, 3354, 10.4049/jimmunol.149.10.3354
Baratto, 2006, Isolation, characterization, and transcriptional analysis of the chitinase chi2 Gene (DQ011663) from the biocontrol fungus Metarhizium anisopliae var. anisopliae, Curr Microbiol., 53, 217, 10.1007/s00284-006-0078-6
Boetzer, 2011, Scaffolding pre-assembled contigs using SSPACE, Bioinformatics, 27, 578, 10.1093/bioinformatics/btq683
Boetzer, 2012, Toward almost closed genomes with GapFiller, Genome Biol., 13, R56, 10.1186/gb-2012-13-6-r56
Bolton, 2008, The novel Cladosporium fulvum lysin motif effector Ecp6 is a virulence factor with orthologues in other fungal species, Mol Microbiol., 69, 119, 10.1111/j.1365-2958.2008.06270.x
Bushley, 2013, Isolation of the MAT1-1 mating type idiomorph and evidence for selfing in the Chinese medicinal fungus Ophiocordyceps sinensis, Fungal Biol., 117, 599, 10.1016/j.funbio.2013.06.001
Bushley, 2013, The genome of Tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster, PLoS Genet., 9, e1003496, 10.1371/journal.pgen.1003496
Cantarel, 2008, MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes, Genome Res., 18, 188, 10.1101/gr.6743907
Charnley, 2003, Fungal pathogens of insects: cuticle degrading enzymes and toxins, Adv Bot Res., 40, 241, 10.1016/S0065-2296(05)40006-3
Cresnar, 2011, Cytochrome P450 enzymes in the fungal kingdom, Biochim Biophys Acta., 1814, 29, 10.1016/j.bbapap.2010.06.020
Cuskin, 2012, How nature can exploit nonspecific catalytic and carbohydrate binding modules to create enzymatic specificity, Proc Natl Acad Sci U S A., 109, 20889, 10.1073/pnas.1212034109
da Silva, 2005, Cuticle-induced endo/exoacting chitinase CHIT30 from Metarhizium anisopliae is encoded by an ortholog of the chi3 gene, Res Microbiol., 156, 382, 10.1016/j.resmic.2004.10.013
de las Mercedes Dana, 2001, Regulation of chitinase 33 (chit33) gene expression in Trichoderma harzianum, Curr Genet., 38, 335, 10.1007/s002940000169
Donatti, 2008, Production and regulation of cuticle-degrading proteases from Beauveria bassiana in the presence of Rhammatocerus schistocercoides cuticle, Curr Microbiol., 56, 256, 10.1007/s00284-007-9071-y
Duplessis, 2011, Obligate biotrophy features unraveled by the genomic analysis of rust fungi, Proc Natl Acad Sci U S A., 108, 9166, 10.1073/pnas.1019315108
Fan, 2011, High-throughput insertion mutagenesis and functional screening in the entomopathogenic fungus Beauveria bassiana, J Invertebr Pathol., 106, 274, 10.1016/j.jip.2010.11.003
Fang, 2005, Cloning of Beauveria bassiana chitinase gene Bbchit1 and its application to improve fungal strain virulence, Appl Environ Microbiol., 71, 363, 10.1128/AEM.71.1.363-370.2005
Ferreira, 2005, The ergosterol biosynthesis pathway, transporter genes, and azole resistance in Aspergillus fumigatus, Med Mycol., 43, S313, 10.1080/13693780400029114
Ferrer-Sevillano, 2007, Novel phacB-encoded cytochrome P450 monooxygenase from Aspergillus nidulans with 3-hydroxyphenylacetate 6-hydroxylase and 3,4-dihydroxyphenylacetate 6-hydroxylase activities, Eukaryot Cell., 6, 514, 10.1128/EC.00226-06
Finn, 2011, HMMER web server: interactive sequence similarity searching, Nucleic Acids Res., 39, W29, 10.1093/nar/gkr367
Freimoser, 2005, Variation in gene expression patterns as the insect pathogen Metarhizium anisopliae adapts to different host cuticles or nutrient deprivation in vitro, Microbiology, 151, 361, 10.1099/mic.0.27560-0
Galagan, 2003, The genome sequence of the filamentous fungus Neurospora crassa, Nature, 422, 859, 10.1038/nature01554
Gao, 2011, Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum, PLoS Genet., 7, e1001264, 10.1371/journal.pgen.1001264
Gardiner, 2013, Cross-kingdom gene transfer facilitates the evolution of virulence in fungal pathogens, Plant Sci., 210, 151, 10.1016/j.plantsci.2013.06.002
Gasteiger, 2005, Protein identification and analysis tools on the ExPASy server, The proteomics protocols handbook, 571, 10.1385/1-59259-890-0:571
Gruber, 2011, Analysis of subgroup C of fungal chitinases containing chitin-binding and LysM modules in the mycoparasite Trichoderma atroviride, Glycobiology, 21, 122, 10.1093/glycob/cwq142
Han, 2013, Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3, Mol Biol Evol., 30, 1987, 10.1093/molbev/mst100
Hane, 2008, RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences, BMC Bioinformatics, 9, 478, 10.1186/1471-2105-9-478
Haragsim, 2001, Biological control of Varroa mites in honeybee hives with Hirsutella thompsonii
Hartl, 2012, Fungal chitinases: diversity, mechanistic properties and biotechnological potential, Appl Microbiol Biotechnol., 93, 533, 10.1007/s00253-011-3723-3
Herrero-Galán, 2008, The insecticidal protein hirsutellin A from the mite fungal pathogen Hirsutella thompsonii is a ribotoxin, Proteins, 72, 217, 10.1002/prot.21910
Herrero-Galán, 2013, Hirsutellin A: a paradigmatic example of the insecticidal function of fungal ribotoxins, Insects, 4, 339, 10.3390/insects4030339
Hood, 2005, Repeat-induced point mutation and the population structure of transposable elements in Microbotryum violaceum, Genetics, 170, 1081, 10.1534/genetics.105.042564
Hu, 2013, Genome survey uncovers the secrets of sex and lifestyle in caterpillar fungus, Chin Sci Bull., 58, 2846, 10.1007/s11434-013-5929-5
Huang, 1997, Characterization of a new ribotoxin gene (c-sar) from Aspergillus clavatus, Toxicon, 35, 383, 10.1016/S0041-0101(96)00170-5
Ihrmark, 2010, Comparative molecular evolution of Trichoderma chitinases in response to mycoparasitic interactions, Evol Bioinform Online., 6, 1, 10.4137/EBO.S4198
Jablonowski, 2001, Saccharomyces cerevisiae cell wall chitin, the Kluyveromyces lactis zymocin receptor, Yeast, 18, 1285, 10.1002/yea.776
Jawallapersand, 2014, 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, 9, e107209, 10.1371/journal.pone.0107209
Jin, 2009, Carboxylate transporter gene JEN1 from the entomopathogenic fungus Beauveria bassiana is involved in conidiation and virulence, Appl Environ Microbiol., 76, 254, 10.1128/AEM.00882-09
Kao, 2001, Mitogillin and related fungal ribotoxins, Methods Enzymol., 341, 324, 10.1016/S0076-6879(01)41161-X
Karlsson, 2009, Evolution of family 18 glycoside hydrolases: diversity, domain structures and phylogenetic relationships, J Mol Microbiol Biotechnol., 16, 208, 10.1159/000151220
Kirk, 2008, Dictionary of the fungi, 10th ed.
Klix, 2010, Functional characterization of MAT1-1-specific mating-type genes in the homothallic ascomycete Sordaria macrospora provides new insights into essential and nonessential sexual regulators, Eukaryot Cell., 9, 894, 10.1128/EC.00019-10
Klosterman, 2011, Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens, PLoS Pathog., 7, e1002137, 10.1371/journal.ppat.1002137
Kubicek, 2011, Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma, Genome Biol., 12, R40, 10.1186/gb-2011-12-4-r40
Lang, 2000, Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion, Science, 289, 1546, 10.1126/science.289.5484.1546
Lauge, 1998, Successful search for a resistance gene in tomato targeted against a virulence factor of a fungal pathogen, Proc Natl Acad Sci U S A., 95, 9014, 10.1073/pnas.95.15.9014
Lechner, 2011, Proteinortho: detection of (co-)orthologs in large-scale analysis, BMC Bioinformatics, 12, 124, 10.1186/1471-2105-12-124
Lee, 2010, The evolution of sex: a perspective from the fungal kingdom, Microbiol Mol Biol Rev., 74, 298, 10.1128/MMBR.00005-10
Letunic, 2012, SMART 7: recent updates to the protein domain annotation resource, Nucleic Acids Res., 40, D302, 10.1093/nar/gkr931
Lin, 1995, Production of type II ribotoxins by Aspergillus species and related fungi in Taiwan, Toxicon, 33, 105, 10.1016/0041-0101(94)00140-4
Liu, 2002, Molecular evidence for teleomorph-anamorph connections in Cordyceps based on ITS-5.8S rDNA sequences, Mycol Res., 106, 1100, 10.1017/S0953756202006378
Lombard, 2014, The carbohydrate-active enzymes database (CAZy) in 2013, Nucleic Acids Res., 42, D490, 10.1093/nar/gkt1178
Lowe, 1997, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res., 25, 955, 10.1093/nar/25.5.0955
Medema, 2011, antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences, Nucleic Acids Res., 39, W339, 10.1093/nar/gkr466
Meerupati, 2013, Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi, PLoS Genet., 9, e1003909, 10.1371/journal.pgen.1003909
Mishra, 1995, Molecular biology of nucleases, 46
Molnar, 2010, Secondary metabolites from entomopathogenic Hypocrealean fungi, Nat Prod Rep., 27, 1241, 10.1039/c001459c
Murphy, 2011, Curation of characterized glycoside hydrolases of fungal origin, Database (Oxford), 2011, bar020, 10.1093/database/bar020
Nagano, 2002, One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions, J Mol Biol., 321, 741, 10.1016/S0022-2836(02)00649-6
Nittler, 2005, Identification of Histoplasma capsulatum transcripts induced in response to reactive nitrogen species, Mol Biol Cell., 16, 4792, 10.1091/mbc.E05-05-0434
Oßwald, 2014, A highly unusual polyketide synthase directs dawenol polyene biosynthesis in Stigmatella aurantiaca, J Biotechnol, 10.1016/j.jbiotec.2014.07.447
Paterson, 2008, Cordyceps: a traditional Chinese medicine and another fungal therapeutic biofactory?, Phytochemistry, 69, 1469, 10.1016/j.phytochem.2008.01.027
Pattemore, 2014, The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species, BMC Genomics, 15, 660, 10.1186/1471-2164-15-660
Pedrini, 2010, Molecular characterization and expression analysis of a suite of cytochrome P450 enzymes implicated in insect hydrocarbon degradation in the entomopathogenic fungus Beauveria bassiana, Microbiology, 156, 2549, 10.1099/mic.0.039735-0
Pei, 2003, PCMA: fast and accurate multiple sequence alignment based on profile consistency, Bioinformatics, 19, 427, 10.1093/bioinformatics/btg008
Quevillon, 2005, InterProScan: protein domains identifier, Nucleic Acids Res., 33, W116, 10.1093/nar/gki442
Saier, 2014, The transporter classification database, Nucleic Acids Res., 42, D251, 10.1093/nar/gkt1097
Saito, 2003, Distribution and evolution of chitinase genes in Streptomyces species: involvement of gene-duplication and domain-deletion, Antonie Van Leeuwenhoek, 84, 7, 10.1023/A:1024463113606
Samson, 1980, Taxonomy of the acarine parasite Hirsutella thompsonii, Mycologia, 72, 359, 10.2307/3759259
Schultz, 1998, SMART, a simple modular architecture research tool: identification of signaling domains, Proc Natl Acad Sci U S A., 95, 5857, 10.1073/pnas.95.11.5857
Seidl, 2008, Chitinases of filamentous fungi: a large group of diverse proteins with multiple physiological functions, Fungal Biol Rev., 22, 36, 10.1016/j.fbr.2008.03.002
Seidl, 2005, A complete survey of Trichoderma chitinases reveals three distinct subgroups of family 18 chitinases, FEBS J., 272, 5923, 10.1111/j.1742-4658.2005.04994.x
Selker, 1987, Rearrangement of duplicated DNA in specialized cells of Neurospora, Cell, 51, 741, 10.1016/0092-8674(87)90097-3
Shoun, 2012, Fungal denitrification and nitric oxide reductase cytochrome P450nor, Philos Trans R Soc Lond B Biol Sci., 367, 1186, 10.1098/rstb.2011.0335
Spanu, 2010, Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism, Science, 330, 1543, 10.1126/science.1194573
St. Leger, 1992, Cloning and regulatory analysis of starvation-stress gene, ssgA, encoding a hydrophobin-like protein from the entomopathogenic fungus, Metarhizium anisopliae, Gene, 120, 119, 10.1016/0378-1119(92)90019-L
St. Leger, 2010, Genetic engineering of fungal biocontrol agents to achieve greater efficacy against insect pests, Appl Microbiol Biotechnol., 85, 901, 10.1007/s00253-009-2306-z
Stanke, 2005, AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints, Nucleic Acids Res., 33, W465, 10.1093/nar/gki458
Stergiopoulos, 2010, Tomato Cf resistance proteins mediate recognition of cognate homologous effectors from fungi pathogenic on dicots and monocots, Proc Natl Acad Sci U S A., 107, 7610, 10.1073/pnas.1002910107
Stergiopoulos, 2012, In silico characterization and molecular evolutionary analysis of a novel superfamily of fungal effector proteins, Mol Biol Evol., 29, 3371, 10.1093/molbev/mss143
Sung, 2007, Phylogenetic classification of Cordyceps and the clavicipitaceous fungi, Stud Mycol., 57, 5, 10.3114/sim.2007.57.01
Swofford, 2003, PAUP*: phylogenetic analysis using parsimony (* and other methods). Version 4.0
Takaya, 2002, Transcriptional control of nitric oxide reductase gene (CYP55) in the fungal denitrifier Fusarium oxysporum, Biosci Biotechnol Biochem., 66, 1039, 10.1271/bbb.66.1039
Tamura, 2013, MEGA6: Molecular Evolutionary Genetics Analysis version 6.0, Mol Biol Evol., 30, 2725, 10.1093/molbev/mst197
Tatusov, 2000, The COG database: a tool for genome-scale analysis of protein functions and evolution, Nucleic Acids Res., 28, 33, 10.1093/nar/28.1.33
Tomura, 1994, Nitric oxide reductase cytochrome P-450 gene, CYP 55, of the fungus Fusarium oxysporum containing a potential binding-site for FNR, the transcription factor involved in the regulation of anaerobic growth of Escherichia coli, J Biochem., 116, 88, 10.1093/oxfordjournals.jbchem.a124508
Tzelepis, 2014, Functional analysis of the C-II subgroup killer toxin-like chitinases in the filamentous ascomycete Aspergillus nidulans, Fungal Genet Biol., 64, 58, 10.1016/j.fgb.2013.12.009
Ubhayasekera, 2012, Bacterial and fungal chitinase chiJ orthologs evolve under different selective constraints following horizontal gene transfer, BMC Res Notes., 5, 581, 10.1186/1756-0500-5-581
Van den Ackerveken, 1993, Characterization of two putative pathogenicity genes of the fungal tomato pathogen Cladosporium fulvum, Mol Plant Microbe Interact., 6, 210, 10.1094/MPMI-6-210
Wang, 2014, Comparative transcriptomic analysis of the heat stress response in the filamentous fungus Metarhizium anisopliae using RNA-Seq, Appl Microbiol Biotechnol., 98, 5589, 10.1007/s00253-014-5763-y
Wang, 2007, The MAD1 adhesin of Metarhizium anisopliae links adhesion with blastospore production and virulence to insects, and the MAD2 adhesin enables attachment to plants, Eukaryot Cell., 6, 808, 10.1128/EC.00409-06
Weibelzahl, 2009, Epizootic of Acalitus vaccinii (Acari: Eriophyidea) caused by Hirsutella thompsonii on southern highbush blueberry in north-central Florida, Fla Entomol., 92, 601, 10.1653/024.092.0412
Weinzierl, 2005, Microbial insecticides
Winnenburg, 2006, PHI-base: a new database for pathogen host interactions, Nucleic Acids Res., 34, D459, 10.1093/nar/gkj047
Xiao, 2012, Genomic perspectives on the evolution of fungal entomopathogenicity in Beauveria bassiana, Sci Rep., 2, 483, 10.1038/srep00483
Xu, 2011, Structure and function of WD40 domain proteins, Protein Cell, 2, 202, 10.1007/s13238-011-1018-1
Yin, 2012, dbCAN: a web resource for automated carbohydrate-active enzyme annotation, Nucleic Acids Res., 40, W445, 10.1093/nar/gks479
Zhang, 2009, Mitogen-activated protein kinase hog1 in the entomopathogenic fungus Beauveria bassiana regulates environmental stress responses and virulence to insects, Appl Environ Microbiol., 75, 3787, 10.1128/AEM.01913-08
Zhang, 2010, Requirement of a mitogen-activated protein kinase for appressorium formation and penetration of insect cuticle by the entomopathogenic fungus Beauveria bassiana, Appl Environ Microbiol., 76, 2262, 10.1128/AEM.02246-09
Zhang, 2012, CYP52X1, representing new cytochrome P450 subfamily, displays fatty acid hydroxylase activity and contributes to virulence and growth on insect cuticular substrates in entomopathogenic fungus Beauveria bassiana, J Biol Chem., 287, 13477, 10.1074/jbc.M111.338947
Zhao, 2014, Host-to-pathogen gene transfer facilitated infection of insects by a pathogenic fungus, PLoS Pathog., 10, e1004009, 10.1371/journal.ppat.1004009