Harnessing the power of phylogenomics to disentangle the directionality and signatures of interkingdom host jumping in the parasitic fungal genus Tolypocladium

LITERATURE CITED

• Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104–2105, doi:10.1093/bioinformatics/bti263
   PubMed Web of Science ®Google Scholar
• Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T. 2013. antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Research 41:1–9, doi:10.1093/nar/gkt449
   PubMed Web of Science ®Google Scholar
• Borel JF. 2002. History of the discovery of cyclosporin and of its early pharmacological development. Wiener klinische Wochenschrift 114:433–437.
   Web of Science ®Google Scholar
• Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10: e1003537, doi:10.1371/journal.pcbi.1003537
   PubMed Web of Science ®Google Scholar
• Bushley KE, Raja R, Jaiswal P, Cumbie JS, Nonogaki M, Boyd AE, Owensby CA, Knaus BJ, Elser J, Miller D, Di Y, McPhail KL, Spatafora JW. 2013. The genome of Tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster. PLoS Genetics 9: 1003496, doi:10.1371/journal.pgen.1003496
   Web of Science ®Google Scholar
• Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, Moore B, Holt C, Alvarado AS, Yandell M. 2008. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Research 18:188–196, doi:10.1101/gr.6743907
   PubMed Web of Science ®Google Scholar
• Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ, Zhou S, Schwartz DC, Freitag M, Ma LJ, Danchin EGJ, Henrissat B, Coutinho PM, Nelson DR, Straney D, Napoli CA, Barker BM, Gribskov M, Rep M, Kroken S, Molnár I, Rensing C, Kennell JC, Zamora J, Farman ML, Selker EU, Salamov A, Shapiro H, Pangilinan J, Lindquist E, Lamers C, Grigoriev IV, Geiser DM, Covert SF, Temporini E, VanEtten HD. 2009. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genetics 5:e1000618, doi:10.1371/journal.pgen.1000618
   Google Scholar
• Cuomo CA, Güldener U, Xu J, Trail F, Turgeon BG, Pietro A Di, Walton JD, Ma L, Baker SE, Rep M, Adam G, Antoniw J, Baldwin T, Calvo S, Chang Y, Harris LJ, Hilburn K, Kennell JC, Kroken S, Magnuson JK, Muehlbauer G, Münsterkötter M, Nelson D, Donnell KO, Ouellet T, Qi W, Quesneville H, Roncero MIG, Seong K-Y, Tetko IV, Urban M, Waalwijk C, Ward TJ, Yao J, Birren BW, Kistler HC. 2007. The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317:1400–1402.
   PubMed Web of Science ®Google Scholar
• Desjardins AE, Hohn TM, McCormick SP. 1993. Trichothecene in Fusarium species: chemistry, genetics, and significance. Microbiology Reviews 57:595–604.
   PubMedGoogle Scholar
• Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29:1969–1973, doi:10.1093/molbev/mss075
   PubMed Web of Science ®Google Scholar
• Druzhinina IS, Seidl-Seiboth V, Herrera-Estrella A, Horwitz BA, Kenerley CM, Monte E, Mukherjee PK, Zeilinger S, Grigoriev I V, Kubicek CP. 2011. Trichoderma: the genomics of opportunistic success. Nature Reviews Microbiology 9:749–759, doi:10.1038/nrmicro2637
   PubMed Web of Science ®Google Scholar
• Eddy SR. 2011. Accelerated profile HMM searches. PLoS Computational Biology 7:1002195, doi:10.1371/journal.pcbi.1002195
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792–1797, doi:10.1093/nar/gkh340
   PubMed Web of Science ®Google Scholar
• Enright AJ, Dongen S Van, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 30:1575–1584, doi:10.1093/nar/30.7.1575
   PubMed Web of Science ®Google Scholar
• Gandolfo MA, Nixon KC, Crepet WL. 2002. Triuridaceae fossil flowers from the upper cretaceous of New Jersey. American Journal of Botany 89:1940–1957.
   PubMed Web of Science ®Google Scholar
• Gao Q, Jin K, Ying S, Zhang Y, Xiao G, Shang Y, Hu X, Xie X, Zhou G, Peng G, Luo Z, Huang W, Wang B, Fang W, Wang S, Zhong Y, Ma L, Leger RJS, Zhao G, Pei Y, Feng M, Xia Y, Wang C. 2011. Genome sequencing and comparative transcriptomics of the model entomopathogenic Fungi Metarhizium anisopliae and M. acridum. PLoS Genetics 7:e1001264, doi:10.1371/journal.pgen.1001264
   PubMed Web of Science ®Google Scholar
• Gazis R, Skaltsas D, Chaverri P. 2014. Novel endophytic lineages of Tolypocladium provide new insights into the ecology and evolution of Cordyceps-like fungi. Mycologia 106:1090–1105, doi:10.3852/13-346
   PubMed Web of Science ®Google Scholar
• Gershenzon J, Dudareva N. 2007. The function of terpene natural products in the natural world. Nature Chemical Biology 3:408–414, doi:10.1038/nchembio.2007.5
   PubMed Web of Science ®Google Scholar
• Gordon A. 2011. FASTQ/A short-reads pre-processing tools. [cited 2013 Nov 15]. Available from: http://hannonlab.cshl.edu/fastx_toolkit/
   Google Scholar
• Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, Palma F di, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29:644–652, doi:10.1038/nbt.1883
   PubMed Web of Science ®Google Scholar
• Hu X, Zhang YJ, Xiao GH, Zheng P, Xia YL, Zhang XY, St Leger RJ, Liu XZ, Wang CS. 2013. Genome survey uncovers the secrets of sex and lifestyle in caterpillar fungus. Chinese Science Bulletin 58:2846–2854, doi:10.1007/s11434-013-5929-5
   Google Scholar
• Huson DH, Scornavacca C. 2012. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Systematic Biology 61:1061–1067, doi:10.1093/sysbio/sys062
   PubMed Web of Science ®Google Scholar
• Jeffries P, Young TWK. 1994. Interfungal parasitic relationships. Wallingford, UK: CAB International. 296 p.
   Google Scholar
• Kepler R, Ban S, Nakagiri A, Bischoff J, Hywel-Jones N, Owensby CA, Spatafora JW. 2013. The phylogenetic placement of hypocrealean insect pathogens in the genus Polycephalomyces: an application of One Fungus One Name. Fungal Biology 117:611–622, doi:10.1016/j.funbio.2013.06.002
   PubMed Web of Science ®Google Scholar
• Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC, Wolfe KH, Fedorova ND. 2010. SMURF: genomic mapping of fungal secondary metabolite clusters. Fungal Genetics and Biology 47:736–741, doi:10.1016/j.fgb.2010.06.003
   PubMed Web of Science ®Google Scholar
• Kobayasi Y, Shimizu D. 1960. Monographic studies on Cordyceps 1. Group parasitic on Elaphomyces. Bulletin of the National Science Museum, Tokyo 5:69–85.
   Google Scholar
• Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canbäck B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Doré J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Högberg N, Johansson T, Khouja H-R, LaButti K, Lahrmann U, Levasseur A, Lindquist EA, Lipzen A, Marmeisse R, Martino E, C R, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm RA, Perotto S, Peter M, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A, Mycorrhizal Genomics Initiative Consortium, Tunlid A, Grigoriev IV, Hibbett DS, Martin F. 2015. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nature Genetics 47:410–415, doi:10.1038/ng.3223
   PubMed Web of Science ®Google Scholar
• Korf I. 2004. Gene finding in novel genomes. BMC Bioinformatics 5:59, doi:10.1186/1471-2105-5-59
   Web of Science ®Google Scholar
• Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, Döhren H von, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gómez-Rodríguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernandez-Onate, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lubeck M, Lubeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Weist A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV. 2011. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biology 12: R40, doi:10.1186/gb-2011-12-4-r40
   Google Scholar
• Lebrigand K, He LD, Thakur N, Arguel MJ, Polanowska J, Henrissat B, Record E, Magdelenat G, Barbe V, Raffaele S, Barbry P, Ewbank JJ. 2016. Comparative genomic analysis of Drechmeria coniospora reveals core and specific genetic requirements for fungal endoparasitism of nematodes. PLoS Genetics 12: e1006017 , doi:10.1371/journal.pgen.1006017
   PubMed Web of Science ®Google Scholar
• Lepage BA, Currah RS, Stockey RA, Rothwell GW. 1997. Fossil ectomycorrhizae from the middle Eocene. American Journal of Botany 84:410–412, doi:10.2307/2446014
   PubMed Web of Science ®Google Scholar
• Li L, Stoeckert CJJ, Roos DS. 2003. OrthoMCL: identification of ortholog groups for Eukaryotic genomes. Genome Research 13:2178–2189, doi:10.1101/gr.1224503
   PubMed Web of Science ®Google Scholar
• Lind AL, Wisecaver JH, Lameiras C, Wiemann P, Palmer JM, Keller NP, Rodrigues F, Goldman GH, Rokas A. 2017. Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species. PLoS Biology 15:e2003583.
   PubMed Web of Science ®Google Scholar
• Lorito M. 1996. Synergistic interaction between cell wall degrading enzymes and membrane affecting compounds. Molecular Plant-Microbe Interactions 9:206, doi:10.1094/MPMI-9-0206
   Web of Science ®Google Scholar
• Maddison WP. 1997. Gene trees in species trees. Systematic Biology 46:523–536.
   Web of Science ®Google Scholar
• Mains EB. 1957. Species of Cordyceps parasitic on Elaphomyces. Bulletin of the Torrey Botanical Club 84:243–251.
   Google Scholar
• Malmierca MG, Cardoza RE, Alexander NJ, McCormick SP, Collado IG, Hermosa R, Monte E, Gutiérrez S. 2013. Relevance of trichothecenes in fungal physiology: disruption of tri5 in Trichoderma arundinaceum. Fungal Genetics and Biology 53:22–33, doi:10.1016/j.fgb.2013.02.001
   PubMed Web of Science ®Google Scholar
• Malmierca MG, Cardoza RE, Alexander NJ, McCormick SP, Hermosa R, Monte E, Gutiérrez S. 2012. Involvement of Trichoderma trichothecenes in the biocontrol activity and induction of plant defense-related genes. Applied and Environmental Microbiology 78:4856–4868, doi:10.1128/AEM.00385-12
   PubMed Web of Science ®Google Scholar
• Marçais G, Kingsford C. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27:764–770, doi:10.1093/bioinformatics/btr011
   PubMed Web of Science ®Google Scholar
• Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EGJ, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, Leon AL de, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS. 2008. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature Biotechnology 26:553–560, doi:10.1038/nbt1403
   PubMed Web of Science ®Google Scholar
• Nikoh N, Fukatsu T. 2000. Interkingdom host jumping underground: phylogenetic analysis of entomoparasitic fungi of the genus Cordyceps. Molecular Biology and Evolution 17:629–638, doi:10.1093/oxfordjournals.molbev.a026341
   PubMed Web of Science ®Google Scholar
• Ortiz-Urquiza A, Keyhani NO. 2013. Action on the surface: entomopathogenic Fungi versus the insect cuticle. Insects 4:357–374, doi:10.3390/insects4030357
   PubMedGoogle Scholar
• Parker EJ, Scott DB. 2004. Indole-diterpene biosynthesis in ascomycetous fungi. In: An Z, ed. Handbook of industrial mycology. Marcel Dekker: New York, NY. p. 405–426.
   Google Scholar
• Parra G, Bradnam K, Korf I. 2007. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061–1067, doi:10.1093/bioinformatics/btm071
   PubMed Web of Science ®Google Scholar
• Parra G, Bradnam K, Ning Z, Keane T, Korf I. 2009. Assessing the gene space in draft genomes. Nucleic Acids Research 37:289–297, doi:10.1093/nar/gkn916
   PubMed Web of Science ®Google Scholar
• Poinar GO, Thomas GM. 1984. A fossil entomogenous fungus from Dominican amber. Experientia 40:578–579.
   Google Scholar
• Price AL, Jones NC, Pevzner PA. 2005. De novo identification of repeat families in large genomes. Bioinformatics 21:351–358, doi:10.1093/bioinformatics/bti1018
   PubMed Web of Science ®Google Scholar
• Quandt CA, Bushley KE, Spatafora JW. 2015a. The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics. BMC Genomics 16: 553, doi:10.1186/s12864-015-1777-9
   PubMed Web of Science ®Google Scholar
• Quandt CA, Di Y, Elser J, Jaiswal P, Spatafora JW. 2016. Differential expression of genes involved in host recognition, attachment, and degradation in the mycoparasite Tolypocladium ophioglossoides. G3: Genes|Genomes|Genetics 6:731–741, doi:10.1534/g3.116.027045
   Web of Science ®Google Scholar
• Quandt CA, Kepler RM, Gams W, Araújo JPM, Ban S, Evans HC, Hughes D, Humber R, Hywel-Jones N, Li Z, Luangsa-Ard JJ, Rehner SA, Sanjuan T, Sato H, Shrestha B, Sung G-H, Yao Y-J, Zare R, Spatafora JW. 2014. Phylogenetic-based nomenclatural proposals for Ophiocordycipitaceae (Hypocreales) with new combinations in Tolypocladium. IMA Fungus 5:121–134, doi:10.5598/imafungus.2014.05.01.12
   PubMed Web of Science ®Google Scholar
• Quandt CA, Kohler A, Hesse CN, Sharpton TJ, Martin F, Spatafora JW. 2015b. Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome. Environmental Microbiology 17, doi:10.1111/1462-2920.12840
   PubMed Web of Science ®Google Scholar
• Robbertse B, Yoder RJ, Boyd A, Reeves J, Spatafora JW. 2011. Hal: an automated pipeline for phylogenetic analyses of genomic data. PLoS Currents Tree of Life 7 Feb, doi:10.1371/currents.RRN1213
   Google Scholar
• Röhrich CR, Iversen A, Jaklitsch WM, Voglmayr H, Berg A, Dörfelt H, Thrane U, Vilcinskas A, Nielsen KF, Döhren H von, Brückner H, Degenkolb T. 2012. Hypopulvins, novel peptaibiotics from the polyporicolous fungus Hypocrea pulvinata, are produced during infection of its natural hosts. Fungal Biology 116: 1219–1231, doi:10.1016/j.funbio.2012.10.003
   Google Scholar
• Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, Calie PJ, Fleetwood DJ, Haws DC, Moore N, Oeser B, Panaccione DG, Schweri KK, Voisey CR, Farman ML, Jaromczyk JW, Roe BA, O’Sullivan DM, Scott B, Tudzynski P, An Z, Arnaoudova EG, Bullock CT, Charlton ND, Chen L, Cox M, Dinkins RD, Florea S, Glenn AE, Gordon A, Guldener U, Harris DR, Hollin W, Jaromczyk J, Johnson RD, Khan AK, Leistner E, Leuchtmann A, Li C, Liu J, Liu J, Liu M, Mace W, Machado C, Nagabhyru P, Pan J, Schmid J, Sugawara K, Steiner U, Takach JE, Tanaka E, Webb JS, Wilson EV, Wiseman JL, Yoshida R, Zeng Z. 2013. Plant-symbiotic Fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid loci. PLoS Genetics 9:1003323, doi:10.1371/journal.pgen.1003323
   PubMed Web of Science ®Google Scholar
• Shaw SR. 1988. Euphorine phylogeny: the evolution of diversity in host-utilization by parasitoid wasps (Hymenoptera: Braconidae). Ecological Entomology 13:323–335.
   Web of Science ®Google Scholar
• Silva DN, Talhinhas P, Cai L, Manuel L, Gichuru EK, Loureiro A, Várzea V, Paulo OS, Batista D. 2012. Host-jump drives rapid and recent ecological speciation of the emergent fungal pathogen Colletotrichum kahawae. Molecular Ecology 21:2655–2670, doi:10.1111/j.1365-294X.2012.05557.x
   PubMed Web of Science ®Google Scholar
• Smit AF, Green P. 1996. RepeatMasker. [cited 2013 Dec 12]. Available from: http://www.repeatmasker.org/
   Google Scholar
• Sorenson WG, Frazer DG, Jarvis BB, Simpson J, Robinson VA. 1987. Trichothecene mycotoxins in aerosolized conidia of Stachybotrys atra. Applied and Environmental Microbiology 53:1370–1375.
   PubMed Web of Science ®Google Scholar
• Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690, doi:10.1093/bioinformatics/btl446
   PubMed Web of Science ®Google Scholar
• Stanke M, Morgenstern B. 2005. AUGUSTUS: a Web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Research 33:465–467, doi:10.1093/nar/gki458
   PubMed Web of Science ®Google Scholar
• Sung G-H, Hywel-Jones NL, Sung J-M, Luangsa-ard JJ, Shrestha B, Spatafora JW. 2007. Phylogenetic classification of Cordyceps and the clavicipitaceous fungi. Studies in Mycology 57:5–59.
   PubMed Web of Science ®Google Scholar
• Sung G, Poinar GO, Spatafora JW. 2008. The oldest fossil evidence of animal parasitism by fungi supports a Cretaceous diversification of fungal–arthropod symbioses. Molecular Phylogenetics and Evolution 49:495–502, doi:10.1016/j.ympev.2008.08.028
   PubMed Web of Science ®Google Scholar
• Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56:564–577, doi:10.1080/10635150701472164
   PubMed Web of Science ®Google Scholar
• Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M. 2008. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Research 18:1979–1990, doi:10.1101/gr.081612.108
   PubMed Web of Science ®Google Scholar
• Than C, Ruths D, Nakhleh L. 2008. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics 9:322, doi:10.1186/1471-2105-9-322
   Web of Science ®Google Scholar
• Wang G, Liu Z, Lin R, Li E, Mao Z, Ling J, Yang Y, Yin WB, Xie B. 2016. Biosynthesis of antibiotic Leucinostatins in bio-control fungus Purpureocillium lilacinum and their inhibition on Phytophthora revealed by genome mining. PLoS Pathogens 12(7): e1005685. doi:10.1371/journal.ppat.1005685
   Web of Science ®Google Scholar
• Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, MacHi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJC, Yoo HS, Zhang C, Zhang Y, Sobral BW. 2014. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Research 42:581–591, doi:10.1093/nar/gkt1099
   PubMed Web of Science ®Google Scholar
• Wu S, Zhu Z, Fu L, Niu B, Li W. 2011. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 12:444, doi:10.1186/1471-2164-12-444
   Web of Science ®Google Scholar
• Xiao G, Ying S-H, Zheng P, Wang Z-L, Zhang S, Xie X-Q, Shang Y, St Leger RJ, Zhao G-P, Wang C, Feng M-G. 2012. Genomic perspectives on the evolution of fungal entomopathogenicity in Beauveria bassiana. Scientific Reports 2:483, doi:10.1038/srep00483
   Web of Science ®Google Scholar
• Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y. 2012. DbCAN: a Web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Research 40:445–451, doi:10.1093/nar/gks479
   PubMed Web of Science ®Google Scholar
• Young CA, Felitti S, Shields K, Spangenberg G, Johnson RD, Bryan GT, Saikia S, Scott B. 2006. A complex gene cluster for indole-diterpene biosynthesis in the grass endophyte Neotyphodium lolii. Fungal Genetics and Biology 43:679–693, doi:10.1016/j.fgb.2006.04.004
   PubMed Web of Science ®Google Scholar
• Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18:821–829, doi:10.1101/gr.074492.107
   PubMed Web of Science ®Google Scholar
• Ziêtara MS, Lumme J. 2002. Speciation by host switch and adaptive radiation in a fish parasite genus Gyrodactylus (Monogenea, Gyrodactylidae). Evolution 56:2445–2458, doi:10.1111/j.0014-3820.2002.tb00170.x
   PubMed Web of Science ®Google Scholar