The chemical ecology and biotechnological potential of metabolites from endophytic and rhizosphere fungi are receiving much attention. A collection of 17 sugarcane-derived fungi were identified and assessed by PCR for the presence of polyketide synthase (PKS) genes. The fungi were all various genera of ascomycetes, the genomes of which encoded 36 putative PKS sequences, 26 shared sequence homology with β-ketoacyl synthase domains, while 10 sequences showed homology to known fungal C-methyltransferase domains. A neighbour-joining phylogenetic analysis of the translated sequences could group the domains into previously established chemistry-based clades that represented non-reducing, partially reducing and highly reducing fungal PKSs. We observed that, in many cases, the membership of each clade also reflected the taxonomy of the fungal isolates. The functional assignment of the domains was further confirmed by in silico secondary and tertiary protein structure predictions. This genome mining study reveals, for the first time, the genetic potential of specific taxonomic groups of sugarcane-derived fungi to produce specific types of polyketides. Future work will focus on isolating these compounds with a view to understanding their chemical ecology and likely biotechnological potential. © 2011 Springer Science+Business Media, LLC.633565577Amnuaykanjanasin, A., Phonghanpot, S., Sengpanich, N., Cheevadhanarak, S., Tanticharoen, M., Insect-specific polyketide synthases (PKSs), potential PKS-nonribosomal peptide synthetase hybrids, and novel PKS clades in tropical fungi (2009) Appl Environ Microbiol, 75, pp. 3721-3732Amnuaykanjanasin, A., Punya, J., Paungmoung, P., Rungrod, A., Tachaleat, A., Pongpattanakitshote, S., Cheevadhanarak, S., Tanticharoen, M., Diversity of type I polyketide synthase genes in the wood-decay fungus Xylaria sp. BCC 1067 (2005) FEMS Microbiol Lett, 251, pp. 125-136Ansari, M.Z., Sharma, J., Gokhale, R.S., Mohanty, D., In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites (2008) BMC Bioinformatics, 9, p. 454Arnold, K., Bordoli, L., Kopp, J., Schwede, T., The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling (2006) Bioinformatics, 22, pp. 195-201Atoui, A., Dao, H.P., Mathieu, F., Lebrihi, A., Amplification and diversity analysis of ketosynthase domains of putative polyketide synthase genes in Aspergillus ochraceus and Aspergillus carbonarius producers of ochratoxin A (2006) Mol Nutr Food Res, 50, pp. 488-493Bach, T.J., Lichtenthaler, H.K., Inhibition by mevinolin of plant growth, sterol formation and pigment acumulation (1983) Physiol Plant, 59, pp. 50-60Ballance, D.J., Sequences important for gene expression in filamentous fungi (1986) Yeast, 2, pp. 229-236Bills, G., Overy, D., Genilloud, O., Pelaez, F., Contribution of pharmaceutical antibiotics and secondary metabolite discovery to the understanding of microbial defence and antagonism (2009) Defensive Mutualism in Microbial Symbiosis, 27. , J. M. White and M. S. Torres (Eds.), Boca Raton: CRCBingle, L.E., Simpson, T.J., Lazarus, C.M., Ketosynthase domain probes identify two subclasses of fungal polyketide synthase genes (1999) Fungal Genet Biol, 26, pp. 209-223Cox, R.J., Polyketides, proteins and genes in fungi: programmed nano-machines begin to reveal their secrets (2007) Org Biomol Chem, 5, pp. 2010-2026da Silva, M., Passarini, M.R., Bonugli, R.C., Sette, L.D., Cnidarian-derived filamentous fungi from Brazil: isolation, characterisation and RBBR decolourisation screening (2008) Environ Technol, 29, pp. 1331-1339Eriksson, O.E., Hawksworth, D.L., Saccharicola, a new genus for two Leptosphaeria species on sugar cane (2003) Mycologia, 95, pp. 426-433Galgoczy, L., Papp, T., Lukacs, G., Leiter, E., Pocsi, I., Vagvolgyi, C., Interactions between statins and Penicillium chrysogenum antifungal protein (PAF) to inhibit the germination of sporangiospores of different sensitive Zygomycetes (2007) FEMS Microbiol Lett, 270, pp. 109-115Gardes, M., Bruns, T.D., ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts (1993) Mol Ecol, 2, pp. 113-118Ginolhac, A., Jarrin, C., Gillet, B., Robe, P., Pujic, P., Tuphile, K., Bertrand, H., Nalin, R., Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones (2004) Appl Environ Microbiol, 70, pp. 5522-5527Gontang, E.A., Gaudencio, S.P., Fenical, W., Jensen, P.R., Sequence-based analysis of secondary-metabolite biosynthesis in marine actinobacteria (2010) Appl Environ Microbiol, 76, pp. 2487-2499Grube, M., Blaha, J., On the phylogeny of some polyketide synthase genes in the lichenized genus Lecanora (2003) Mycol Res, 107, pp. 1419-1426Guerrero, A., Rosell, G., Biorational approaches for insect control by enzymatic inhibition (2005) Curr Med Chem, 12, pp. 461-469Henson, J.M., Butler, M.J., Day, A.W., The dark sede of the mycelium: melanins of phytopathogenic fungi (1999) Annu Rev Phytopathol, 37, pp. 447-471Hertweck, C., The biosynthetic logic of polyketide diversity (2009) Angew Chem Int Ed Engl, 48, pp. 4688-4716Hoffmeister, D., Keller, N.P., Natural products of filamentous fungi: enzymes, genes, and their regulation (2007) Nat Prod Rep, 24, pp. 393-416Hopwood, D.A., Khosla, C., Genes for polyketide secondary metabolic pathways in microorganisms and plants (1992) Ciba Found Symp, 171, pp. 88-106. , discussion 106-112Howard, R.J., Ferrari, M.A., Roach, D.H., Money, N.P., Penetration of hard substrates by a fungus employing enormous turgor pressures (1991) Proc Natl Acad Sci USA, 88, pp. 11281-11284Huang, C.S., Chang, S.L., Leafinfection with citrus black spot and perithecial development in relation to ascospore discharge of Guignardia citricarpa Kiely (1972) J Taiwan Agric Res, 21, pp. 256-263Huang, W., Jia, J., Edwards, P., Dehesh, K., Schneider, G., Lindqvist, Y., Crystal structure of beta-ketoacyl-acyl carrier protein synthase II from E. coli reveals the molecular architecture of condensing enzymes (1998) EMBO J, 17, pp. 1183-1191Kagan, R.M., Clarke, S., Widespread occurrence of three sequence motifs in diverse S-adenosylmethionine-dependent methyltransferases suggests a common structure for these enzymes (1994) Arch Biochem Biophys, 310, pp. 417-427Katz, J.E., Dlakic, M., Clarke, S., Automated identification of putative methyltransferases from genomic open reading frames (2003) Mol Cell Proteomics, 2, pp. 525-540Kelley, L.A., Sternberg, M.J., Protein structure prediction on the Web: a case study using the Phyre server (2009) Nat Protoc, 4, pp. 363-371Kim, T.K., Hewavitharana, A.K., Shaw, P.N., Fuerst, J.A., Discovery of a new source of rifamycin antibiotics in marine sponge actinobacteria by phylogenetic prediction (2006) Appl Environ Microbiol, 72, pp. 2118-2125Kroken, S., Glass, N.L., Taylor, J.W., Yoder, O.C., Turgeon, B.G., Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes (2003) Proc Natl Acad Sci USA, 100, pp. 15670-15675Kupfer, D.M., Drabenstot, S.D., Buchanan, K.L., Lai, H., Zhu, H., Dyer, D.W., Roe, B.A., Murphy, J.W., Introns and splicing elements of five diverse fungi (2004) Eukaryot Cell, 3, pp. 1088-1100Langfelder, K., Streibel, M., Jahn, B., Haase, G., Brakhage, A.A., Biosynthesis of fungal melanins and their importance for human pathogenic fungi (2003) Fungal Genet Biol, 38, pp. 143-158Lee, T., Yun, S.H., Hodge, K.T., Humber, R.A., Krasnoff, S.B., Turgeon, G.B., Yoder, O.C., Gibson, D.M., Polyketide synthase genes in insect and nematode-associated fungi (2001) Appl Microbiol Biotechnol, 56, pp. 181-187Macreadie, I.G., Johnson, G., Schlosser, T., Macreadie, P.I., Growth inhibition of Candida species and Aspergillus fumigatus by statins (2006) FEMS Microbiol Lett, 262, pp. 9-13Magnani, G.S., Didonet, C.M., Cruz, L.M., Picheth, C.F., Pedrosa, F.O., Souza, E.M., Diversity of endophytic bacteria in Brazilian sugarcane (2010) Genet Mol Res, 9, pp. 250-258Martin, J.L., McMillan, F.M., SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold (2002) Curr Opin Struct Biol, 12, pp. 783-793Mathieu, M., Zeelen, J.P., Pauptit, R.A., Erdmann, R., Kunau, W.H., Wierenga, R.K., The 2.8 A crystal structure of peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: a five-layered alpha beta alpha beta alpha structure constructed from two core domains of identical topology (1994) Structure, 2, pp. 797-808Mayer, K.M., Ford, J., Macpherson, G.R., Padgett, D., Volkmann-Kohlmeyer, B., Kohlmeyer, J., Murphy, C., Wright, J.L., Exploring the diversity of marine-derived fungal polyketide synthases (2007) Can J Microbiol, 53, pp. 291-302Mendes, R., Pizzirani-Kleiner, A.A., Araujo, W.L., Raaijmakers, J.M., Diversity of cultivated endophytic bacteria from sugarcane: genetic and biochemical characterization of Burkholderia cepacia complex isolates (2007) Appl Environ Microbiol, 73, pp. 7259-7267Metz, J.G., Roessler, P., Facciotti, D., Levering, C., Dittrich, F., Lassner, M., Valentine, R., Browse, J., Production of polyunsaturated fatty acids by polyketide synthases in both prokaryotes and eukaryotes (2001) Science, 293, pp. 290-293Miller, D.J., Ouellette, N., Evdokimova, E., Savchenko, A., Edwards, A., Anderson, W.F., Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain (2003) Protein Sci, 12, pp. 1432-1442Nicholson, T.P., Rudd, B.A., Dawson, M., Lazarus, C.M., Simpson, T.J., Cox, R.J., Design and utility of oligonucleotide gene probes for fungal polyketide synthases (2001) Chem Biol, 8, pp. 157-178Olsen, J.G., Kadziola, A., von Wettstein-Knowles, P., Siggaard-Andersen, M., Larsen, S., Structures of beta-ketoacyl-acyl carrier protein synthase I complexed with fatty acids elucidate its catalytic machinery (2001) Structure, 9, pp. 233-243Peres, N.A., Harakava, R., Carroll, G.C., Adaskaveg, J.E., Timmer, L.W., Comparisonof molecular procedures for detection and identification of Guignardia citricarpa and G. mangiferae (2007) Plant Dis, 91, pp. 525-531Sauer, M., Lu, P., Sangari, R., Kennedy, S., Polishook, J., Bills, G., An, Z., Estimating polyketide metabolic potential among nonsporulatingfungal endophytes of Vaccinium macrocarpon (2002) Mycol Res, 1006, pp. 460-470Schmitt, I., Kautz, S., Lumbsch, H.T., 6-MSAS-like polyketide synthase genes occur in lichenized ascomycetes (2008) Mycol Res, 112, pp. 289-296Schmitt, I., Martin, M.P., Kautz, S., Lumbsch, H.T., Diversity of non-reducing polyketide synthase genes in the Pertusariales (lichenized Ascomycota): a phylogenetic perspective (2005) Phytochemistry, 66, pp. 1241-1253Schulz, B., Boyle, C., The endophytic continuum (2005) Mycol Res, 109, pp. 661-686Schumann, J., Hertweck, C., Advances in cloning, functional analysis and heterologous expression of fungal polyketide synthase genes (2006) J Biotechnol, 124, pp. 690-703Soanes, D.M., Alam, I., Cornell, M., Wong, H.M., Hedeler, C., Paton, N.W., Rattray, M., Talbot, N.J., Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis (2008) PLoS One, 3, pp. e2300Stierle, A., Strobel, G., Stierle, D., Taxol and taxane production by Taxomyces andreanae, an endophytic fungus of Pacific yew (1993) Science, 260, pp. 214-216Stuart, R.M., Romao, A.S., Pizzirani-Kleiner, A.A., Azevedo, J.L., Araujo, W.L., Culturable endophytic filamentous fungi from leaves of transgenic imidazolinone-tolerant sugarcane and its non-transgenic isolines (2010) Arch Microbiol, 192, pp. 307-313Tan, R.X., Zou, W.X., Endophytes: a rich source of functional metabolites (2001) Nat Prod Rep, 18, pp. 448-459Varga, J., Rigo, K., Kocsube, S., Farkas, B., Pal, K., Diversity of polyketide synthase gene sequences in Aspergillus species (2003) Res Microbiol, 154, pp. 593-600Weissman, K.J., Introduction to polyketide biosynthesis (2009) Methods Enzymol, 459, pp. 3-16White, T.J., Bruns, T., Lee, S., Taylor, J., Amplification and direct sequencing of fungal ribosomal DNA genes for phylogenies (1990) PCR Protocols: A Guide to Methods and Applications, pp. 312-315. , M. A. Innis, D. H. Gelfand, J. J. Snisky, and T. J. White (Eds.), New York: Academic