Abstract
Endophytes live inter- and/or intracellularly inside healthy aboveground tissues of plants without causing disease. Endophytic fungi are found in virtually every vascular plant species examined. The origins of this symbiotic relationship between endophytes go back to the emergence of vascular plants. Endophytic fungi receive nutrition and protection from their hosts while the plants benefit from the production of fungal secondary metabolites, which enhance the host plants’ resistance to herbivores, pathogens, and various abiotic stresses. Endophytic fungi have attracted increased interest as potential sources of secondary metabolites with agricultural, industrial, and medicinal use. This chapter provides detailed protocols for isolation of genomic DNA from fungal endophytes and its use in polymerase chain reaction-based amplification of the internal transcribed spacer region between the conserved flanking regions of the small and large subunit of ribosomal RNA for barcoding purposes.
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References
Tan RX and Zou WX (2001) Endophytes: a rich source of functional metabolites. Natural Product Reports 18(4):448–459
Rodriguez RJ, White JF, Arnold AE, et al (2009) Fungal endophytes: diversity and Âfunctional roles. New Phytologist 182(2): 314–330
Zhang HW, Song YC, and Tan RX (2006) Biology and chemistry of endophytes. Nat Prod Rep 23(5):753–771
Seifert KA (2009) Progress towards DNA barcoding of fungi. Molecular Ecology Resources 9:83–89
McLaughlin DJ, Hibbett DS, Lutzoni F, et al (2009) The search for the fungal tree of life. Trends Microbiol 17(11):488–497
Stajich JE, Berbee ML, Blackwell M, et al (2009) The fungi. Curr Biol 19(18): R840–845
Saikkonen K, Faeth SH, Helander M, et al (1998) Fungal endophytes: A continuum of interactions with host plants. Annual Review of Ecology and Systematics 29:319–343
Belesky DP and Bacon CW (2009) Tall fescue and associated mutualistic toxic fungal endophytes in agroecosystems. Toxin Reviews 28(2–3):102–117
Schardl CL, Grossman RB, Nagabhyru P, et al (2007) Loline alkaloids: Currencies of mutualism. Phytochemistry 68(7):980–996
Schulz B, Boyle C, Draeger S, et al (2002) Endophytic fungi: a source of novel biologically active secondary metabolites. Mycological Research 106:996–1004
Strobel G (2006) Harnessing endophytes for industrial microbiology. Current opinion in microbiology 9(3):240–244
Strobel G and Daisy B (2003) Bioprospecting for microbial endophytes and their natural products. Microbiol Mol Biol Rev 67(4):491–502
Strobel G, Daisy B, Castillo U, et al (2004) Natural products from endophytic microorganisms. Journal of natural products 67(2):257–268
Sucher NJ and Carles MC (2008) Genome-based approaches to the authentication of medicinal plants. Planta Med 74(6):603–623
Hebert PD, Cywinska A, Ball SL, et al (2003) Biological identifications through DNA barcodes. Proc Biol Sci 270(1512):313–321
Stockinger H, Kruger M, and Schussler A (2010) DNA barcoding of arbuscular mycorrhizal fungi. New Phytol 187(2):461–474
Hebert PD and Gregory TR (2005) The promise of DNA barcoding for taxonomy. Syst Biol 54(5):852–859
Chase MW and Fay MF (2009) Barcoding of Plants and Fungi. Science 325(5941):682–683
Martin KJ and Rygiewicz PT (2005) Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiol 5:28
White T, Bruns T, Lee S, et al (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M, Gelfand D, Sninsky J, & White T (ed) PCR Protocols: A Guide to Methods and Applications. Academic Press Inc, New York
Wang B, Priest MJ, Davidson A, et al (2007) Fungal endophytes of native Gossypium species in Australia. Mycol Res 111(3):347–354
Egger KN (1995) Molecular Analysis of Ectomycorrhizal Fungal Communities. Can J Bot 73:S1415–S1422
Gardes M and Bruns TD (1993) Its Primers with Enhanced Specificity for Basidiomycetes – Application to the Identification of Mycorrhizae and Rusts. Mol Ecol 2(2): 113–118
Gargas A and DePriest PT (1996) A nomenclature for fungal PCR primers with examples from intron-containing SSU rDNA. Mycologia 88(5):745–748
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Diaz, P.L., Hennell, J.R., Sucher, N.J. (2012). Genomic DNA Extraction and Barcoding of Endophytic Fungi. In: Sucher, N., Hennell, J., Carles, M. (eds) Plant DNA Fingerprinting and Barcoding. Methods in Molecular Biology, vol 862. Humana Press. https://doi.org/10.1007/978-1-61779-609-8_14
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DOI: https://doi.org/10.1007/978-1-61779-609-8_14
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