Skip to main content
SpringerLink
Log in

DNA Barcoding for Diagnosis and Monitoring of Fungal Plant Pathogens

  • Chapter
  • First Online:
Molecular Markers in Mycology

Part of the book series: Fungal Biology ((FUNGBIO))

  • In the original version of Chapter 5, illustrations 1–10 had permission issues. In the current version, Chapter 5 has been replaced with a new, revised chapter with one original figure replacing the previous 10 illustrations.

Abstract

Plant pathogenic fungi cause significant economic crop yield losses every year. Proper identification up to species level is a critical initial step in any investigation of plant infection, whether it is research driven or compelled by the need for rapid and accurate diagnostics during disease outbreak. Further, it is also helpful in making decision with respect to the monetary loss and investment to follow necessary disease management practices. The recent developments of DNA barcoding technology have drastically translated the epitome of species identification and show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, ecological studies, diagnostics and monitoring of fungal plant pathogens. This chapter provides a vision on the current use and impact of DNA barcoding approaches in diagnosis and monitoring of fungal plant pathogens. Moreover, an effort has been put forward to understand various marker genes associated with barcode process, their suitability, limitation and applicability in diagnostic and monitoring of fungal plant pathogens.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

Change history

  • 27 July 2017

    An erratum has been published.

References

  • Abdelfattah A, Li Destri Nicosia MG, Cacciola SO, Droby S, Schena L. Metabarcoding analysis of fungal diversity in the phyllosphere and carposphere of olive (Olea europaea). PLoS One. 2015;110(7):e0131069. doi:10.1371/journal.pone.0131069.

    Article  CAS  Google Scholar 

  • Alaei H, Baeyena S, Maes M, Höfte M, Heungens K. Molecular detection of Puccinia horiana in Chrysanthemum x morifolium through conventional and real-time PCR. J Microbiol Methods. 2009;76:136–45.

    CAS  PubMed  Google Scholar 

  • Ali MA, Gyulai G, Hidvégi N, Kerti B, et al. The changing epitome of species identification-DNA barcoding. Saudi J Biol Sci. 2014;21(3):204–31.

    Google Scholar 

  • Aroca A, Raposo R. PCR-based strategy to detect and identify species of Phaeoacremonium causing grapevine diseases. Appl Environ Microbiol. 2007;73:2911–8. doi:10.1128/AEM.02176-06.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aroca A, Raposo R, Lunello P. A biomarker for the identification of four Phaeoacremonium species using the β-tubulin gene as the target sequence. Appl Microbiol Biotechnol. 2008;80:1131–40.

    CAS  PubMed  Google Scholar 

  • Atkins SD, Clark IM. Fungal molecular diagnostics: a mini review. J Appl Genet. 2004;45(1):3–15.

    PubMed  Google Scholar 

  • Balajee SA, Borman AM, Brandt ME, et al. Sequence-based identification of Aspergillus, Fusarium, and Mucorales species in the clinical mycology laboratory: where are we and where should we go from here? J Clin Microbiol. 2009;47:877–84.

    CAS  PubMed  Google Scholar 

  • Begerow D, Nilsson H, Unterseher M, Maier W. Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Appl Microbiol Biotechnol. 2010;87:99–108.

    CAS  PubMed  Google Scholar 

  • Belfield GP, Tuite MF. Translation elongation factor 3: a fungus-specific translation factor? Mol Microbiol. 2006;9:411–8.

    Google Scholar 

  • Berry D, Mahfoudh KB, Wagner M, Loy A. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl Environ Microbiol. 2011;77:7846–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bilodeau GJ, Koike ST, Uribe P, Martin FN. Development of an assay for rapid detection and quantification of Verticillium dahliae in soil. Phytopathology. 2012;102:331–43.

    CAS  PubMed  Google Scholar 

  • Bilodeau GJ, Martin FN, Coffey MD, Blomquist CL. Development of a multiplex assay for genus- and species-specific detection of Phytophthora based on differences in mitochondrial gene order. Phytopathology. 2014;104(7):733–48. doi:10.1094/PHYTO-09-13-0263-R.

    Article  CAS  PubMed  Google Scholar 

  • Brodersen DE, Nissen P. The social life of ribosomal proteins. FEBS J. 2005;272:2098–108.

    CAS  PubMed  Google Scholar 

  • Bruns TD, White TJ, Talyor JW. Fungal molecular systematics. Annu Rev Ecol Syst. 1991;22:525–64.

    Google Scholar 

  • Budge GE, Shaw MW, Colyer A, Pietravalle S, Boonham N. Molecular tools to investigate Rhizoctonia solani distribution in soil. Plant Pathol. 2009;58:1071–80.

    CAS  Google Scholar 

  • Cai L, Hyde KD, Taylor PWJ, Weir BS, Waller J, et al. A polyphasic approach for studying Colletotrichum. Fungal Divers. 2009;39:183–204.

    Google Scholar 

  • Carbone I, Kohn LM. A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia. 1999;91:553–6.

    CAS  Google Scholar 

  • Ceasar AS, Ignacimuthu S. Genetic engineering of crop plants for fungal resistance: role of antifungal genes. Biotechnol Lett. 2012;34:995–1002. doi:10.1007/s10529-012-0871-1.

    Article  CAS  PubMed  Google Scholar 

  • Chen Y, Roxby R. Characterization of a Phytophthora infestans gene involved in vesicle transport. Gene. 1996;181:89–94.

    CAS  PubMed  Google Scholar 

  • Chen W, Djama ZR, Coffey MD, Martin FN, et al. Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species. Phytopathology. 2013;103:43–54. doi:10.1094/PHYTO-04-12-0092-R.

    Article  CAS  PubMed  Google Scholar 

  • Cho S, Mitchell A, Regier JC, Mitter C, Poole RW, Friedlander TP, Zhao S. A highly conserved gene for low level phylogenetics: elongation factor-1 alpha recovers morphology-based tree for heliothine moths. Mol Biol Evol. 1995;12:650–6.

    CAS  PubMed  Google Scholar 

  • Collado-Romero M, Mercado-Blanco J, Olivares-García C, Jiménez-Díaz RM. Phylogenetic analysis of Verticillium dahliae vegetative compatibility groups. Phytopathology. 2008;98:1019–28.

    CAS  PubMed  Google Scholar 

  • Crouch JA, Clarke BB, Hillman BI. Unraveling evolutionary relationships among the divergent lineages of Colletotrichum causing anthracnose disease in turfgrass and corn. Mycology. 2006;96(1):46–60. doi:10.1094/PHYTO-96-0046.

    Article  CAS  Google Scholar 

  • Crouch JA, Szabo LJ. Real-time PCR detection and discrimination of the southern and common corn rust pathogens Puccinia polysora and Puccinia sorghi. Plant Dis. 2011;95:624–32.

    PubMed  Google Scholar 

  • Crouch JA, Clarke BB, Hillman BI. What is the value of ITS sequence data in Colletotrichum systematics and species diagnosis? A case study using the falcate-spored graminicolous Colletotrichum group. Mycologia. 2009a;101:648–56.

    PubMed  Google Scholar 

  • Crouch JA, Tredway LP, Clarke BB, Hillman BI. Phylogenetic and population genetic divergence correspond with habitat for the pathogen Colletotrichum cereale and allied taxa across diverse grass communities. Mol Ecol. 2009b;18(1):123–35.

    CAS  PubMed  Google Scholar 

  • Crous PW, Groenewald JZ, Summerell BA, Wingfield BD, Wingfield MJ. Co-occurring species of Teratosphaeria on eucalyptus. Persoonia. 2009;22:38–48.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Crous PW, Hawksworth DL, Wingfield MJ. Identifying and naming plant-pathogenic fungi: past, present, and future. Annu Rev Phytopathol. 2015;53:247–67. doi:10.1146/annurev-phyto-080614-120245.

    Article  CAS  PubMed  Google Scholar 

  • Cummings MP. GARLI (Genetic Algorithm for Rapid Likelihood Inference). Dictionary of Bioinformatics and Computational Biology. 2014. doi: 10.1002/9780471650126.dob0912.

  • Damm U, Woudenberg JHC, Cannon PF, Crous PW. Colletotrichum species with curved conidia from herbaceous hosts. Fungal Divers. 2009;39:45–87.

    Google Scholar 

  • Daniel HM, Meyer W. Evaluation of ribosomal RNA and actin gene sequences for the identification of ascomycetous yeasts. Int J Food Microbiol. 2003;86:61–78.

    CAS  PubMed  Google Scholar 

  • Daniel HM, Sorrell TC, Meyer W. Partial sequence analysis of the actin gene and its potential for studying the phylogeny of Candida species and their teleomorphs. Int J Syst Evol Microbiol. 2001;51:1593–606.

    CAS  PubMed  Google Scholar 

  • Davey JW, Hohenlohe PA, Etter PD, Boone JQ, et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet. 2011;12:499–510.

    CAS  PubMed  Google Scholar 

  • de Beer ZW, Duong TA, Barnes I, Wingfield BD, Wingfield MJ. Redefining Ceratocystis and allied genera. Stud Mycol. 2014;79:187–219.

    PubMed  PubMed Central  Google Scholar 

  • De Boer SH, López MM. New grower-friendly methods for plant pathogen monitoring. Annu Rev Phytopathol. 2012;50:197–218.

    PubMed  Google Scholar 

  • Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O. Phylogeny.Fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008;36(Web Server):W465–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Dita MA, Waalwijk C, Buddenhagen IW, Souza Jr MT, Kema GHJ. A molecular diagnostic for tropical race 4 of the banana fusarium wilt pathogen. Plant Pathol. 2010;59:348–57.

    CAS  Google Scholar 

  • Dixon LJ, Schlub RL, Pernezny K, Datnoff LE. Host specialization and phylogenetic diversity of Corynespora cassiicola. Phytopathology. 2009;99(9):1015–27.

    CAS  PubMed  Google Scholar 

  • Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007;7:214. doi:10.1186/1471-2148-7-214.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duressa D, Rauscher G, Koike ST, Mou B, Hayes RJ, Maruthachalam K, Subbarao KV, Klosterman SJ. A real-time PCR assay for detection and quantification of Verticillium dahliae in spinach seed. Phytopathology. 2012;102:443–51.

    CAS  PubMed  Google Scholar 

  • Fang Y, Ramasamy RP. Current and prospective methods for plant disease detection. Biosensors. 2015;4:537–61. doi:10.3390/bios5030537.

    Article  CAS  Google Scholar 

  • Farris JS. Methods for computing Wagner trees. Syst Zool. 1970;19:83–92.

    Google Scholar 

  • Feau N, Vialle A, Allaire M, Maier W, Hamelin RC. DNA barcoding in the rust genus Chrysomyxa and its implications for the phylogeny of the genus. Mycologia. 2011;103(6):1250–66.

    PubMed  Google Scholar 

  • Feau N, Vialle A, Allaire M, Tanguay P, Joly DL, Frey P, Callan BE, Hamelin RC. Fungal pathogen (mis-) identifications: a case study with DNA barcodes on Melampsora rusts of aspen and white poplar. Mycol Res. 2009;113:713–24. doi:10.1016/j.mycres.2009.02.007.

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J. Cases in which parsimony and compatibility methods will be positively misleading. Syst Zool. 1978;27:401–10.

    Google Scholar 

  • Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39:783–91.

    PubMed  Google Scholar 

  • Felsenstein J. Phylip (phylogeny inference package). Seattle: Department of Genetics, University of Washington; 1995.

    Google Scholar 

  • Fraaije BA, Lowell DJ, Coelho JM, Baldwin S, Hollomon DW. PCR-based assay to assess wheat varietal resistance to blotch (Septoria tritici and Stagonospora nodorum) and rust (Puccinia striiformis and Puccinia recondita) diseases. Eur J Plant Pathol. 2001;107:905–17.

    CAS  Google Scholar 

  • Frederick RD, Snyder CL, Peterson GL, Bonde MR. Polymerase chain reaction assays for the detection and discrimination of the soybean rust pathogens Phakopsora pachyrhizi and P. meibomiae. Phytopathology. 2002;92:217–27.

    CAS  PubMed  Google Scholar 

  • Gao R, Zhang G. Potential of DNA barcoding for detecting quarantine fungi. Phytopathology. 2013;103(11):1103–7.

    CAS  PubMed  Google Scholar 

  • Geiser DM, Jiménez-Gasco M, Kang S, Makalowska I, Veeraraghavan N, et al. FUSARIUM-ID v. 1.0: a DNA sequence database for identifying Fusarium. Eur J Plant Pathol. 2004;110:473–9.

    CAS  Google Scholar 

  • Geiser DM, Klich MA, Frisvad JC, Peterson SW, Varga J, Samson RA. The current status of species recognition and identification in Aspergillus. Stud Mycol. 2007;59:1–10. doi:10.3114/sim.2007.59.01.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gilbert D. Sequence file format conversion with command-line readseq. Curr Protoc Bioinformatics. 2003;00:1E:A.1E.1–A.1E.4.

    Google Scholar 

  • Gilmore SR, Gräfenhahn T, Louis-Seize G, Seifert KA. Multiple copies of cytochrome oxidase 1 in species of the fungal genus Fusarium. Mol Ecol Resour. 2009;9:90–8.

    CAS  PubMed  Google Scholar 

  • Glass NL, Donaldson GC. Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Appl Environ Microbiol. 1995;61(4):1323–30.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Glienke C, Pereira OL, Stringari D, Fabris J, Kava-Cordeiro V, Galli-Terasawa L, Cunnington J, Shivas RG, Groenewald JZ, Crous PW. Endophytic and pathogenic Phyllosticta species, with reference to those associated with citrus black spot. Persoonia. 2011;26:47–56.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Glynn NC, Dixon LJ, Castlebury LA, Szabo LJ, Comstock JC. PCR assays for the sugarcane rust pathogens Puccinia kuehnii and P. melanocephala and detection of a SNP associated with geographical distribution in P. kuehnii. Plant Pathol. 2010;59:703–11.

    CAS  Google Scholar 

  • Goloboff PA, Farris JS, Nixon KC. TNT, a free program for phylogenetic analysis. Cladistics. 2008;24(5):774–86.

    Google Scholar 

  • Gomez-Alpizar L, CH H, Oliva R, Forbes G, Ristaino JB. Phylogenetic relationships of Phytophthora andina, a new species from the highlands of Ecuador that is closely related to the Irish potato famine pathogen Phytophthora infestans. Mycologia. 2008;100:590–602.

    CAS  PubMed  Google Scholar 

  • Greganova E, Altmann M, Buetikofer P. Unique modifications of translation elongation factors. FEBS J. 2011;278:2613–24.

    CAS  PubMed  Google Scholar 

  • Groenewald JZ, Nakashima C, Nishikawa J, Shin HD, Park JH, Jama AN, Groenewald M, Braun U, Crous PW. Species concepts in Cercospora: spotting the weeds among the roses. Stud Mycol. 2013;75(1):115–70. doi:10.3114/sim0012.

    Article  CAS  PubMed  Google Scholar 

  • Guerber JC, Liu B, Correll JC, Johnston PR. Characterization of diversity in Colletotrichum acutatum sensu lato by sequence analysis of two gene introns, mtDNA and intron RFLPs, and mating compatibility. Mycologia. 2003;95:872–95.

    CAS  PubMed  Google Scholar 

  • Guindon S, Delsuc F, Dufayard JF, Gascuel O. Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol. 2009;537:113–37. doi:10.1007/978-1-59745-251-9_6.

    Article  CAS  PubMed  Google Scholar 

  • Guo D, Jing J, Hu W, Navi SS, Jing L. Internal transcribed spacer sequence analysis of Puccinia helianthi Schw. And its application in detection of sunflower rust. J Phytopathol. 2016;164(2):141–6. doi:10.1111/jph.12404.

    Article  CAS  Google Scholar 

  • Guo Y, Li W, Sun H, Ning W, Hanshou Y, Chen H. Detection and quantification of Rhizoctonia cerealis in soil using real-time PCR. J Gen Plant Pathol. 2012;78:247–54.

    CAS  Google Scholar 

  • Hajibabaei M, Shokralla S, Zhou X, Singer GAC, Baird DJ. Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One. 2011;6:e17497.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95–8.

    CAS  Google Scholar 

  • Hatsch D, Phalip V, Jeltsch JM. Use of genes encoding cellobiohydrolase-C and topoisomerase II as targets for phylogenetic analysis and identification of Fusarium. Res Microbiol. 2004;155(4):290–6.

    CAS  PubMed  Google Scholar 

  • Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. Identification of birds through DNA barcodes. PLoS Biol. 2004;2(10):e312. doi:10.1371/journal.pbio.0020312.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Herder JE, Valentini A, Bellemain E, Dejean T, van Delft CWJJ, et al. Environmental DNA-A review of the possible applications for the detection of invasive species. Stitching RAVON, Nijmegen. Report 2013–2014; 2014.

    Google Scholar 

  • Hibbett DS. Ribosomal RNA and fungal systematics. Trans Mycol Soc. 1992;33:533–56.

    CAS  Google Scholar 

  • Hillis DM, Huelsenbeck JP, Swofford DL. Hobgoblin of phylogenetics ? Nature. 1994;369:363–4.

    CAS  PubMed  Google Scholar 

  • Hollingsworth PM, Graham SW, Little DP. Choosing and using a plant DNA barcode. PLoS One. 2011;6:e19254.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hong S-Y, Kang M-R, Cho E-J, Kim H-K, Yun S-H. Specific PCR detection of four quarantine Fusarium species in Korea. Plant Pathol J. 2010;26:409–16.

    CAS  Google Scholar 

  • Huelsenbeck JP, Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics. 2001;17(8):754–5.

    CAS  PubMed  Google Scholar 

  • Hunter GC, Wingfield BD, Crous PW, Wingfield MJ. A multi-gene phylogeny for species of Mycosphaerella occurring on eucalyptus leaves. Stud Mycol. 2006;55:147–61.

    PubMed  PubMed Central  Google Scholar 

  • Inderbitzin P, Bostock RM, Trouillas FP, Michailides TJ. A six locus phylogeny reveals high species diversity in Botryosphaeriaceae from California almond. Mycologia. 2010;102:1350–68.

    CAS  PubMed  Google Scholar 

  • James P, Whelen S, Hall BD. The RET1 gene of yeast encodes the second-largest subunit of RNA polymerase III. J Biol Chem. 1991;266:5616–24.

    CAS  PubMed  Google Scholar 

  • Ji Y, Ashton L, Pedley SM, Edwards DP, Tang Y, Nakamura A, Kitching R, Dolman PM, Woodcock P, Edwards FA, Larsen TH, Hsu WW, Benedick S, Hamer KC, Bruce C, Wang X, Levi T, Lott M, Emerson BC, Yu DW. Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecol Lett. 2013;16:1245–57.

    PubMed  Google Scholar 

  • Joly S, Davies TJ, Archambault A, Bruneau A, et al. Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead. Mol Ecol Resour. 2014;14:221–32. doi:10.1111/1755-0998.12173.

    Article  CAS  PubMed  Google Scholar 

  • Kageyama K, Senda M, Asano T, Suga H, Ishiguro K. Intra-isolate heterogeneity of the ITS region of rDNA in Pythium helicoides. Mycol Res. 2007;111:416–23.

    CAS  PubMed  Google Scholar 

  • Kang S, Mansfield MA, Park B, Geiser DM, Ivors KL, Coffey MD, Grünwald NJ, Martin FN, Lévesque CA, Blair JE. The promise and pitfalls of sequence-based identification of plant pathogenic fungi and oomycetes. Phytopathology. 2010;100:732–7.

    PubMed  Google Scholar 

  • Kashyap PL, Kumar S, Gurjar MS, Singh A, et al. Phytopathogenomics in plant disease management: a paradigm shift. In: Prasad D, Ray DP, editors. Biotechnological approaches in crop protection. New Delhi: Biotech Book publsihers; 2013. p. 241–62.

    Google Scholar 

  • Kashyap PL, Kumar S, Srivastava AK. Nanodiagnostics for plant pathogens. Environ Chem Lett. 2017;15:7–13. doi:10.1007/s10311-016-0580-4.

    Article  CAS  Google Scholar 

  • Kashyap PL, Rai P, Sharma S, Chakdar H, Kumar S, Pandiyan K, Srivastava AK. Nanotechnology for the detection and diagnosis of plant pathogens. In: Ranjan S, et al., editors. Nanoscience in Food and Agriculture 2, sustainable Agriculture reviews 21. Cham: Springer International Publishing; 2016a. doi:10.1007/978-3-319-39306-3_8.

    Chapter  Google Scholar 

  • Kashyap PL, Rai S, Kumar S, Srivastava AK. Genetic diversity, mating types and phylogenetic analysis of Indian races of Fusarium oxysporum f. Sp. ciceris from chickpea. Arch Phytopathol Plant Protect. 2016b;49:533–53. doi:10.1080/03235408.2016.1243024.

    Article  Google Scholar 

  • Kashyap PL, Rai S, Kumar S, Srivastava AK, Anandaraj M, Sharma AK. Mating type genes and genetic markers to decipher intraspecific variability among Fusarium udum isolates from pigeonpea. J Basic Microbiol. 2015;55:846–56. doi:10.1002/jobm.201400483.

    Article  CAS  PubMed  Google Scholar 

  • Kashyap PL, Sanghera GS, Wani SH, Shafi W, et al. Genes of microorganisms: paving way to tailor next generation fungal disease resistant crop plants. Not Sci Biol. 2011;3:147–57.

    CAS  Google Scholar 

  • Katoh K, Misawa K, Kuma K, Miyataa T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30(14):3059–66.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28(12):1647–9. doi:10.1093/bioinformatics/bts199.

    Article  PubMed  PubMed Central  Google Scholar 

  • Khiyami MA, Almoammar H, Awad YM, Alghuthaym MA, et al. Plant pathogen nanodiagnostic techniques: forthcoming changes? Biotechnol Biotechnol Equip. 2014;28(5):775–85. doi:10.1080/13102818.2014.960739.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kibbe WA. OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res. 2007;35(Web Server issue):W43–6. doi:10.1093/nar/gkm234.

    Article  PubMed  PubMed Central  Google Scholar 

  • Knutsen AK, Torp M, Holst-Jensen A. Phylogenetic analyses of the Fusarium poae, F. sporotrichioides and F. langsethiae species complex based on partial sequences of the translation elongation factor-1 alpha gene. Int J Food Microbiol. 2004;95:287–95.

    CAS  PubMed  Google Scholar 

  • Korpelainen H, Pietiläinen M, Huotari T. Effective detection of indoor fungi by metabarcoding. Ann Microbiol. 2016;66:495–8. doi:10.1007/s13213-015-1118-x.

    Article  CAS  Google Scholar 

  • Kress WJ, García-Robledo C, Uriarte M, Erickson DL. DNA barcodes for ecology, evolution, and conservation. Trends Ecol Evol. 2015;30(1):25–35. doi:10.1016/j.tree.2014.10.008.

    Article  PubMed  Google Scholar 

  • Kristensen R, Torp M, Kosiak B, Holst-Jensen A. Phylogeny and toxigenic potential is correlated in Fusarium species as revealed by partial translation elongation factor 1 alpha gene sequences. Mycol Res. 2005;109:173–86.

    CAS  PubMed  Google Scholar 

  • Kroon LP, Bakker FT, van den Bosch GB, Bonants PJ, Flier WG. Phylogenetic analysis of Phytophthora species based on mitochondrial and nuclear DNA sequences. Fungal Genet Biol. 2004;41:766–82.

    CAS  PubMed  Google Scholar 

  • Kumar S, Singh R, Kashyap PL, Srivastava AK. Rapid detection and quantification of Alternaria solani in tomato. Sci Hortic. 2013;151:184–9.

    CAS  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23:2947–8.

    CAS  PubMed  Google Scholar 

  • Lewis CT, Bilkhu S, Robert V, et al. Identification of fungal DNA barcode targets and PCR primers based on Pfam protein families and taxonomic hierarchy. Open Appl Inform J. 2011;5:30–44.

    Google Scholar 

  • Lievens B, Houterman PM, Rep M. Effector gene screening allows unambiguous identification of Fusarium oxysporum f. Sp. lycopersici races and discrimination from other formae speciales. FEMS Microbiol Lett. 2009;300:201–15.

    CAS  PubMed  Google Scholar 

  • Liu YJ, Whelen S, Hall BD. Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit. Mol Biol Evol. 1999;16:1799–808.

    CAS  PubMed  Google Scholar 

  • Lutzoni F, Kauff F, Cox CJ, McLaughlin D, et al. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am J Bot. 2004;91:1446–80.

    PubMed  Google Scholar 

  • Maddison WP, Maddison DR. MacClade version 3: analysis of phylogeny and character evolution. Sunderland: Sinauer Associates; 1992.

    Google Scholar 

  • Malkus A, Linda CP, Sabina MZ, Kuang-ren C, Jonathan S, et al. RNA polymerase II gene (RPB2) encoding the second largest protein subunit in Phaeosphaeria nodorum and P. avenaria. MycolRes. 2006;110:1152–64.

    CAS  Google Scholar 

  • Mann SK, Kashyap PL, Sanghera GS, Singh G, Singh S. RNA interference: an eco-friendly tool for plant disease management. Transgenic Plant J. 2008;2:110–26.

    Google Scholar 

  • Martin FN, Tooley PW. Phylogenetic relationships among Phytophthora species inferred from sequence analysis of mitochondrially encoded cytochrome oxidase I and II genes. Mycologia. 2003;95:269–84.

    CAS  PubMed  Google Scholar 

  • Martínez-Espinoza AD, León-Ramírez CG, Singh N, Ruiz-Herrera J. Use of PCR to detect infection of differentially susceptible maize cultivars using Ustilago maydis strains of variable virulence. Int Microbiol. 2003;6(2):117–20.

    PubMed  Google Scholar 

  • McCartney HA, Foster SJ, Fraaije BA, Ward E. Molecular diagnostics for fungal plant pathogens. Pest Manag Sci. 2003;59:129–42.

    CAS  PubMed  Google Scholar 

  • Mehl HL, Epstein L. Identification of Fusarium solani f. Sp. cucurbitae race 1 and race 2 with PCR and production of disease-free pumpkin seeds. Plant Dis. 2007;91:1288–92.

    CAS  PubMed  Google Scholar 

  • Merget B, Koetschan C, Hackl T, Förster F, Dandekar T, Müller T, Schultz J, Wolf M. The ITS2 database. J Vis Exp. 2012;61:3806. doi:10.3791/3806.

    Article  CAS  Google Scholar 

  • Mesapogu S, Babu BK, Bakshi A, Reddy SS, Saxena S. Rapid detection and quantification of Fusarium udum in soil and plant samples using real-time PCR. J Plant Pathol Microbiol. 2011;2:107. doi:10.4172/2157-7471.1000107.

    Article  CAS  Google Scholar 

  • Meusnier I, Singer GA, Landry JF, Hickey DA, Hebert PD, Hajibabaei M. A universal DNA mini-barcode for biodiversity analysis. BMC Genomics. 2008;9:214. doi:10.1186/1471-2164-9-214.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miller SA, Beed FD, Harmon CL. Plant disease diagnostic capabilities and networks. Annu Rev Phytopathol. 2009;l47:15–38.

    Google Scholar 

  • Mitchell A, Cho S, Regier JC, Mitter C, Poole RW, et al. Phylogenetic utility of elongation factor-1 alpha in Noctuoidea (Insecta: Lepidoptera): the limits of synonymous substitution. Mol Biol Evol. 1997;14:381–90.

    CAS  PubMed  Google Scholar 

  • Moriwaki J, Tsukiboshi T. Colletotrichum echinochloae, a new species on Japanese barnyard millet (Echinochloa utilis). Mycoscience. 2009;50:273–80. doi:10.1007/s10267-009-0485-1.

    Article  Google Scholar 

  • Mostert L, Groenewald JZ, Summerbell RC, Gams W, Crous PW. Taxonomy and pathology of Togninia (Diaporthales) and its Phaeoacremonium anamorphs. Stud Mycol. 2006;54:1–115.

    Google Scholar 

  • Mulè G, Susca A, Stea G, Moretti A. Specific detection of the toxigenic species Fusarium proliferatum and F. oxysporum from asparagus plants using primers based on calmodulin gene sequences. FEMS Microbiol Lett. 2004;230:235–40.

    PubMed  Google Scholar 

  • Myburg H, Gryzenhout M, Wingfield BD, Wingfield MJ. β-tubulin and histone H3 gene sequences distinguish Cryphonectria cubensis from South Africa, Asia, and South America. Can J Bot. 2002;80:590–6.

    CAS  Google Scholar 

  • Myllys L, Stenroos S, Thell A. New genes for phylogenetic studies of lichenized fungi: glyceraldehyde-3-phosphate dehydrogenase and beta-tubulin genes. Lichenologist. 2002;34(3):237–46.

    Google Scholar 

  • Naidoo K, Steenkamp ET, Coetzee MPA, Wingfield MJ, Wingfield BD. Concerted evolution in the ribosomal RNA cistron. PLoS One. 2013;8(3):e59355. doi:10.1371/journal.pone.0059355.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nam JM, Stoeva SI, Mirkin CA. Bio-bar-code-based DNA detection with PCR-like sensitivity. J Am Chem Soc. 2004;126(19):5932–3.

    CAS  PubMed  Google Scholar 

  • Nguyen HD, Seifert KA. Description and DNA barcoding of three new species of Leohumicola from South Africa and the United States. Persoonia. 2008;21:57–69. doi:10.3767/003158508X361334.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nitschke E, Nihlgard M, Varrelmann M. Differentiation of eleven Fusarium spp. isolated from sugar beet, applying restriction fragment analysis of polymerase chain reaction–amplified translation elongation factor 1α gene fragment. Phytopathology. 2009;99:921–9.

    CAS  PubMed  Google Scholar 

  • O’Donnell K, Cigelnik E, Nirenberg HI. Molecular systematics and phylogeography of the Gibberella fujikoroi species complex. Mycologia. 1998a;90:465–93.

    Google Scholar 

  • O’Donnell K, Kistler HC, Cigelnik E, Ploetz RC. Multiple evolutionary origins of the fungus causing Panama disease of banana: concordant evidence from nuclear and mitochondrial gene genealogies. Proc Natl Acad Sci U S A. 1998b;95:2044–9.

    PubMed  PubMed Central  Google Scholar 

  • O’Donnell K, Cigelnik E. Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are non orthologous. Mol Phylogenet Evol. 1997;7(1):103–16.

    PubMed  Google Scholar 

  • O’Donnell K, Rooney AP, Proctor RH, Brown DW, McCormick SP, et al. Phylogenetic analysis of RPB1 and RPB2 support a middle cretaceous origin for a clade comprising all agriculturally and medically important fusaria. Fungal Genet Biol. 2013;52:20–31. doi:10.1016/j.fgb.2012.12.004.

    Article  CAS  PubMed  Google Scholar 

  • Okubara PA, Harrison LA, Gatch EW, Vandemark G, Schroeder KL, du Toit LJ. Development and evaluation of a TaqMan real-time PCR assay for Fusarium oxysporum f. Sp. spinaciae. Plant Dis. 2013;97:927–37.

    CAS  PubMed  Google Scholar 

  • Okubara PA, Schroeder KL, Paulitz TC. Identification and quantification of Rhizoctonia solani and R. oryzae using real-time polymerase chain reaction. Phytopathology. 2008;98:837–47. doi:10.1094/PHYTO-98-7-0837.

    Article  CAS  PubMed  Google Scholar 

  • Orgiazzi A, Dunbar MB, Panagos P, Groot GA, Lemanceau P. Soil biodiversity and DNA barcodes: opportunities and challenges. Soil Biol Biochem. 2015;80:244–50.

    CAS  Google Scholar 

  • Packer L, Gibbs J, Sheffield C, Hanner R. DNA barcoding and the mediocrity of morphology. Mol Ecol Resour. 2009;9:42–50.

    PubMed  Google Scholar 

  • Page RD. Visualizing phylogenetic trees using TreeView. Curr Protoc Bioinformatics. 2002;00:6.2:6.2.1–6.2.15. doi: 10.1002/0471250953.bi0602s01.

  • Pannecoucque J, Hofte M. Detection of rDNA ITS polymorphism in Rhizoctonia solani AG 2-1 isolates. Mycologia. 2009;101:26–33.

    CAS  PubMed  Google Scholar 

  • Pavan-Kumar A, Gireesh-Babu P, Lakra WS. DNA metabarcoding: a new approach for rapid biodiversity assessment. J Cell Sci Mol Biol. 2015;2(1):111.

    Google Scholar 

  • Pedley KF. PCR-based assays for the detection of Puccinia horiana on chrysanthemums. Plant Dis. 2009;93:1252–8.

    CAS  PubMed  Google Scholar 

  • Pond SL, Frost SD, Muse SV. HyPhy: hypothesis testing using phylogenies. Bioinformatics. 2005;21(5):676–9.

    CAS  PubMed  Google Scholar 

  • Posada D, Crandall KA. MODELTEST: testing the model of DNA substitution. Bioinformatics. 1998;14(9):817–8.

    CAS  PubMed  Google Scholar 

  • Pouzoulet J, Mailhac N, Couderc C, Besson X, Daydé J, Lummerzheim M, Jacques A. A method to detect and quantify Phaeomoniella chlamydospora and Phaeoacremonium aleophilum DNA in grapevine-wood samples. Appl Microbiol Biotechnol. 2013;97:10163–75. doi:10.1007/s00253-013-5299-6.

    Article  CAS  PubMed  Google Scholar 

  • Prigigallo MI, Abdelfattah A, Cacciola SO, Faedda R, Sanzani SM, Cooke DEL, Schena L. Metabarcoding analysis of Phytophthora diversity using genus-specific primers and 454 pyrosequencing. Phytopathology. 2016;106(3):305–13. doi:10.1094/PHYTO-07-15-0167-R.

    Article  CAS  PubMed  Google Scholar 

  • Quaedvlieg W, Groenewald JZ, de Jesus Y-MM, Crous PW. DNA barcoding of Mycosphaerella species of quarantine importance to Europe. Persoonia. 2012;29:101–15. doi:10.3767/003158512X661282.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Quaedvlieg W, Kema GHJ, Groenewald JZ, Verkley GJM, Seifbarghi S, Razavi M, Mirzadi Gohari A, Mehrabi R, Crous PW. Zymoseptoria gen. Nov.: a new genus to accommodate Septoria-like species occurring on graminicolous hosts. Persoonia. 2011;26:57–69.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Quaedvlieg W, Verkley GJM, Shin H-D, Barreto RW, Alfenas AC, Swart WJ, Groenewald JZ, Crous PW. Sizing up Septoria. Stud Mycol. 2013;75:307–90.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rai S, Kashyap PL, Kumar S, Srivastava AK, Ramteke PW. Comparative analysis of microsatellites in five different antagonistic Trichoderma species for diversity assessment. World J Microbiol Biotechnol. 2016a;32:8.

    PubMed  Google Scholar 

  • Rai S, Kashyap PL, Kumar S, Srivastava AK, Ramteke PW. Identification, characterization and phylogenetic analysis of antifungal Trichoderma from tomato rhizosphere. SpringerPlus. 2016b;5:1939. doi:10.1186/s40064-016-3657-4.

    Article  PubMed  PubMed Central  Google Scholar 

  • Rehner SA, Buckley E. A Beauveria phylogeny inferred from nuclear ITS and EF1-alpha sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia. 2005;97:84–9810. 3852/mycologia.97.1.84

    CAS  PubMed  Google Scholar 

  • Riit T, Tedersoo L, Drenkhan R, Runno-Paurson E, Kokko H, Anslan S. Oomycete-specific ITS primers for identification and metabarcoding. MycoKeys. 2016;14:17–30. Doi.org/10.3897/mycokeys.14.9244

    Google Scholar 

  • Robert V, Szoke S, Eberhardt U, et al. The quest for a general and reliable fungal DNA barcode. Open Appl Inform J. 2011;5:45–61.

    CAS  Google Scholar 

  • Robideau GP, De Cock AWAM, Coffey MD, Voglmayr H, et al. DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer. Mol Ecol Resour. 2011;11:1002–11.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Romero MP, Wise KA. Development of molecular assays for detection of Stenocarpella maydis and Stenocarpella macrospora in corn. Plant Dis. 2015;99:761–9.

    CAS  PubMed  Google Scholar 

  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4(4):406–25.

    CAS  PubMed  Google Scholar 

  • Sampietro DA, Marín P, Iglesias J, Presello DA, Vattuone MA, Catalan CA, Gonzalez Jaen MT. A molecular based strategy for rapid diagnosis of toxigenic Fusarium species associated to cereal grains from Argentina. Fungal Biol. 2010;114:74–81. doi:10.1016/j.mycres.2009.10.008.

    Article  CAS  PubMed  Google Scholar 

  • Santamaria M, Vicario S, Pappadà G, Scioscia G, Scazzocchio C, Saccone C. Towards barcode markers in fungi: an intron map of Ascomycota mitochondria. BMC Bioinformatics. 2009;10:S15.

    PubMed  PubMed Central  Google Scholar 

  • Sasikumar AN, Perez WB, Goss Kinzy T. The many roles of eukaryotic elongation factor 1 complex. Wiley Interdisciplinary Rev RNA. 2012;3:543–55.

    CAS  Google Scholar 

  • Saunders GW. Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Phil Trans Royal Soci B BiolSci. 2005;360:1879–88.

    CAS  Google Scholar 

  • Schena L, Cooke DL. Assessing the potential of regions of the nuclear and mitochondrial genome to develop a “molecular tool box” for the detection and characterization of Phytophthora species. J Microbiol Methods. 2006;67(1):70–85.

    CAS  PubMed  Google Scholar 

  • Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. PNAS. 2012;109(16):6241–6. doi:10.1073/pnas.1117018109.

    Article  PubMed  PubMed Central  Google Scholar 

  • Schroeder KL, Okubara PA, Tambong JT, Lévesque CA, Paulitz TC. Identification and quantification of pathogenic Pythium spp. from soils in eastern Washington using real-time polymerase chain reaction. Phytopathology. 2006;96:637–47.

    CAS  PubMed  Google Scholar 

  • Schubert K, Groenewald JZ, Braun U, Dijksterhuis J, Starink M, et al. Biodiversity in the Cladosporium herbarum Complex (Davidiellaceae, Capnodiales), with standardisation of methods for Cladosporium taxonomy and diagnostics. Stud Mycol. 2007;58:105–56.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Schwenkbier L, Pollok S, König S, Urban M, et al. Towards on-site testing of Phytophthora species. Anal Methods. 2015;7:211–7.

    CAS  Google Scholar 

  • Seibel PN, Müller T, Dandekar T, Schultz J, Wolf M. 4SALE – a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics. 2006;7:498. doi:10.1186/1471-2105-7-498.

    Article  PubMed  PubMed Central  Google Scholar 

  • Seifert KA. Progress towards DNA barcoding of fungi. Mol Ecol Resour. 2009;9:83–9.

    CAS  PubMed  Google Scholar 

  • Seifert KA, Samson RA, Dewaard JR, et al. Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. PNAS. 2007;104:3901–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sharma R, Polkade AV, Shouche YS. Species concept’ in microbial taxonomy and systematic. Curr Sci. 2015;108:1804–14.

    CAS  Google Scholar 

  • Sharma S, Rai P, Rai S, Srivastava M, Kashyap PL, Sharma A, Kumar S. Genomic revolution in crop disease diagnosis: a review. In: Singh SS, editor. Plants and microbes in an ever changing environment. Nova Science Publishers; 2017. p. 257–93.

    Google Scholar 

  • Shimomoto Y, Sato T, Hojo H, Morita Y, Takeuchi S, et al. Pathogenic and genetic variation among isolates of Corynespora cassiicola in Japan. Plant Pathol. 2011;60:253–60.

    CAS  Google Scholar 

  • Shishido M, Sato K, Yoshida N, Tsukui R, Usami T. PCR-based assays to detect and quantify Phomopsis sclerotioides in plants and soil. J General Plant Pathol. 2010;76:21–30.

    CAS  Google Scholar 

  • Singh R, Kumar S, Kashyap PL, Srivastava AK, Mishra S, et al. Identification and characterization of microsatellite from Alternaria brassicicola to assess cross-species transferability and utility as a diagnostic marker. Mol Biotechnol. 2013;56:1049–59.

    Google Scholar 

  • Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3. doi:10.1093/bioinformatics/btu033.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Steenkamp ET, Wingfield BD, Coutinho TA, Wingfield MJ, Marasas WFO. Differentiation of Fusarium subglutinans f. Sp. pini by histone gene sequence data. Appl Environ Microbiol. 1999;65(8):3401–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Steenkamp ET, Wingfield BD, Coutinho TA, Zeller KA, Wingfield MJ, Marasas WFO, Leslie JF. PCR-Based identification of MAT-1 and MAT-2 in the Gibberella fujikuroi species complex. Appl Environ Microbiol. 2000;66(10):4378–82.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Stephenson SA, Green J, Manners J, Maclean DJ. Cloning and characterisation of glutamine synthetase from Colletotrichum gloeosporioides and demonstration of elevated expression during pathogenesis on Stylosanthes guianensis. Curr Genet. 1997;31:447–54. doi:10.1007/s002940050228.

    Article  CAS  PubMed  Google Scholar 

  • Stielow JB, Lévesque CA, Seifert KA, Meyer W, Irinyi L, et al. One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes. Persoonia. 2015;35:242–63.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sundelin T, Collinge DB, Lübeck M. A cultivation independent, PCR-based protocol for the direct identification of plant pathogens in infected plant material. Eur J Plant Pathol. 2009;123(4):473–6.

    CAS  Google Scholar 

  • Swofford DL. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Sunderland: Sinauer Associates; 2002a.

    Google Scholar 

  • Swofford DL. PAUP: phylogenetic analysis using maximum parsimony (and other method). Version 4.0b10. Sunderland: Sinauer; 2002b.

    Google Scholar 

  • Swofford DL, Olsen GJ, Waddell PJ, Hillis DM. Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK, editors. Molecular systematics. 2nd ed. Sunderland: Sinauer; 1996. p. 407–514.

    Google Scholar 

  • Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E. Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol. 2012;21:2045–50.

    CAS  PubMed  Google Scholar 

  • Tambong JT, de Cock AW, Tinker NA, Lévesque CA. Oligonucleotide array for identification and detection of Pythium species. Appl Environ Microbiol. 2006;72:2691–706.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;10:2731–9.

    Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–9. doi:10.1093/molbev/mst197.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Templeton MD, Rikkerink EHA, Solon SL, Crowhurst RN. Cloning and molecular characterization of the glyceraldehyde-3-phosphate dehydrogenase-encoding gene and cDNA from the plant pathogenic fungus Glomerella cingulata. Gene. 1992;122(1):225–30.

    CAS  PubMed  Google Scholar 

  • Thines M. Characterization and phylogeny of repeated elements giving rise to exceptional length of ITS2 in several downy mildew genera (Peronosporaceae). Fungal Genet Biol. 2007;44:199–207.

    CAS  PubMed  Google Scholar 

  • Thomsen PF, Willerslev E. Environmental DNA – an emerging tool in conservation for monitoring past and present biodiversity. Biol Conserv. 2015;183:4–18.

    Google Scholar 

  • Thon MR, Royse DJ. Evidence for two independent lineages of shiitake of the americas (Lentinula boryana) based on rDNA and beta tubulin gene sequences. Mol Phylogenet Evol. 1999;13:520–4.

    CAS  PubMed  Google Scholar 

  • Úrbez-Torres JR, Haag P, Bowen P, Lowery T, O’Gorman DT. Development of a DNA macroarray for the detection and identification of fungal pathogens causing decline of young grapevines. Phytopathology. 2015;105:1373–88.

    PubMed  Google Scholar 

  • Verkley GJM, Starink-Willemse M, van IA, Abeln ECA. Phylogenetic analyses of Septoria species based on the ITS and LSU-D2 regions of nuclear ribosomal DNA. Mycologia. 2004;96:558–71.

    CAS  PubMed  Google Scholar 

  • Vilgalys R, Hester M. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol. 1990;172:4239–46.

    Google Scholar 

  • Weir BS, Johnston PR, Damm U. The Colletotrichum gloeosporioides species complex. Stud Mycol. 2012;73(1):115–80. doi:10.3114/sim0011.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • White TJ, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninksky JJ, White TJ, editors. PCR protocols: a guide to method and amplifications. San Diego, CA: Academic; 1990. p. 315–22.

    Google Scholar 

  • Wolf M, Ruderisch B, Dandekar T, Schultz J, Müller T. ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments. Bioinformatics. 2008;24(20):2401–2. doi:10.1093/bioinformatics/btn453.

    Article  CAS  PubMed  Google Scholar 

  • Xu J. Fungal DNA barcoding. Genome. 2016;59(11):913–32. doi:10.1139/gen-2016-0046.

    Article  CAS  PubMed  Google Scholar 

  • Yadav MK, Babu BK, Saxena AK, Singh BP, Singh K, et al. Real-time PCR assay based on topoisomerase- II Gene for detection of Fusarium udum. Mycopathologia. 2011;171:373–81.

    PubMed  Google Scholar 

  • Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586–91.

    CAS  PubMed  Google Scholar 

  • Yao C, Frederiksen RA, Magill CW. Length heterogeneity in ITS2 and the methylation status of CCGG and GCGC sites in the rRNA genes of the genus Peronosclerospora. Curr Genet. 1992;22:415–20.

    CAS  PubMed  Google Scholar 

  • Zhao P, Luo J, Zhuang W-Y. Practice towards DNA barcoding of the nectriaceous fungi. Fungal Divers. 2011;46:183–91. doi:10.1007/s13225-010-0064-y.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, 275103, India

    Prem Lal Kashyap, Pallavi Rai, Hillol Chakdar & Alok K. Srivastava

  2. ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Regional Station, Flowerdale, Shimla, 171002, India

    Prem Lal Kashyap

  3. ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India

    Sudheer Kumar

Authors
  1. Prem Lal Kashyap
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pallavi Rai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sudheer Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hillol Chakdar
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Alok K. Srivastava
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Prem Lal Kashyap .

Editor information

Editors and Affiliations

  1. Department of Biotechnology, Mizoram University, Aizawl, Mizoram, India

    Bhim Pratap Singh

  2. Department of Biochemistry, National University of Ireland Galway, Galway, Ireland

    Vijai Kumar Gupta

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Kashyap, P.L., Rai, P., Kumar, S., Chakdar, H., Srivastava, A.K. (2017). DNA Barcoding for Diagnosis and Monitoring of Fungal Plant Pathogens. In: Singh, B.P., Gupta, V.K. (eds) Molecular Markers in Mycology. Fungal Biology. Springer, Cham. https://doi.org/10.1007/978-3-319-34106-4_5

Download citation

Publish with us

Policies and ethics

Search

Navigation