Phylogeny of Canadian ergot fungi and a detection assay by real-time polymerase chain reaction

LITERATURE CITED

• Alderman SC, Halse RR, White JF. 2004. A reevaluation of the host range and geographical distribution of Claviceps species in the United States. Plant Disease 88:63–81.
   PubMed Web of Science ®Google Scholar
• Alm T. 2003. The witch trials of Finnmark, Northern Norway, during the 17th century: evidence for ergotism as a contributing factor. Economic Botany 57:403–416.
   Web of Science ®Google Scholar
• Barger G. 1931. Ergot and Ergotism: a monograph based on the Dohme lecture delivered in Johns Hopkins University, Baltimore. London and Edinburgh: Gurney and Jackson. p. 20–84.
   Google Scholar
• Billing M. 1996. The Crusades: five centuries of holy wars. New York: Sterling Publishing Company.
   Google Scholar
• Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT 2009. The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments. Clin Chem 55:611–622.
   Google Scholar
• Caporael LR. 1976. Ergotism: the satan loosed in Salem? Science 192:21–26.
   Google Scholar
• Chen J, Moinard M, Xu J, Wang S, Foulongne-Oriol M, Zhao R, Hyde KD, Callac P. 2016. Genetic analyses of the Internal Transcribed Spacer sequences suggest introgression and duplication in the medicinal mushroom Agaricus subrufescens. PLoS ONE 11:e0156250.
   Web of Science ®Google Scholar
• Crosignani PG. 2006. Current treatment issues in female hyperprolactinaemia. European Journal of Obstetrics & Gynecology and Reproductive Biology 125:152–164.
   PubMed Web of Science ®Google Scholar
• de Groot ANJA, van Dongen PWJ, Vree TB, Hekster YA, van Roosmalen J. 1998. Ergot alkaloids: current status and review of clinical pharmacology and therapeutic use compared with other oxytocics in obstetrics and gynaecology. Drugs 56:523–535.
   Web of Science ®Google Scholar
• Douhan GW, Smith ME, Huyrn KL, Westbrook A, Beerli P, Fisher AJ. 2008. Multigene analysis suggests ecological speciation in the fungal pathogen Claviceps purpurea. Molecular Ecology 17:2276–2286.
   PubMed Web of Science ®Google Scholar
• Eich E, Pertz H. 1999. Antimicrobial and antitumor effects of ergot alkaloids and their derivatives. In: Kren V, Cvak L, eds. Ergot: the genus Claviceps. Amsterdam, The Netherlands: Harwood Academic Publishers (republished 2006 by Taylor and Francis e-Library). p. 441–449.
   Google Scholar
• Fišerová A, Pospíšil M. 1999. Role of ergot alkaloids in the immune system. In: Kren V, Cvak L, eds. Ergot: the genus Claviceps. Amsterdam, The Netherlands: Harwood Academic Publishers (republished 2006 by Taylor and Francis e-Library). p. 451–467.
   Google Scholar
• Geiser DM, del Mar Jiménez-Gasco M, Kang S, Makalowska I, Veeraraghavan N, Ward TJ, Zhang N, Kuldau GA, O’Donnell K. 2004. FUSARIUM-ID v. 1.0: a DNA sequence database for identifying Fusarium. European Journal of Plant Pathology 110:473–479.
   Web of Science ®Google Scholar
• Geiser DM, Klich MA, Frisvad JC, Peterson SW, Varga J, Samson RA. 2007. The current status of species recognition and identification in Aspergillus. Studies in Mycology 59:1–10.
   PubMed Web of Science ®Google Scholar
• Grantham NS, Reich BJ, Pacifici K, Laber EB, Menninger HL, Henley JB, Barberán A, Leff JW, Fierer N, Dunn RR. 2015. Fungi identify the geographic origin of dust samples. PLoS ONE 10:e0122605.
   Web of Science ®Google Scholar
• Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41:95–98.
   Google Scholar
• Katoh K, Kuma K-i, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33:511–518.
   PubMed Web of Science ®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, Mentjies P, Drummond A. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649.
   PubMed Web of Science ®Google Scholar
• Lindner DL, Banik MT. 2011. Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus. Mycologia 103:731–740.
   PubMed Web of Science ®Google Scholar
• Liu YJ, Whelen S, Hall BD. 1999. Phylogenetic relationships among Ascomycetes: evidence from an RNA polymerase II subunit. Molecular Biology and Evolution 16:1799–1808.
   PubMed Web of Science ®Google Scholar
• Loveless AR. 1971. Conidial evidence for host restriction in Claviceps purpurea. Transactions of the British Mycological Society 56:419–434.
   Google Scholar
• Loveless AR, Peach JM. 1986. Evidence from ascospores for host restriction in Claviceps purpurea. Transactions of the British Mycological Society 86:603–610.
   Google Scholar
• Menzies JG, Turkington TK. 2015. An overview of the ergot (Claviceps purpurea) issue in western Canada: challenges and solutions. Canadian Journal of Plant Pathology 37:40–51.
   Web of Science ®Google Scholar
• Micale V, Incognito T, Ignoto A, Rampello L, Spartà M, Drago F. 2006. Dopaminergic drugs may counteract behavioral and biochemical changes induced by models of brain injury. European Neuropsychopharmacology 16:195–203.
   Web of Science ®Google Scholar
• Miedaner T, Geiger HH. 2015. Biology, genetics, and management of ergot (Claviceps spp.) in rye, sorghum, and pearl millet. Toxins 7:659–678.
   Google Scholar
• Negård M, Uhlig S, Kauserud H, Andersen T, Høiland K, Vrålstad T. 2015. Links between genetic groups, indole alkaloid profiles and ecology within the grass-parasitic Claviceps purpurea species complex. Toxins 7:1431–1456.
   PubMed Web of Science ®Google Scholar
• Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson K-H. 2008. Intraspecific ITS variability in the Kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evolutionary Bioinformatics 4:193–201.
   PubMed Web of Science ®Google Scholar
• Nylander JAA. 2004. MrModeltest v2. Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. [cited 2018 Apr 23]. Available from: https://github.com/nylander/MrModeltest2
   Google Scholar
• O’Donnell K, Cigelnik E. 1997. Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Molecular Phylogenetics and Evolution 7:103–116.
   PubMed Web of Science ®Google Scholar
• O’Donnell K, Gueidan C, Sink S, Johnston PR, Crous PW, Glenn A, Riley R, Zitomer NC, Colyer P, Waalwijk C. 2009. A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex. Fungal Genetics and Biology 46:936–948.
   PubMed Web of Science ®Google Scholar
• Okabe I, Arakawa M, Matsumoto N. 2001. ITS polymorphism within a single strain of Sclerotium rolfsii. Mycoscience 42:107–113.
   Google Scholar
• Osmundson TW, Robert VA, Schoch CL, Baker LJ, Smith A, Robich G, Mizzan L, Garbelotto MM. 2013. Filling gaps in biodiversity knowledge for macrofungi: contributions and assessment of an herbarium collection DNA barcode sequencing project. PLoS ONE 8:e62419.
   PubMed Web of Science ®Google Scholar
• Pažoutová S, Olsovska J, Linka M, Kolinska R, Flieger M. 2000. Chemoraces and habitat specialization of Claviceps purpurea populations. Applied and Environmental Microbiology 66:5419–5425.
   PubMed Web of Science ®Google Scholar
• Pažoutová S, Pešicová K, Chudíčková M, Šrůtka P, Kolařík M. 2015. Delimitation of cryptic species inside Claviceps purpurea. Fungal Biology 119:7–26.
   PubMed Web of Science ®Google Scholar
• Pertz H, Eich E. 1999. Ergot alkaloids and their derivatives as ligands for serotoninergic, dopaminergic, and adrenergic receptors. In: Kren V, Cvak L, eds. Ergot: the genus Claviceps. Amsterdam, The Netherlands: Harwood Academic Publishers (republished 2006 by Taylor and Francis e-Library). p. 411–440
   Google Scholar
• Píchová K, Pažoutová S, Kostovčík M, Chudíčková M, Stodůlková E, Novák P, Flieger M, van der Linde E, Kolařík M. 2018. Evolutionary history of ergot with a new infrageneric classification (Hypocreales: Clavicipitaceae: Claviceps). Molecular Phylogenetics and Evolution 123:73–87.
   PubMed Web of Science ®Google Scholar
• Rehner SA, Buckley E. 2005. A Beauveria phylogeny inferred from nuclear ITS and EF1-α sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia 97:84–98.
   PubMed Web of Science ®Google Scholar
• Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61:539–542.
   PubMed Web of Science ®Google Scholar
• Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Fungal Barcoding Consotium. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America 109:6241–6246.
   Google Scholar
• Seifert KA. 2008. Persoonial reflections: integrating DNA barcoding into the mycological sciences. Persoonia 21:161–166.
   Google Scholar
• Stäger R. 1903. Infectionsversuche mit Gramineen-bewohnenden Claviceps-Arten. Botanische Zeitung 61:111–158.
   Google Scholar
• Stäger R. 1922. Beitrag zur Verbreitungsbiologie der Claviceps-sklerotien. Zentralblatt für Bakteriologie, Parasitenkunde und Infektionkrankheiten und Hygiene. Abt II:329–339.
   Google Scholar
• Stielow JB, Lévesque CA, Seifert KA, Meyer W, Iriny L, Smits D, Renfurm R, Verkley GJM, Groenewald M, Chaduli D, Lomascolo A, Welti S, Lesage-Meessen L, Favel A, Al-Hatmi AMS, Damm U, Yilmaz N, Houbraken J, Lombard L, Quaedvlieg W, Binder M, Vaas LAI, Vu D, Yurkov A, Begerow D, Roehl O, Guerreiro M, Fonseca A, Samerpitak K, van Diepeningen AD, Dolatabadi S, Moreno LF, Casaregola S, Mallet S, Jacques N, Roscini L, Egidi E, Bizet C, Garcia-Hermoso D, Martín MP, Deng S, Groenewald JZ, Boekhout T, de Beer ZW, Barnes I, Duong TA, Wingfield MJ, de Hoog GS, Crous PW, Lewis CT, Hambleton S, Moussa TAA, Al-Zahrani HS, Almaghrabi OA, Louis-Seize G, Assabgui R, McCormick W, Omer G, Dukik K, Cardinali G, Eberhardt U, de Vries M, Robert V. 2015. One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes. Persoonia 35:242–263.
   PubMed Web of Science ®Google Scholar
• Sung G-H, Sung J-M, Hywel-Jones NL, Spatafora JW. 2007. A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach. Molecular Phylogenetics and Evolution 44:1204–1223.
   PubMed Web of Science ®Google Scholar
• Swofford DL. 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods). version 4.0 b10. Sunderland, Massachusetts: Sinauer Associates.
   Google Scholar
• Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou NS, Wijesundera R, Ruiz LV, Vasco-Palacios AM, Thu PQ, Suija A, Smith ME, Sharp C, Saluveer E, Saitta A, Rosas M, Riit T, Ratkowsky D, Pritsch K, Põldmaa K, Piepenbring M, Phosri C, Peterson M, Parts K, Pärtel K, Otsing E, Nouhra E, Njouonkou AL, Nilsson RH, Morgado LN, Mayor J, May TW, Majuakim L, Lodge DJ, Lee SS, Larsson K-H, Kohout P, Hosaka K, Hiiesalu I, Henkel TW, Harend H, Guo L-d, Greslebin A, Grelet G, Geml J, Gates G, Dunstan W, Dunk C, Drenkhan R, Dearnaley J, De Kesel A, Dang T, Chen X, Buegger F, Brearley FQ, Bonito G, Anslan S, Abell S, Abarenkov K. 2014. Global diversity and geography of soil fungi. Science 346:1256688.
   PubMed Web of Science ®Google Scholar
• Tenberge KB. 2006. Biology and life strategy of the ergot fungi. In: Kren V, Cvak L, eds. Ergot: the genus Claviceps. Amsterdam, The Netherlands: Harwood Academic Publishers (republished 2006 by Taylor and Francis e-Library). p. 25–56.
   Google Scholar
• Tulasne LR. 1853. Mémoire sur l’ergot des Glumacées. Annales des Sciences Naturelles Botanique 20:5–56.
   Google Scholar
• van der Linde EJ, Pešicová K, Pažoutová S, Stodůlková E, Flieger M, Kolařík M. 2016. Ergot species of the Claviceps purpurea group from South Africa. Fungal Biology 120:917–930.
   Web of Science ®Google Scholar
• White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenies. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR protocols: a guide to methods and applications. San Diego, California: Academic Press. p. 315–322.
   Google Scholar
• Woo PCY, Leung S-Y, To KKW, Chan JFW, Ngan AHY, Cheng VCC, Lau SKP, Yuen K-Y. 2010. Internal transcribed spacer region sequence heterogeneity in Rhizopus microsporus: implications for molecular diagnosis in clinical microbiology laboratories. Journal of Clinical Microbiology 48:208–214.
   PubMed Web of Science ®Google Scholar
• Wörheide G, Nichols SA, Goldberg J. 2004. Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies. Molecular Phylogenetics and Evolution 33:816–830.
   PubMed Web of Science ®Google Scholar
• Xu J. 2016. Fungal DNA barcoding. Genome 59:913–932.
   PubMed Web of Science ®Google Scholar
• Xue AG, Chen Y, Ai-Rewashdy Y. 2017. Diseases of spring wheat in central and eastern Ontario in 2017. Canadian Plant Disease Survey 98:148–149.
   Google Scholar
• Zahariev M, Chen W, Visagie CM, Lévesque CA. 2018. Cluster oligonucleotide signatures for rapid identification by sequencing. BMC Bioinformatics 19:395.
   Web of Science ®Google Scholar
• Zwickl DJ. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion [PhD dissertation]. Austin, Texas: The University of Texas at Austin. [cited 2018 May 29]. GARLI 2.0 available from: http://code.google.com/p/garli/
   Google Scholar