USE OF RAPD-PCR AND ITS MARKERS FOR IDENTIFICATION OF Diaporthe/Phomopsis FROM FRUIT TREES IN SOUTH-EASTERN POLAND
Barbara Abramczyk
Institute of Soil Science and Plant Cultivation – State Research Institute, PuławyEwa Król
University of Life Sciences in LublinAbstrakt
In recent years, it has been reported the increasing harmfulness of Diaporthe/Phomopsis spp. in the orchards and nurseries worldwide. They cause nonspecific
symptoms which in combination with the morphological similarity of the cultures and difficult sporulation creates problems with their correct identification using classical methods. This implies the need to integrate advanced molecular techniques to identify the strain on the species level. The aim of this research was to determine the identity and genetically characterize forty isolates of Diaporthe/Phomopsis obtained in 2010–2012 from the shoots of selected fruit trees grown in the south-eastern Poland. Using the RAPD-PCR technique the genetic similarity within studied population has been demonstrated irrespectively of the origin and type of the host plant from which the isolates derived. Based on the comparative analysis of the non-coding sequence of the ITS regions (ITS1, 5.8S rDNA, ITS2) with the sequences available in NCBI database the studied Diaporthe isolates were identified as Diaporthe eres species complex not described previously on fruit trees under Polish conditions.
Słowa kluczowe:
Diaporthe eres species complex, molecular identification, orchard plants, fungiBibliografia
Adaskaveg, J.E., Förster, H., Conell, J.H. (1999). First report of fruit rot and associated branch dieback of almond in California caused by Phomopsis species tentatively identified as P. amygdali. Plant Dis., 83(11), 1073.
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lippman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol., 215, 403–410.
Ash, G.J., Stodart, B., Sakuanrungsirikul, S., Anschaw, E., Crump, N., Hailstones, D., Harper, J.D.I. (2010). Genetic characterization of a novel Phomopsis sp., a putative biocontrol agent for Carthamus lanatus. Mycologia, 102,54–61.
Chen, W.Q., Ntahimpera, N., Morgan, D.P., Michailides, T.J. (2002 a). Mycoflora of Pistacia vera in the central valley, California. Mycotaxon, 83, 147–158.
Chen, Y.Q., Jiang, Z., Qi, P.K. (2002 b). Application of RAPD and ITS region sequence analyses on classification and identification of Phomopsis. Mycosystema, 21, 39–46.
Cristescu, C. (2007). The morphology and anatomy of structure somatic and reproductive of species of Phomopsis Sacc. Bubak. Bul. Grăd. Bot. Iasi Tom., 14,19–27.
Crous, P.W. (2005). Impact of molecular phylogenetics on the taxonomy and diagnostics of fungi. Bull. OEPP/EPPO 35,47–51.
De Guido, M.A., Pollastro, S., Carlucci, A., De Miccolis Angelini, R.M., Faretra, F. (2003). Phomopsis viticola is easily transformed with hph and Bml gens. J. Plant Pathol., 85, 1, 43–52.
Dereeper, A., Guignon, V., Blanc, G., Audic, S., Buffet, S., Chevenet, F., Dufayard, J.F., Guindon, S., Lefort, V., Lescot, M., Claverie, J.M., Gascuel, O. (2008). Phylogeny. fr: robust phylogenetic analysis for the non-specialist. Nucl. Acids Res., 1(36),W465–9. doi: 10.1093/nar/gkn180
Diogo, E.L.F., Santos, J.M., Phillips, A.J.L. (2010). Phylogeny, morphology and pathogenicity of Diaporthe and Phomopsis species on almond in Portugal. Fung. Div., 44, 107–115.
Farr, D.F., Castlebury, L.A., Pardo-Schultheiss, R.A. (1999). Phomopsis amygdali causes peach shoot blight of cultivated peach trees in the southeastern United States. Mycologia, 91, 1008–1015.
Farr, D.F., Castlebury, L.A., Rossman, A.Y. (2002). Morphological and molecular characterization of Phomopsis vaccinii and additional isolates of Phomopsis from blueberry and cranberry in the eastern United States. Mycologia, 94, 494–504.
Garcia-Vallve, S., Palau, J., Romeu, A. (1999). Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis. Mol. Biol. Evol., 16(9), 1125–1134.
Gomes, R.R., Glienke, C., Videira, S.I.R., Lombard, L., Groenewald, J.Z., Crous, P.W. (2013). Diaporthe, a genus of endophytic, saprobic and plant pathogenic fungi. Persoonia, 31,1–41.
Hewitt, W.B., Pearson, R.C. (1988). Phomopsis cane and leaf spot. In: Compendium of grape diseases, Pearson, R.C., Goheen, A.C. (eds). APS Press, Minnesota, 16–18.
http://genomes.urv.cat/UPGMA/
http://phylogeny.lirmm.fr/phylo_cgi/index.cgi
http://www.ncbi.nlm.nih.gov
http://www.ncbi.nml.nih.gov/BLAST/
Hyde, K.D., McKenzie, E.H.C., KoKo, T.W. (2011). Towards incorporating anamorphic fungi in a natural classification – checklist and notes for 2010. Mycosphere, 2, 1–88.
Karaoglanidis, G.S., Bardas, G. (2006). First report of Phomopsis fruit decay on apple caused by Phomopsis mali in Greece. Plant Dis, 90(3), 375.
Kirk, P.M., Cannon, P.M., Minter, D.W., Stalpens, J.A. (2008). ainsworth & bisby’s dictionary of fungi. 10th Editions. 2008 CAB International; 640 pp.
Król, E. (2002 a). Determination of genetic variability within Phomosis spp. using RAPD method. Phytopathol. Pol., 25, 35–46.
Król, E. (2005 b). Identification and differentiation of Phomopsis spp. isolates from grapevine and some other plant species. Phytopathol. Pol., 35, 151–156.
Król, E. (2006). Chitosan activity in an inhibition of in vitro growth of Phomopsis viticola and protection of grapevine canes against the pathogen. Phytopathol. Pol., 39, 155–162.
Król, E. (2007). Phomopsis viticola Sacc. jako patogen winorośli na świecie i w Polsce. Post. Nauk Roln., 4, 85–96.
Król, E., Kowalik, B. (2010). Charakterystyka grzybów rodzaju Phomopsis wyizolowanych z roślin sadowniczych. Zesz. Prob. Post. Nauk Rol./Progr. Plant Prot. Res., 554, 53–59.
Król, E., Kowalik, B. (2011). Grzyby z rodzaju Phomopsis występujące na pędach roślin sadowniczych. Post. Nauk Roln., 2, 31–42.
Machowicz-Stefaniak, Z. (1993). Phomopsis viticola Sacc. (Sphaeropsidales Deuteromycotina) nowy w Polsce patogen pędów winorośli. Acta Mycol., 28, 157–160.
Michailides, T.J., Thomidis, T. (2006). First report of Phomopsis amygdali causing fruit rot on peaches in Greece. Plant Dis., 90(12), 1551.
Mostert, L., Crous, P.W., Kang, C.J., Phillips, A.J.L. (2001). Species of Phomopsis and a Libertella sp. occurring on grapevines with specific reference to South Africa: morphological, cultural, molecular and pathological characterization. Mycologia, 93, 145–166.
Nei, M., Li, W.H. (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA, 76, 5269–5273.
Rehner, S.A., Uecker, F.A., (1994). Nuclear ribosomal internal transcribed spacer phylogeny and host diversity in the coelomycete Phomopsis. Can. J. Bot., 72, 1666–1674.
Rodeva, R., Stoyanova, Z., Pandeva, R. (2009). A new fruit disease of pepper in Bulgaria caused by Phomopsis capsici. Acta Hortic., 830, 551–556.
Santos, J.M., Phillips, A.J.L. (2009). Resolving the complex of Diaporthe (Phomopsis) species occurring on Foeniculum vulgare in Portugal. Fung. Div., 34, 111–125.
Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V., Spouge, J.L., Levesque, A.C., Chen, W., Fungal Barcoding Consortium (2012). Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. USA, 109, 6241–6246.
Sutton, B.C. (1980). The Coelomycetes, fungi imperfecti with picnidia, acervuli and stroma. Commonwealth Mycological Institute, Kew, Surrey.
Tamura, K., Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol., 10, 512–526.
Taylor, J.W., Jacobson, D.J., Kroken, S., Kasuga, T., Geiser, D.M., Hibbett, D.S., Fisher, M.C. (2000). Phylogenetic species recognition and species concepts in fungi. Fung. Gen. Biol., 31, 21–32.
Udayanga, D., Liu, X. X., McKenzie, E.H.C., Chukeatirote, E., Bahkali, A.H., Hyde, K.D. (2011). The genus Phomopsis: biology, applications, species concepts and names of common phytopathogens. Fung. Div., 50, 189–225.
Udayanga, D., Liu, X., Crous, P.W., McKenzie, E.H.C., Chukeatirote, E., Hyde, K.D. (2012 a). A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis). Fung. Div., 56, 157–171.
Udayanga, D., Liu, X., McKenzie, E.H.C., Chukeatirote, E., Hyde, K.D. (2012 b). Multi-locus phylogeny reveals three new species of Diaporthe from Thailand. Crypt. Mycol., 33, 295–309.
Udayanga, D., Castlebury, L.A., Rossman, A.Y., Hyde, K.D. (2014 a). Species limits in Diaporthe: molecular re-assessment of D. citri, D. cytosporella, D. foeniculina and D. rudis. Persoonia, 32, 83–101.
Udayanga, D., Castlebury, L.A., Rossman, A.Y., Chukeatirote, E., Hyde, K.D. (2014 b). Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex. Fung. Div., 67, 203–229.
Uddin, W., Stevenson, K.L., Pardo-Schultheiss, R.A. (1997). Pathogenicity of a species of Phomopsis causing a shoot blight on peach in Georgia and evaluation of possible infection courts. Plant Dis., 81, 983–989.
Uddin, W., Stevenson, K.L., Pardo-Schultheiss, R.A., Rehner, S.A. (1998). Pathogenic and molecular characterization of three Phomopsis isolates from peach, plum and Asian pear. Plant Dis., 82, 732–737.
Uecker, F.A., (1988). A world list of Phomopsis names with notes on nomenclature, morphology and biology. Mycol. Mem., 13, 321 ss.
van Niekerk, J.M., Groenewald, J.Z., Farr, D.F., Fourie, P.H., Hallen, F., Crous, P.W. (2005). Reassessment of Phomopsis species on grapevines. Austral. Plant Pathol., 34, 27–39.
van Rensburg, J.C.J., Lamprecht, S.C., Groenewald, J.Z., Castlebury, L.A., Crous, P.W. (2006). Characterisation of Phomopsis spp. associated with die-back of rooibos (Aspalathus linearis) in South Africa. Stud. Mycol., 55, 65–74.
White, T.J., Bruns, T., Lee, S., Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR protocols: A guide to methods and applications, Innis, M., Gelfand, D., Sninsky, J., White T. (eds.). Academic Press, San Diego, Calif, 315–322.
Williams, J.K.G., Kubelik, A.R., Livak, K.J., Rafalsky, J.A., Tyngey, S.V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl. Acid. Res., 18, 6531–6535.
Zhang, A.W., Riccioni, L., Pedersen, W.L., Kollipara, K.P., Hartman, G.L. (1998). Molecular identification and phylogenetic grouping of Diaporthe phaseolorum and Phomopsis longicolla isolates from soybean. Phytopathology, 88, 1306–1314.
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lippman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol., 215, 403–410.
Ash, G.J., Stodart, B., Sakuanrungsirikul, S., Anschaw, E., Crump, N., Hailstones, D., Harper, J.D.I. (2010). Genetic characterization of a novel Phomopsis sp., a putative biocontrol agent for Carthamus lanatus. Mycologia, 102,54–61.
Chen, W.Q., Ntahimpera, N., Morgan, D.P., Michailides, T.J. (2002 a). Mycoflora of Pistacia vera in the central valley, California. Mycotaxon, 83, 147–158.
Chen, Y.Q., Jiang, Z., Qi, P.K. (2002 b). Application of RAPD and ITS region sequence analyses on classification and identification of Phomopsis. Mycosystema, 21, 39–46.
Cristescu, C. (2007). The morphology and anatomy of structure somatic and reproductive of species of Phomopsis Sacc. Bubak. Bul. Grăd. Bot. Iasi Tom., 14,19–27.
Crous, P.W. (2005). Impact of molecular phylogenetics on the taxonomy and diagnostics of fungi. Bull. OEPP/EPPO 35,47–51.
De Guido, M.A., Pollastro, S., Carlucci, A., De Miccolis Angelini, R.M., Faretra, F. (2003). Phomopsis viticola is easily transformed with hph and Bml gens. J. Plant Pathol., 85, 1, 43–52.
Dereeper, A., Guignon, V., Blanc, G., Audic, S., Buffet, S., Chevenet, F., Dufayard, J.F., Guindon, S., Lefort, V., Lescot, M., Claverie, J.M., Gascuel, O. (2008). Phylogeny. fr: robust phylogenetic analysis for the non-specialist. Nucl. Acids Res., 1(36),W465–9. doi: 10.1093/nar/gkn180
Diogo, E.L.F., Santos, J.M., Phillips, A.J.L. (2010). Phylogeny, morphology and pathogenicity of Diaporthe and Phomopsis species on almond in Portugal. Fung. Div., 44, 107–115.
Farr, D.F., Castlebury, L.A., Pardo-Schultheiss, R.A. (1999). Phomopsis amygdali causes peach shoot blight of cultivated peach trees in the southeastern United States. Mycologia, 91, 1008–1015.
Farr, D.F., Castlebury, L.A., Rossman, A.Y. (2002). Morphological and molecular characterization of Phomopsis vaccinii and additional isolates of Phomopsis from blueberry and cranberry in the eastern United States. Mycologia, 94, 494–504.
Garcia-Vallve, S., Palau, J., Romeu, A. (1999). Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis. Mol. Biol. Evol., 16(9), 1125–1134.
Gomes, R.R., Glienke, C., Videira, S.I.R., Lombard, L., Groenewald, J.Z., Crous, P.W. (2013). Diaporthe, a genus of endophytic, saprobic and plant pathogenic fungi. Persoonia, 31,1–41.
Hewitt, W.B., Pearson, R.C. (1988). Phomopsis cane and leaf spot. In: Compendium of grape diseases, Pearson, R.C., Goheen, A.C. (eds). APS Press, Minnesota, 16–18.
http://genomes.urv.cat/UPGMA/
http://phylogeny.lirmm.fr/phylo_cgi/index.cgi
http://www.ncbi.nlm.nih.gov
http://www.ncbi.nml.nih.gov/BLAST/
Hyde, K.D., McKenzie, E.H.C., KoKo, T.W. (2011). Towards incorporating anamorphic fungi in a natural classification – checklist and notes for 2010. Mycosphere, 2, 1–88.
Karaoglanidis, G.S., Bardas, G. (2006). First report of Phomopsis fruit decay on apple caused by Phomopsis mali in Greece. Plant Dis, 90(3), 375.
Kirk, P.M., Cannon, P.M., Minter, D.W., Stalpens, J.A. (2008). ainsworth & bisby’s dictionary of fungi. 10th Editions. 2008 CAB International; 640 pp.
Król, E. (2002 a). Determination of genetic variability within Phomosis spp. using RAPD method. Phytopathol. Pol., 25, 35–46.
Król, E. (2005 b). Identification and differentiation of Phomopsis spp. isolates from grapevine and some other plant species. Phytopathol. Pol., 35, 151–156.
Król, E. (2006). Chitosan activity in an inhibition of in vitro growth of Phomopsis viticola and protection of grapevine canes against the pathogen. Phytopathol. Pol., 39, 155–162.
Król, E. (2007). Phomopsis viticola Sacc. jako patogen winorośli na świecie i w Polsce. Post. Nauk Roln., 4, 85–96.
Król, E., Kowalik, B. (2010). Charakterystyka grzybów rodzaju Phomopsis wyizolowanych z roślin sadowniczych. Zesz. Prob. Post. Nauk Rol./Progr. Plant Prot. Res., 554, 53–59.
Król, E., Kowalik, B. (2011). Grzyby z rodzaju Phomopsis występujące na pędach roślin sadowniczych. Post. Nauk Roln., 2, 31–42.
Machowicz-Stefaniak, Z. (1993). Phomopsis viticola Sacc. (Sphaeropsidales Deuteromycotina) nowy w Polsce patogen pędów winorośli. Acta Mycol., 28, 157–160.
Michailides, T.J., Thomidis, T. (2006). First report of Phomopsis amygdali causing fruit rot on peaches in Greece. Plant Dis., 90(12), 1551.
Mostert, L., Crous, P.W., Kang, C.J., Phillips, A.J.L. (2001). Species of Phomopsis and a Libertella sp. occurring on grapevines with specific reference to South Africa: morphological, cultural, molecular and pathological characterization. Mycologia, 93, 145–166.
Nei, M., Li, W.H. (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA, 76, 5269–5273.
Rehner, S.A., Uecker, F.A., (1994). Nuclear ribosomal internal transcribed spacer phylogeny and host diversity in the coelomycete Phomopsis. Can. J. Bot., 72, 1666–1674.
Rodeva, R., Stoyanova, Z., Pandeva, R. (2009). A new fruit disease of pepper in Bulgaria caused by Phomopsis capsici. Acta Hortic., 830, 551–556.
Santos, J.M., Phillips, A.J.L. (2009). Resolving the complex of Diaporthe (Phomopsis) species occurring on Foeniculum vulgare in Portugal. Fung. Div., 34, 111–125.
Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V., Spouge, J.L., Levesque, A.C., Chen, W., Fungal Barcoding Consortium (2012). Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. USA, 109, 6241–6246.
Sutton, B.C. (1980). The Coelomycetes, fungi imperfecti with picnidia, acervuli and stroma. Commonwealth Mycological Institute, Kew, Surrey.
Tamura, K., Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol., 10, 512–526.
Taylor, J.W., Jacobson, D.J., Kroken, S., Kasuga, T., Geiser, D.M., Hibbett, D.S., Fisher, M.C. (2000). Phylogenetic species recognition and species concepts in fungi. Fung. Gen. Biol., 31, 21–32.
Udayanga, D., Liu, X. X., McKenzie, E.H.C., Chukeatirote, E., Bahkali, A.H., Hyde, K.D. (2011). The genus Phomopsis: biology, applications, species concepts and names of common phytopathogens. Fung. Div., 50, 189–225.
Udayanga, D., Liu, X., Crous, P.W., McKenzie, E.H.C., Chukeatirote, E., Hyde, K.D. (2012 a). A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis). Fung. Div., 56, 157–171.
Udayanga, D., Liu, X., McKenzie, E.H.C., Chukeatirote, E., Hyde, K.D. (2012 b). Multi-locus phylogeny reveals three new species of Diaporthe from Thailand. Crypt. Mycol., 33, 295–309.
Udayanga, D., Castlebury, L.A., Rossman, A.Y., Hyde, K.D. (2014 a). Species limits in Diaporthe: molecular re-assessment of D. citri, D. cytosporella, D. foeniculina and D. rudis. Persoonia, 32, 83–101.
Udayanga, D., Castlebury, L.A., Rossman, A.Y., Chukeatirote, E., Hyde, K.D. (2014 b). Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex. Fung. Div., 67, 203–229.
Uddin, W., Stevenson, K.L., Pardo-Schultheiss, R.A. (1997). Pathogenicity of a species of Phomopsis causing a shoot blight on peach in Georgia and evaluation of possible infection courts. Plant Dis., 81, 983–989.
Uddin, W., Stevenson, K.L., Pardo-Schultheiss, R.A., Rehner, S.A. (1998). Pathogenic and molecular characterization of three Phomopsis isolates from peach, plum and Asian pear. Plant Dis., 82, 732–737.
Uecker, F.A., (1988). A world list of Phomopsis names with notes on nomenclature, morphology and biology. Mycol. Mem., 13, 321 ss.
van Niekerk, J.M., Groenewald, J.Z., Farr, D.F., Fourie, P.H., Hallen, F., Crous, P.W. (2005). Reassessment of Phomopsis species on grapevines. Austral. Plant Pathol., 34, 27–39.
van Rensburg, J.C.J., Lamprecht, S.C., Groenewald, J.Z., Castlebury, L.A., Crous, P.W. (2006). Characterisation of Phomopsis spp. associated with die-back of rooibos (Aspalathus linearis) in South Africa. Stud. Mycol., 55, 65–74.
White, T.J., Bruns, T., Lee, S., Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR protocols: A guide to methods and applications, Innis, M., Gelfand, D., Sninsky, J., White T. (eds.). Academic Press, San Diego, Calif, 315–322.
Williams, J.K.G., Kubelik, A.R., Livak, K.J., Rafalsky, J.A., Tyngey, S.V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl. Acid. Res., 18, 6531–6535.
Zhang, A.W., Riccioni, L., Pedersen, W.L., Kollipara, K.P., Hartman, G.L. (1998). Molecular identification and phylogenetic grouping of Diaporthe phaseolorum and Phomopsis longicolla isolates from soybean. Phytopathology, 88, 1306–1314.
Barbara Abramczyk
Institute of Soil Science and Plant Cultivation – State Research Institute, Puławy
Institute of Soil Science and Plant Cultivation – State Research Institute, Puławy
Ewa Król
University of Life Sciences in Lublin
University of Life Sciences in Lublin
Licencja
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Autor podpisuje oświadczenie o oryginalności dzieła, wkładzie poszczególnych osób i źródle finansowania.
