A comparison between ITS, D1/D2 LSU rDNA, tub2, and rpb2 regions to delimit Allophoma, Didymella, and Neodidymelliopsis species from the family Didymellaceae

Document Type : Research Paper

Authors

1 Assistant Professor of Plant Pathology, Plant Protection Department, Agriculture Faculty, Shahid Chamran University of Ahvaz, Ahvaz, Khuzestan Province, Iran

2 Biotechnology and Biological Science Research Center, Shahid Chamran University of Ahvaz, Ahvaz, Iran

3 Professor of Plant Pathology, Plant Protection Department, Agriculture Faculty, Shahid Chamran University of Ahvaz, Ahvaz, Khuzestan Province, Iran

Abstract

In this study, 12 native strains and 80 strains from the known species of Allophoma, Didymella, and Neodidymelliopsis were selected. The ITS, D1/D2 LSU rDNA, tub2 and rpb2 regions of the mentioned strains were compared for species delimitation using phylogenetic analysis. The genomic regions of the native strains were amplified using DNA extracted from freeze-dried mycelia and sequenced. The phylogenetic analysis was performed using the maximum likelihood algorithm. The regions of the D1/D2 LSU rDNA, ITS, tub2, and rpb2 delimited 0, 20, 43, and 46 out of 61 species studied, respectively. In the phylogenetic analysis based on combined regions, all datasets (ITS-tub2, ITS-rpb2, tub2-rpb2, ITS-tub2-rpb2, and ITS-28S-tub2-rpb2) could delimit 49 out of the 61 species under survey.Results showed that the sequencing and phylogenetic analysis of the ITS, tub2, and rpb2 regions in combination with morphological studies are necessary for species delimitation of the Allophoma, Didymella and Neodidymelliopsis genera. In a single-locus phylogeny, tub2 or rpb2 genes are the best markers among the genomic regions used.

Keywords


  1. Ahmadpour, S. A., Mehrabi-Koushki, M. & Farokhinejad, R. (2017a). Neodidymelliopsis farokhinejadii sp. nov., an undescribed fungus from dead branches of trees in Iran. Sydowia, 69, 171-182.
  2. Ahmadpour, S. A., Farokhinejad, R. & Mehrabi-Koushki, M. (2017b). Further characterization and pathogenicity of Didymella microchlamydospora causing stem necrosis of Morus nigra in Iran. Mycosphere, 8(7), 835-852.
  3. Ariyawansa, H. A., Hyde, K. D., Jayasiri, S. C., Buyck, B., Chethana, K. T., Dai, D. Q., Dai, Y. C., Daranagama, D. A., Jayawardena, R. S., Lücking, R. & Ghobad-Nejhad, M. (2015). Fungal diversity notes 111-252-taxonomic and phylogenetic contributions to fungal taxa. Fungal Diversity,75, 27-274.
  4. Aveskamp, M., de Gruyter, J., Woudenberg, J., Verkley, G. & Crous, P. W. (2010). Highlights of the Didymellaceae: a polyphasic approach to characterise Phoma and related pleosporalean genera. Studies in Mycology,65, 1-60.
  5. Babaahmadi, G., Mehrabi-Koushki, M. & Hayati J. (2017). Allophoma hayatii sp. nov., an undescribed pathogenic fungus causing dieback of Lantana camara in Iran. Mycological Progress, 17(3), 365-379.
  6. Cannon, P. f., Damm, U., Johnston, P. R. & Weir, B. S. (2012). Colletotrichum – current status and future directions. Studies in Mycology,73, 181-213.
  7. Chen, Q., Jiang, J. R., Zhang, G. Z., Cai, L. & Crous, P. W. (2015). Resolving the Phoma enigma. Studies in Mycology, 82, 137-217.
  8. Chen, Q., Hou, L. W., Duan, W. J., Crous, P. W. & Cai, L. (2017). Didymellaceae revisited. Studies in Mycology, 87, 105-159.
  9. Crouse, J. & Amorese, D. (1987). Ethanol precipitation: ammoni‏um acetate as an alternative to sodium acetate. Focus,9, 3-5.
  10. de Gruyter, J., Aveskamp, M. M., Woudenberg, J. H., Verkley, G. J., Groenewald, J. Z. & Crous, P. W. (2009). Molecular phylogeny of Phoma and allied anamorph genera: towards a reclassification of the Phoma complex. Mycological Research, 113, 508-519.
  11. de Gruyter, J., Woudenberg, J. H., Aveskamp, M. M., Verkley, G. J., Groenewald, J. Z. & Crous, P. W. (2010). Systematic reappraisal of species in Phoma section Paraphoma, Pyrenochaeta and Pleurophoma. Mycologia, 102, 1066-1081.
  12. De Gruyter, J., Woudenberg, J. H. C., Aveskamp, M. M., Verkley, G. J. M., Groenewald, J. Z. & Crous, P. W. (2013). Redisposition of Phoma-like anamorphs in Pleosporales. Studies in Mycology75, 1-36.
  13. Druzhinina, I. S., Kubicek, C. P., Komon-Zelazowska, M., Belayneh-Mulaw, T. B. & Bissett., J. (2010). The Trichoderma harzianum demon: complex speciation history resulting in coexistence of hypothetical biological species, recent agamospecies and numerous relict lineages. BMC Evolutionary Biology, 10, 94-96.
  14. Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
  15. Hyde, K. D., Nilsson, R. H., Alias, S. A., Ariyawansa, H. A., Blair, J. E., Cai, L., de Cock, A. W., Dissanayake, A. J., Glockling, S. L., Goonasekara, I. D. & Gorczak, M. (2014). One stop shop: backbones trees for important phytopathogenic genera: I (2014). Fungal Diversity, 67(1), 21-125.
  16. Hyde, K. D., Hongsanan, S., Jeewon, R., Bhat, D. J., McKenzie, E. H. C., et al. (2016). Fungal Diversity. Notes 367–490: taxonomic and phylogenetic contributions to fungal taxa. Fungal Diversity, 80, 1-270.
  17. Jayawardena, R. S., Hyde, K. D., Damm, U., Cai, L., Liu, M., Li, X. H., Zhang, W., Zhao, W. S. & Yan, J. Y. (2016). Notes on currently accepted species of Colletotrichum. Mycosphere, 7, 1192-1260
  18. Laurence, H. M., Summerell, B. A., Burgess, L. W. & Liew, E. C. Y. (2014). Genealogical concordance phylogenetic species recognition in the Fusarium oxysporum species complex. Fungal Biology, 118, 374-384.
  19. Liu, Y. J., Whelen, S. & Hall, B. D. (1999). Phylogenetic relationships among Ascomycetes: evidence from an RNA polymerse II subunit. Molecular Biology and Evolution, 16, 1799-1808.
  20. Manamgoda, D. S., Cai, L., McKenzie, E. H. C., Crous, P. W., Madrid, H., Chukeatirote, E., Shivas, R. G., Tan, Y. P. & Hyde, K. D. (2012). A phylogenetic and taxonomic re-evaluation of the BipolarisCochliobolusCurvularia complex. Fungal Diversity, 56, 131-144.
  21. O’Donnell, K. (1993). Fusarium and ITS near relatives. In: Reynolds, D. R. & Taylor, J. W. (eds), The Fungal Holomorph: Mitotic, Meiotic and Pleomorphic Speciation in Fungal Systematics. UK: CAB International, pp. 225-233.
  22. Raeder, U. & Broda, P. (1985). Rapid preparation of DNA from filamentous fungi. Letters in Applied Microbiology, 1, 17-20
  23. Short, D. P. G., O’Donnell, K., Thrane, U., Nielsen, K. F., Zhang, N., Juba, J. H. & Geiser, D. M. (2013). Phylogenetic relationships among members of the Fusarium solani species complex in human infections and the descriptions of F. keratoplasticum sp. nov. and F. petroliphilum stat. nov. Fungal Genetics and Biology, 53, 59-70.
  24. Sung, G. H., Sung, J. M., Hywel-Jones, N. L. & Spatafora, J. W. (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.
  25. Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30, 2725-2729.
  26. Valenzuela-Lopez, N., Cano-Lira, J. F., Guarro, J., Sutton, D. A., Wiederhold, N., Crous, P. W. & Stchigel, A. M. (2018). Coelomycetous Dothideomycetes with emphasis on the families Cucurbitariaceae and Didymellaceae. Studies in Mycology, 90, 1-69.
  27. White, T. J., Bruns, T., Lee, S. & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M. A., Gelfand, D. H., Sninsky, J. J. & White, T. J. (eds). PCR Protocols: a guide to methods and applications. Academic Press, New York, USA, pp. 315-322.
  28. Wikee, S., Udayanga, D., Crous, P. W., Chukeatirote, E., McKenzie, E. H. C., Bahkali, A. H., Dai, D. Q. & Hyde, K. D. (2011). Phyllosticta an overview of current status of species recognition. Fungal Diversity, 51, 43-61.
  29. Woudenberg, J., Aveskamp, M., de Gruyter, J., Spiers, A. & Crous, P. (2009). Multiple Didymella teleomorphs are linked to the Phoma clematidina morphotype. Persoonia-Molecular Phylogeny and Evolution of Fungi, 22, 56-62.
  30. Woudenberg, J. H. C., Groenewald, J. Z., Binder, M. & Crous, P. W. (2013). Alternaria redefined. Studies in Mycology, 75, 171-212.