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Türkiye’den Bazı Helvella Türlerinin Moleküler Tanımlanması İçin İki DNA Barkodlama Bölgesinin Karşılaştırılması

Year 2022, Volume: 13 Issue: 3, 111 - 118, 30.12.2022

Şuheda Sümeyye Terman Mustafa Emre Akçay Ayten Dizkırıcı

Abstract

Çalışmada iki nükleer DNA lokusu kullanılarak Türkiye‘den bazı Helvella türlerinin (Helvella acetabulum, H. arctoalpina, H. calycina, H. corium, H. crispa, H. elastica, H. lacunosa, H. leucomelaena, H. leucopus, H. solitaria) filogenetik ilişkileri değerlendirilmiştir. Transkribe edilen aralayıcı bölgeler (ITS) ve translasyon uzama faktörü 1-alfa (TEF1-α) DNA dizileri Maksimum olasılık ve Bayes çıkarım yöntemleri baz alınarak analiz edilmiştir. TEF1-α bölgesi daha az indel ve tutarlı nukleotid varyasyonları içermesine ragmen, ITS bölgesi Helvella türlerinin filogenetik ayrımında daha iyi sonuç verebilir. Fakat her iki bölge de bu cins içerisinde yer alan bazı kriptik türlerin ya da morfotürlerin ayrımında tek başına yeterli olmayabilir.

Keywords

Helvella Barkod ITS TEF1-α Barcode

Project Number

FHD-2022-10113

References

  • Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990). Basic local alignment search tool. J Mol Biol. 215(3):403–410.
  • Dizkirici, A., and Kalmer, A. (2019). Utility of various molecular markers in fungal identification and phylogeny. Nova Hedwigia, 109: 187–224
  • Dulla, E.L., Kathera, C., Gurijala, H.K., Mallakuntla, T.R. and Srinivasan, P. (2016): Highlights of DNA Barcoding in identification of salient microorganisms like fungi. J. Mycol. Méd. 26: 291–297.
  • Doyle, J.J. and Doyle, J.L., 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19:11-15.
  • Hansen, K. and Olariaga, I. (2015). Species limits and relationships within Otidea inferred from multiple gene phylogenies. Persoonia 35: 148–165.
  • Healy, R.A., Smith, M.E., Bonito, G.M., Pfister, D.H., Ge, Z.W., Guevara, G.G., Williams, G., Stafford, K., Kumar, L., Lee, T., Hobart, C., Trappe, J., Vilgalys, R. and Mclaughlin, D.J. (2013). High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales. Molecular Ecology 22: 1717–1732.
  • Hwang, J., Zhao, Q., Yang, Z.L., Wang, Z. and Townsend, J.P. (2015). Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples an example of saddle fungi. Environ Microbiol Rep 7:658–667.
  • Katoh, K. and Standley, M.D. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30(4):772-80.
  • Kesici, S. and Uzun, Y. (2021). Adaklı (Yüksekova/Hakkâri) ve Çevre Köylerde Belirlenen Makromantarlar. The Journal of Fungus 12(2): 148-162.
  • Kirk, P.M., Cannon, P.F., Minter, D.W. and Stalpers, J.A. (2008). Ainsworth & Bisby’s Dictionary of the Fungi, 10th Edition. CABI Europe-UK: [i]-xi, [1]-771.
  • Landvik, S., Kristiansen, R. and Schumacher, T. (1999). Pindara: a miniature Helvella. Mycologia 91: 278–285.
  • Løken, S.B., Skrede, I. and Schumacher, T. (2020). The Helvella corium species aggregate in Nordic countries phylogeny and species delimitation. Fungal Systematics and Evolution 5: 169–186.
  • Maia, L.C., Yano, A.M. and Kimbrough, J.W. (1996). Species of Ascomycota-forming ectomycorrhiza. Mycotaxon, 57:371–390.
  • Maddison, W. and Maddison, D. (2009). MESQUITE: a modular system for evolutionary analysis. Evolution 11 (5).
  • Nguyen, N.H., Landeros, F. and Garibay-Orijel, R. (2013). The Helvella lacunosa species complex in western North America: cryptic species, misapplied names and parasites. Mycologia 105: 1275–1286. Raja, H., Schoch, C.L., Hustad, V., Shearer, C. and Miller, A. (2011). Testing the phylogenetic utility of MCM7 in the Ascomycota. MycoKeys 1: 63–94.
  • Raja, H.A., Miller, A.N., Pearce, C.J. and Oberlies, N.H. (2017). Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community. Journal of Naturel Products 80 (3): 756–770. Rambaut, A., 2010. FigTree v1.3.1. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh.
  • Rehner, S.A. and 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: 84–89.
  • Ronquist, F. and Huelsenbeck, J.P. (2003). MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19: 1572-1574.
  • Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V. and Spouge, J.L. (2012). Fungal Barcoding Consortium (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. PNAS 109: 6241–6246.
  • Skrede, I., Carlsen, T. and Schumacher T. (2017). A synopsis of the saddle fungi (Helvella: Ascomycota) in Europe – species delimitation, taxonomy and typification. Persoonia 39: 201–253.
  • Skrede, I., Gonzalvo, l. B., Mathiesen, C. and Schumacher, T. (2020). The genera Helvella and Dissingia (Ascomycota: Pezizomycetes) in Europe - Notes on species from Spain. Fungal Systematics and Evolution 6: 65–93.
  • Sesli, E., Asan, A., Selçuk, F., (eds.) Abacı Günyar, Ö., Akata, I., Akgül, H., Aktaş, S., Alkan, S., Allı, H., Aydoğdu, H., Berikten, D., Demirel, K., Demirel, R., Doğan, H.H., Erdoğdu, M., Ergül, C,, Eroğlu, G., Giray, G., Halikî Uztan, A., Kabaktepe, Ş., Kadaifçiler, D., Kalyoncu, F., Karaltı, İ., Kaşık, G., Kaya, A., Keleş, A., Kırbağ, S., Kıvanç, M., Ocak, İ., Ökten, S., Özkale, E., Öztürk, C., Sevindik, M., Şen, B., Şen, İ., Türkekul, İ., Ulukapı, M., Uzun, Ya., Uzun, Yu., Yoltaş, A. (2020). Türkiye mantarları listesi (The checklist of fungi of Turkey). Ali Nihat Gökyiğit Vakfı Yayını. İstanbul.
  • Stielow, J.B., Lévesque, C.A., Seifert, K.A., Meyer, W. and Irinyi, L. (2015). One fungus, which genes Development and Assessment of Universal Primers for Potential Secondary Fungal DNA Barcodes. Persoonia 35: 242–263.
  • Tedersoo. L., Hansen, K., Perry, B. A. and Kjoller, R. (2006). Molecular and morphological diversity of pezizalean ectomycorrhiza. New Phytologist 170: 581–596.
  • Wen, J. and Zimmer, E.A. (1996). Phylogeny and Biogeography of Panax L. (the Ginseng Genus, Araliaceae): Inferences from ITS Sequences of Nuclear Ribosomal DNA. Molecular Phylogenetics and Evolution, 6: 167–177.
  • Zhao, Q., Tolgor, B. and Zhao, Y. (2015). Species diversity within the Helvella crispa group (Ascomycota: Helvellaceae) in China. Phytotaxa 239: 130– 142.
  • Zhao, Q., Sulayman, M. and Zhu, X. (2016). Species clarification of the culinary Bachu mushroom in western China. Mycologia 108: 828–836.

Comparison of Two DNA Barcoding Regions for Molecular Identification of Some Helvella Species from Türkiye

Year 2022, Volume: 13 Issue: 3, 111 - 118, 30.12.2022

Şuheda Sümeyye Terman Mustafa Emre Akçay Ayten Dizkırıcı

Abstract

In the present study, phylogenetic relationships of some Helvella species from Türkiye (Helvella acetabulum, H. arctoalpina, H. calycina, H. corium, H. crispa, H. elastica, H. lacunosa, H. leucomelaena, H. leucopus, H. solitaria) were assessed using morphological and molecular characters. DNA sequences of internal transcribed spacer (ITS) and translation elongation factor 1-alpha (TEF1-α) were analyzed based on Bayesian Inference methods. Although, the TEF1-α region has less number of indels and consistent nucleotide variations, ITS region can be preferred for figuring out the phylogeny of Helvella species. However, none of the regions may be sufficient alone for the identification of some cryptic and morphospecies within the genus.

Keywords

Helvella ITS TEF1-α Barcode

Supporting Institution

Scientific Research Project Foundation

Project Number

FHD-2022-10113

References

  • Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990). Basic local alignment search tool. J Mol Biol. 215(3):403–410.
  • Dizkirici, A., and Kalmer, A. (2019). Utility of various molecular markers in fungal identification and phylogeny. Nova Hedwigia, 109: 187–224
  • Dulla, E.L., Kathera, C., Gurijala, H.K., Mallakuntla, T.R. and Srinivasan, P. (2016): Highlights of DNA Barcoding in identification of salient microorganisms like fungi. J. Mycol. Méd. 26: 291–297.
  • Doyle, J.J. and Doyle, J.L., 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19:11-15.
  • Hansen, K. and Olariaga, I. (2015). Species limits and relationships within Otidea inferred from multiple gene phylogenies. Persoonia 35: 148–165.
  • Healy, R.A., Smith, M.E., Bonito, G.M., Pfister, D.H., Ge, Z.W., Guevara, G.G., Williams, G., Stafford, K., Kumar, L., Lee, T., Hobart, C., Trappe, J., Vilgalys, R. and Mclaughlin, D.J. (2013). High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales. Molecular Ecology 22: 1717–1732.
  • Hwang, J., Zhao, Q., Yang, Z.L., Wang, Z. and Townsend, J.P. (2015). Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples an example of saddle fungi. Environ Microbiol Rep 7:658–667.
  • Katoh, K. and Standley, M.D. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30(4):772-80.
  • Kesici, S. and Uzun, Y. (2021). Adaklı (Yüksekova/Hakkâri) ve Çevre Köylerde Belirlenen Makromantarlar. The Journal of Fungus 12(2): 148-162.
  • Kirk, P.M., Cannon, P.F., Minter, D.W. and Stalpers, J.A. (2008). Ainsworth & Bisby’s Dictionary of the Fungi, 10th Edition. CABI Europe-UK: [i]-xi, [1]-771.
  • Landvik, S., Kristiansen, R. and Schumacher, T. (1999). Pindara: a miniature Helvella. Mycologia 91: 278–285.
  • Løken, S.B., Skrede, I. and Schumacher, T. (2020). The Helvella corium species aggregate in Nordic countries phylogeny and species delimitation. Fungal Systematics and Evolution 5: 169–186.
  • Maia, L.C., Yano, A.M. and Kimbrough, J.W. (1996). Species of Ascomycota-forming ectomycorrhiza. Mycotaxon, 57:371–390.
  • Maddison, W. and Maddison, D. (2009). MESQUITE: a modular system for evolutionary analysis. Evolution 11 (5).
  • Nguyen, N.H., Landeros, F. and Garibay-Orijel, R. (2013). The Helvella lacunosa species complex in western North America: cryptic species, misapplied names and parasites. Mycologia 105: 1275–1286. Raja, H., Schoch, C.L., Hustad, V., Shearer, C. and Miller, A. (2011). Testing the phylogenetic utility of MCM7 in the Ascomycota. MycoKeys 1: 63–94.
  • Raja, H.A., Miller, A.N., Pearce, C.J. and Oberlies, N.H. (2017). Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community. Journal of Naturel Products 80 (3): 756–770. Rambaut, A., 2010. FigTree v1.3.1. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh.
  • Rehner, S.A. and 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: 84–89.
  • Ronquist, F. and Huelsenbeck, J.P. (2003). MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19: 1572-1574.
  • Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V. and Spouge, J.L. (2012). Fungal Barcoding Consortium (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. PNAS 109: 6241–6246.
  • Skrede, I., Carlsen, T. and Schumacher T. (2017). A synopsis of the saddle fungi (Helvella: Ascomycota) in Europe – species delimitation, taxonomy and typification. Persoonia 39: 201–253.
  • Skrede, I., Gonzalvo, l. B., Mathiesen, C. and Schumacher, T. (2020). The genera Helvella and Dissingia (Ascomycota: Pezizomycetes) in Europe - Notes on species from Spain. Fungal Systematics and Evolution 6: 65–93.
  • Sesli, E., Asan, A., Selçuk, F., (eds.) Abacı Günyar, Ö., Akata, I., Akgül, H., Aktaş, S., Alkan, S., Allı, H., Aydoğdu, H., Berikten, D., Demirel, K., Demirel, R., Doğan, H.H., Erdoğdu, M., Ergül, C,, Eroğlu, G., Giray, G., Halikî Uztan, A., Kabaktepe, Ş., Kadaifçiler, D., Kalyoncu, F., Karaltı, İ., Kaşık, G., Kaya, A., Keleş, A., Kırbağ, S., Kıvanç, M., Ocak, İ., Ökten, S., Özkale, E., Öztürk, C., Sevindik, M., Şen, B., Şen, İ., Türkekul, İ., Ulukapı, M., Uzun, Ya., Uzun, Yu., Yoltaş, A. (2020). Türkiye mantarları listesi (The checklist of fungi of Turkey). Ali Nihat Gökyiğit Vakfı Yayını. İstanbul.
  • Stielow, J.B., Lévesque, C.A., Seifert, K.A., Meyer, W. and Irinyi, L. (2015). One fungus, which genes Development and Assessment of Universal Primers for Potential Secondary Fungal DNA Barcodes. Persoonia 35: 242–263.
  • Tedersoo. L., Hansen, K., Perry, B. A. and Kjoller, R. (2006). Molecular and morphological diversity of pezizalean ectomycorrhiza. New Phytologist 170: 581–596.
  • Wen, J. and Zimmer, E.A. (1996). Phylogeny and Biogeography of Panax L. (the Ginseng Genus, Araliaceae): Inferences from ITS Sequences of Nuclear Ribosomal DNA. Molecular Phylogenetics and Evolution, 6: 167–177.
  • Zhao, Q., Tolgor, B. and Zhao, Y. (2015). Species diversity within the Helvella crispa group (Ascomycota: Helvellaceae) in China. Phytotaxa 239: 130– 142.
  • Zhao, Q., Sulayman, M. and Zhu, X. (2016). Species clarification of the culinary Bachu mushroom in western China. Mycologia 108: 828–836.
There are 27 citations in total.

Details

Primary Language English
Journal Section RESEARCH ARTICLE
Authors

Şuheda Sümeyye Terman 0000-0002-1244-9716

Mustafa Emre Akçay 0000-0002-9215-3383

Ayten Dizkırıcı 0000-0002-0578-5092

Project Number FHD-2022-10113
Publication Date December 30, 2022
Published in Issue Year 2022 Volume: 13 Issue: 3

Cite

APA Terman, Ş. S., Akçay, M. E., & Dizkırıcı, A. (2022). Comparison of Two DNA Barcoding Regions for Molecular Identification of Some Helvella Species from Türkiye. Mantar Dergisi, 13(3), 111-118. https://doi.org/10.30708/mantar.1202827
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