BibTex RIS Cite

Türkiye’de yayılış gösteren bazı Lecidea, Porpidia ve Lecidella türlerinin liken oluşturan ascomycetes rDNA ITS bölgesinin dizi analizi yöntemi ile tanımlanması

Year 2015, Volume: 72 Issue: 1, 45 - 58, 01.03.2015

Esin Başaran Demet Cansaran -duman İlker Büyük Sümer Aras

Abstract

Amaç: Lecidea cinsine ait türlerin taksonomisi tür içi ve türler arasındaki büyük morfolojik farklılıkların olması nedeniyle oldukça karmaşa göstermektedir. Bu çalışma kapsamında, Lecidea türleri ve onunla ilişkili cinsler olarak bilinen ve Anadolu’da oldukça yaygın olan Lecidella ve Porpidia cins türlerine ait örneklere ait rDNA ITS bölgelerinin analiz edilmesi amaçlanmıştır. Yöntemler: Anadolu’nun farklı bölgelerinden toplanan 11 türe ait 17 liken örneğine ait rDNA ITS dizi analizi verileri incelenmiştir. Diğer ülkelerde dağılım gösteren Lecidea, Lecidella, Lecanora ve Porpidia cinsine ait bazı türlerin sekans analizi bilgileri GenBank’dan www.ncbi.nlm.nih.gov alınmıştır. Filogenetik analizler dört farklı metotla NJ, ME, MP, UPGMA analiz edilmiştir ve analiz sonuçlarında oluşturulan dört faklı filogenetik ağaçta da benzer sonuçlar elde edilmiştir. Bulgular: Minimum-Evolution ME analizine göre oluşturan filogenetik agaca göre Lecidea, Lecidella, Porpidia ve Ganoderma cinslerine ait türlerin dört ana dala ayrılmış olduğu tespit edilmiştir. Minimum-Evolution ME analizde Ganoderma applanatum GU256764 türü dışgrup olarak kullanılmıştır ve çalışılan tüm türlerden ayrı bir dal oluşturmuştur. Çalışılan Lecidea ve onunla ilişkili cinslerin tür ayrımı karşılaştırıldığında genellikle aynı cinsine ait türler ana dala karşı bir dal oluşturmuşlardır. Moleküler filogenetik analizler sonucunda elde edilen sonuçlara göre Lecidea cinsi Lecidella cinsinden ziyade Porpidia cinsine daha yakın bulunmuştur. Çalışılan örneklerden ilgili bölgelerinin DNA dizisinden 4100 nükleotit elde edilmiştir. Bu nükleotidlerin 177 tanesi korunmuş C , 747 nükleotit farklılaşmış V olarak belirlenmiştir. 56 nükleotit çifti transitions, 54 nükleotit çiftide tranversion olarak tespit edilmiştir. Sonuç: Bu çalışma kapsamında Lecidea ve onunla ilişkili cinslerin filogenetik analizi literatürde ilk defa değerlendirilmiştir ve elde edilen sonuçların ileride yapılacak fungus türlerinin moleküler filogenetik yöntemlerle tanımlanması çalışmalarına kaynak sağlayacağı düşünülmektedir.

Keywords

Lecidea Lecidella Porpidia ITS

References

  • 1. Hertel H. Schlüssel für die Arten der Flechtenfamilie Lecideaceae in Europa. Biblioth Lichenol, 1995; 58: 137-80.
  • 2. Hertel H. Ein vorlaufiger Bestimmungsschlüssel für die kryptothallinen, schwarzfrüchtigen, saxicolen Arten der Sammelgattung Lecidea (Lichenes) in der Holarktis. Decheniana, 1975; 127: 37-78.
  • 3. Buschbom J, Mueller G. Resolving evolutionary relationships in the lichen-forming genus Porpidia and related allies (Porpidiaceae, Ascomycota). Mol Phylo Evol, 2004; 32: 66-82.
  • 4. Hertel H. Revision einiger calciphiler Formenkreise der Flechtengattung Lecidea. Nova Hedwig Beih, 1967; 24: 1-174.
  • 5. Brodo IM, Sharnoff SD, Sharnoff S. Lichens of North America, Yale University Press. London, 2001; 390- 633.
  • 6. Ahmadjian V. The lichen symbiosis. New York, Wiley, 1993; 135-40.
  • 7. Gowan SP. The lichen genus Porpidia (Porpidiaceae) in North America. Bryologist, 1989; 92: 25-59.
  • 8. Gowan SP. A character analysis of the secondary products of the Porpidiaceae (lichenized Ascomycetes). System Bot, 1989; 14: 77-90.
  • 9. Gowan SP, Ahti T. Status of the lichen genus Porpidia in eastern Fennoscandinavia. Annal Bot Fenn, 1993; 92: 25-59.
  • 10. Knoph JG. Vorarbeiten zu einer monographie der euthallinen arten der flechtengattung porpidia (Porpidiaceae, Lecanorales) Europas, mit besonderer Berücksichtigung des Alpengebietes. Staatsexamensarbeit, Universitat München, 1984.
  • 11. Schwab AJ. Rostfarbene Arten der Sammelgattung Lecidea (Lecanorales): Revision der Arten Mittelund Nordeuropas. Mitteilungen der Botanischen Staatssammlung München., 1986; 2: 221-476.
  • 12. Fryday AM. Ecology and taxonomy of montane lichen vegetation in the British Isles. Ph. D. Thesis, University of Sheffield, England, 1997.
  • 13. Körber G. Systema Lichenum Germaniae (I–XXXIV). Die Flechten Deutschlands mikroscopisch geprüft, kritisch gesichtet, charakteristisch beschrieben und systematisch geordnet, Breslau, 1855.
  • 14. Zahlbruckner A. Catalogus Lichenum Universalis. Vol. 3, Leipzig, 1925.
  • 15. Fries TM. Lichenographia Scandinavica. Pars I u. II, Uppsala, 1874.
  • 16. Hertel H, Leuckert C. Über Flechtenstoffe und Systematik einiger Arten der Gattungen Lecidea, Placopsis und Trapelia mit C+ rot reagierendem Thallus. Willdenowia, 1969; 5: 369-83.
  • 17. Knoph JG. Untersuchungen an gesteinsbewohnenden xanthonhaltigen Sippen der Flechtengattung Lecidella (Lecanoraceae, Lecanorales) unter besonderer Berücksichtigung von auβereuropaischen Proben exklusive. Am Bibliog Lichen, 1990; 36: 1-183.
  • 18. Leuckert C, Knoph JG, Ziegler HG, Hertel H. Chemotaxonomische studien in der Gattung Lecidella (Lecanoraceae, Lecanorales) I. Lecidella carpathica und Lecidella viridans-Untersuchungen an mittel- und südeuropaischen Proben. Herzogia, 1990; 8: 265-72.
  • 19. Leuckert C, Knoph JG, Hertel H. Chemotaxonomische Studien in derGattung Lecidella (Lecanoraceae, Lecanorales) II. Europaische Arten der Lecidella asema-Gruppe. Herzogia, 1992; 9: 1-17.
  • 20. Leuckert C, Knoph JG. European taxa of saxicolous Lecidella containing chloroxanthones: identification of patterns using thin layer chromatography. Lichennologist, 1992; 24: 383-97.
  • 21. Huneck S, Santesson J. Mitteilung über Flechteninhaltsstoffe. Die Inhaltsstoffe von Lecidella carpathica (Koerb.) Szat. Und die Struktur des Thuringions, eines neuen Xanthons. Zeitsc für Naturfor, 1969; 24b: 756-60.
  • 22. Elix JA, Crook CE. The joint occurrence of chloroxanthones in lichens, and a further thirteen new lichen xanthones. Bryologist, 1992; 95: 52-64.
  • 23. Song KM, Osborn TC, Williams PH. Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs), I. Genome evolution of diploid and amphidiploid species. Theor App Genet, 1988; 75: 784-94.
  • 24. Miller JC, Tanksley SD. RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor App Genet, 1990; 80(4): 437-48.
  • 25. Wheeler WC, Honeycutt RL. Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications. Mol Biol Evol, 1988; 5: 90-6.
  • 26. Bridge PD, Arora DK, Reddy CA, Elander RP. Applications of PCR in Mycology. In: PCR Applications in Studies of Lichen-Forming Fungi (Crespo A, Cubero OF and Grube M, eds. USA: Cab International, 1998; 231-69.
  • 27. Dizkırıcı A, Kaya Z, Cabi E, Doğan M. Phylogenetic relationships of Elymus L. and related genera (Poaceae) based on the nuclear ribosomal internal transcribed spacer sequences. Turk J Bot, 2010; 34: 467-78.
  • 28. Torres RA, Gunal M, Humleben V. GC balance in the International Transcribed Spacers ITS1 and ITS2 of nuclear ribosomal RNA genes. J Mol Evol, 1990; 30: 170-81.
  • 29. White TJ, Bruns T, Taylor J. Amplification and direct sequencing of fungal ribosomal genes for phylogenetics. In: PCR protocols: A guide to Methods and Applications (Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. San Diego: Academic press, 1990; 315-22.
  • 30. Porter CH, Collins FH. Species-diagnostic difference in a ribosomal DNA internal transcribed spacer from the sibling species Anopheles freeborni and Anopheles hermsi (Diptera: Culicidae). Am J Trop Med Hyg, 1991; 45: 271–9.
  • 31. Aras S, Cansaran D. Isolation of DNA for sequence analysis from herbarium material of some lichen species. Turk J Bot, 2006; 30: 449-53.
  • 32. Gardes M, Bruns TD. ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol Ecol, 1993; 2: 113-8.
  • 33. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformat, 2007; 23: 2947-48.
  • 34. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol., 2007; 24: 1596-99.
  • 35. Ruprecht U, Lumbsch T, Brunauer G, Allan-Green TG, Turk R. Diversity of Lecidea (Lecideaceae, Ascomycota) species revealed by molecular data and morphological charaers. Antar Sci, 2010; 22(6): 727-41.
  • 36. Aras S, Cansaran D, Türk AÖ, Kandemir I, Candan M. Resolving genetic relationships in manna group of lichens from genus Aspicilia. Afr J Biotech, 2007; 6(9): 1154-60.
  • 37. Cansaran D, Aras S, Kandemir I, Halıcı MG. Phylogenetic relations of Rhizoplaca Zopf. From Anatolia Inferred from ITS sequence data. Zeit Naturfor, 2006; 61c: 405-12.
  • 38. Hertel H. Progress and problems in taxonomy of Antarctic saxicolous lecideoid lichens. Bibliot Lichenol, 1987; 25: 219-42.

Identification of some Lecidea, Porpidia and Lecidella species lichen-forming ascomycetes distributed in Turkey by sequence analysis of rDNA ITS region

Year 2015, Volume: 72 Issue: 1, 45 - 58, 01.03.2015

Esin Başaran Demet Cansaran -duman İlker Büyük Sümer Aras

Abstract

Objective: The taxonomy of Lecidea is extremely complex because of the enormous morphological variation within and between species. The aim of this study was to analyse the rDNA ITS regions of Lecidea species and related genus called Lecidella and Porpidia which are widely spreaded in Anatolia, Turkey. Methods: The ITS rDNA sequence information of 17 samples from 11 species which were collected from different provinces of Anatolia were generated. Some of the specimens from Lecidea, Lecidella, Lecanora and Porpidia genus were also taken from the GenBank www.ncbi.nlm.nih.gov . The phylogenetic analysis was performed by the help of four different methods NJ, ME, MP, UPGMA and these different methods manifested similar results. Results: Minimum-Evolution ME dendrogram revealed that species of Lecidea, Lecidella, Porpidia and Ganoderma sp. genus were distributed into four main branches. Ganoderma applanatum GU256764 which was considered as outgroup formed one of the branches, while the other species were collected on the other branchs. Generally the species which belong to the same genus, combined in one branch towards to the origin. In accordance with the results derived from molecular phylogenetic analysis, genus Lecidea is found closer Porpidia rather than Lecidella morphologically. Numerable 4100 nucleotides were obtained from DNA sequences of related region of studied samples. It was indicated that 177 nucleotides of those regions were stable C , 747 nucleotides were variable V . It was confirmed that there were transitions in 56 nucleotide pairs, tranversion in 54 nucleotide pairs of compared samples. Conclusion: In this study, the results of phylogenetic analysis of the genus Lecidea and other similar groups were firstly evaluated and the results will not be only a guide but also will provide a resource for next researchers.

Keywords

Lecidea Lecidella Porpidia ITS

References

  • 1. Hertel H. Schlüssel für die Arten der Flechtenfamilie Lecideaceae in Europa. Biblioth Lichenol, 1995; 58: 137-80.
  • 2. Hertel H. Ein vorlaufiger Bestimmungsschlüssel für die kryptothallinen, schwarzfrüchtigen, saxicolen Arten der Sammelgattung Lecidea (Lichenes) in der Holarktis. Decheniana, 1975; 127: 37-78.
  • 3. Buschbom J, Mueller G. Resolving evolutionary relationships in the lichen-forming genus Porpidia and related allies (Porpidiaceae, Ascomycota). Mol Phylo Evol, 2004; 32: 66-82.
  • 4. Hertel H. Revision einiger calciphiler Formenkreise der Flechtengattung Lecidea. Nova Hedwig Beih, 1967; 24: 1-174.
  • 5. Brodo IM, Sharnoff SD, Sharnoff S. Lichens of North America, Yale University Press. London, 2001; 390- 633.
  • 6. Ahmadjian V. The lichen symbiosis. New York, Wiley, 1993; 135-40.
  • 7. Gowan SP. The lichen genus Porpidia (Porpidiaceae) in North America. Bryologist, 1989; 92: 25-59.
  • 8. Gowan SP. A character analysis of the secondary products of the Porpidiaceae (lichenized Ascomycetes). System Bot, 1989; 14: 77-90.
  • 9. Gowan SP, Ahti T. Status of the lichen genus Porpidia in eastern Fennoscandinavia. Annal Bot Fenn, 1993; 92: 25-59.
  • 10. Knoph JG. Vorarbeiten zu einer monographie der euthallinen arten der flechtengattung porpidia (Porpidiaceae, Lecanorales) Europas, mit besonderer Berücksichtigung des Alpengebietes. Staatsexamensarbeit, Universitat München, 1984.
  • 11. Schwab AJ. Rostfarbene Arten der Sammelgattung Lecidea (Lecanorales): Revision der Arten Mittelund Nordeuropas. Mitteilungen der Botanischen Staatssammlung München., 1986; 2: 221-476.
  • 12. Fryday AM. Ecology and taxonomy of montane lichen vegetation in the British Isles. Ph. D. Thesis, University of Sheffield, England, 1997.
  • 13. Körber G. Systema Lichenum Germaniae (I–XXXIV). Die Flechten Deutschlands mikroscopisch geprüft, kritisch gesichtet, charakteristisch beschrieben und systematisch geordnet, Breslau, 1855.
  • 14. Zahlbruckner A. Catalogus Lichenum Universalis. Vol. 3, Leipzig, 1925.
  • 15. Fries TM. Lichenographia Scandinavica. Pars I u. II, Uppsala, 1874.
  • 16. Hertel H, Leuckert C. Über Flechtenstoffe und Systematik einiger Arten der Gattungen Lecidea, Placopsis und Trapelia mit C+ rot reagierendem Thallus. Willdenowia, 1969; 5: 369-83.
  • 17. Knoph JG. Untersuchungen an gesteinsbewohnenden xanthonhaltigen Sippen der Flechtengattung Lecidella (Lecanoraceae, Lecanorales) unter besonderer Berücksichtigung von auβereuropaischen Proben exklusive. Am Bibliog Lichen, 1990; 36: 1-183.
  • 18. Leuckert C, Knoph JG, Ziegler HG, Hertel H. Chemotaxonomische studien in der Gattung Lecidella (Lecanoraceae, Lecanorales) I. Lecidella carpathica und Lecidella viridans-Untersuchungen an mittel- und südeuropaischen Proben. Herzogia, 1990; 8: 265-72.
  • 19. Leuckert C, Knoph JG, Hertel H. Chemotaxonomische Studien in derGattung Lecidella (Lecanoraceae, Lecanorales) II. Europaische Arten der Lecidella asema-Gruppe. Herzogia, 1992; 9: 1-17.
  • 20. Leuckert C, Knoph JG. European taxa of saxicolous Lecidella containing chloroxanthones: identification of patterns using thin layer chromatography. Lichennologist, 1992; 24: 383-97.
  • 21. Huneck S, Santesson J. Mitteilung über Flechteninhaltsstoffe. Die Inhaltsstoffe von Lecidella carpathica (Koerb.) Szat. Und die Struktur des Thuringions, eines neuen Xanthons. Zeitsc für Naturfor, 1969; 24b: 756-60.
  • 22. Elix JA, Crook CE. The joint occurrence of chloroxanthones in lichens, and a further thirteen new lichen xanthones. Bryologist, 1992; 95: 52-64.
  • 23. Song KM, Osborn TC, Williams PH. Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs), I. Genome evolution of diploid and amphidiploid species. Theor App Genet, 1988; 75: 784-94.
  • 24. Miller JC, Tanksley SD. RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor App Genet, 1990; 80(4): 437-48.
  • 25. Wheeler WC, Honeycutt RL. Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications. Mol Biol Evol, 1988; 5: 90-6.
  • 26. Bridge PD, Arora DK, Reddy CA, Elander RP. Applications of PCR in Mycology. In: PCR Applications in Studies of Lichen-Forming Fungi (Crespo A, Cubero OF and Grube M, eds. USA: Cab International, 1998; 231-69.
  • 27. Dizkırıcı A, Kaya Z, Cabi E, Doğan M. Phylogenetic relationships of Elymus L. and related genera (Poaceae) based on the nuclear ribosomal internal transcribed spacer sequences. Turk J Bot, 2010; 34: 467-78.
  • 28. Torres RA, Gunal M, Humleben V. GC balance in the International Transcribed Spacers ITS1 and ITS2 of nuclear ribosomal RNA genes. J Mol Evol, 1990; 30: 170-81.
  • 29. White TJ, Bruns T, Taylor J. Amplification and direct sequencing of fungal ribosomal genes for phylogenetics. In: PCR protocols: A guide to Methods and Applications (Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. San Diego: Academic press, 1990; 315-22.
  • 30. Porter CH, Collins FH. Species-diagnostic difference in a ribosomal DNA internal transcribed spacer from the sibling species Anopheles freeborni and Anopheles hermsi (Diptera: Culicidae). Am J Trop Med Hyg, 1991; 45: 271–9.
  • 31. Aras S, Cansaran D. Isolation of DNA for sequence analysis from herbarium material of some lichen species. Turk J Bot, 2006; 30: 449-53.
  • 32. Gardes M, Bruns TD. ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol Ecol, 1993; 2: 113-8.
  • 33. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformat, 2007; 23: 2947-48.
  • 34. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol., 2007; 24: 1596-99.
  • 35. Ruprecht U, Lumbsch T, Brunauer G, Allan-Green TG, Turk R. Diversity of Lecidea (Lecideaceae, Ascomycota) species revealed by molecular data and morphological charaers. Antar Sci, 2010; 22(6): 727-41.
  • 36. Aras S, Cansaran D, Türk AÖ, Kandemir I, Candan M. Resolving genetic relationships in manna group of lichens from genus Aspicilia. Afr J Biotech, 2007; 6(9): 1154-60.
  • 37. Cansaran D, Aras S, Kandemir I, Halıcı MG. Phylogenetic relations of Rhizoplaca Zopf. From Anatolia Inferred from ITS sequence data. Zeit Naturfor, 2006; 61c: 405-12.
  • 38. Hertel H. Progress and problems in taxonomy of Antarctic saxicolous lecideoid lichens. Bibliot Lichenol, 1987; 25: 219-42.
There are 38 citations in total.

Details

Primary Language English
Journal Section Research Article
Authors

Esin Başaran This is me

Demet Cansaran -duman This is me

İlker Büyük This is me

Sümer Aras This is me

Publication Date March 1, 2015
Published in Issue Year 2015 Volume: 72 Issue: 1

Cite

APA Başaran, E., Cansaran -duman, D., Büyük, İ., Aras, S. (2015). Identification of some Lecidea, Porpidia and Lecidella species lichen-forming ascomycetes distributed in Turkey by sequence analysis of rDNA ITS region. Türk Hijyen Ve Deneysel Biyoloji Dergisi, 72(1), 45-58.
AMA Başaran E, Cansaran -duman D, Büyük İ, Aras S. Identification of some Lecidea, Porpidia and Lecidella species lichen-forming ascomycetes distributed in Turkey by sequence analysis of rDNA ITS region. Turk Hij Den Biyol Derg. March 2015;72(1):45-58.
Chicago Başaran, Esin, Demet Cansaran -duman, İlker Büyük, and Sümer Aras. “Identification of Some Lecidea, Porpidia and Lecidella Species Lichen-Forming Ascomycetes Distributed in Turkey by Sequence Analysis of RDNA ITS Region”. Türk Hijyen Ve Deneysel Biyoloji Dergisi 72, no. 1 (March 2015): 45-58.
EndNote Başaran E, Cansaran -duman D, Büyük İ, Aras S (March 1, 2015) Identification of some Lecidea, Porpidia and Lecidella species lichen-forming ascomycetes distributed in Turkey by sequence analysis of rDNA ITS region. Türk Hijyen ve Deneysel Biyoloji Dergisi 72 1 45–58.
IEEE E. Başaran, D. Cansaran -duman, İ. Büyük, and S. Aras, “Identification of some Lecidea, Porpidia and Lecidella species lichen-forming ascomycetes distributed in Turkey by sequence analysis of rDNA ITS region”, Turk Hij Den Biyol Derg, vol. 72, no. 1, pp. 45–58, 2015.
ISNAD Başaran, Esin et al. “Identification of Some Lecidea, Porpidia and Lecidella Species Lichen-Forming Ascomycetes Distributed in Turkey by Sequence Analysis of RDNA ITS Region”. Türk Hijyen ve Deneysel Biyoloji Dergisi 72/1 (March 2015), 45-58.
JAMA Başaran E, Cansaran -duman D, Büyük İ, Aras S. Identification of some Lecidea, Porpidia and Lecidella species lichen-forming ascomycetes distributed in Turkey by sequence analysis of rDNA ITS region. Turk Hij Den Biyol Derg. 2015;72:45–58.
MLA Başaran, Esin et al. “Identification of Some Lecidea, Porpidia and Lecidella Species Lichen-Forming Ascomycetes Distributed in Turkey by Sequence Analysis of RDNA ITS Region”. Türk Hijyen Ve Deneysel Biyoloji Dergisi, vol. 72, no. 1, 2015, pp. 45-58.
Vancouver Başaran E, Cansaran -duman D, Büyük İ, Aras S. Identification of some Lecidea, Porpidia and Lecidella species lichen-forming ascomycetes distributed in Turkey by sequence analysis of rDNA ITS region. Turk Hij Den Biyol Derg. 2015;72(1):45-58.