Phylogenetic analysis of some fungi species in West Kazakhstan based on nuclear ribosomal DNA ITS sequences


  • Emre SEVİNDİK Aydın Adnan Menderes University, Faculty of Agriculture, Department of Agricultural Biotechnology, South Campus, Cakmar (TR)
  • Assemgul N. SARSENOVA L.N. Gumilyov Eurasian National University, Department of General Biology and Genomics, Satpayev str. 2, Nur-Sultan (KZ)
  • Abiev S. ABIEVICH L.N. Gumilyov Eurasian National University, Department of General Biology and Genomics, Satpayev str. 2, Nur-Sultan (KZ)
  • Erengül SOFYALIOĞLU Aydın Adnan Menderes University, Faculty of Agriculture, Department of Agricultural Biotechnology, South Campus, Cakmar (TR)
  • Darbayeva T. ESENOMANOVNA Makhambet Utemisov West Kazakhstan University, N. Nazarbayev ave.162, Uralsk (KZ)
  • Cafer EKEN Aydın Adnan Menderes University, Faculty of Agriculture, Department of Agricultural Biotechnology, South Campus, Cakmar, Aydin (TR)



fungi, phylogenetic analysis, ITS, West Kazakhstan


In this study, phylogenetic analysis of some fungal species distributed in West Kazakhstan was performed based on ITS sequences. All of the mushroom samples were collected from different regions of West Kazakhstan and brought to the laboratory. Total genomic DNA was extracted using a GeneMark commercial kit. ITS1 and ITS4 primers were used for the amplification of the ITS region in PCR analyses. The resulting DNA sequences were then edited using BioEdit and FinchTV. For phylogenetic analysis used MEGA 6.0 program. As a result of the study, ITS sequences ranged from 532 to 715 nucleotides, while the divergence values of the sequences differed between 0.000 and 0.468. The maximum likelihood tree constructed using ITS sequences consists of two clades. According to the phylogenetic analysis results obtained using other fungal species, ITS results were found to be a good indicator for the differentiation of fungal genera.


Abacı Ö, Haliki A (2005). Fungal tanıda polimeraz zincir reaksiyonu. Orlab On-Line Mikrobiyoloji Dergisi 3(10):1-9.

Akata I, Altuntaş D, Sahin E, Allı H, Kabaktepe Ş (2021). A note on Battarrea phalloides in Turkey. Mantar Dergisi 12(1):1-9.

Angelini P, Compagno R, Arcangeli A, Bistocchi G, Gargano ML, Venanzoni R, Venturella G (2016). Macrofungal diversity and ecology in two Mediterranean forest ecosystems. Plant Biosystem 150(3):540-549.

Avin FA, Bhassu S, Shin TY, Sabaratnam V (2012). Molecular classification and phylogenetic relationships of selected edible Basidiomycetes species. Molecular Biology Reports 39(7):7355-7364.

Badotti F, Fonseca PLC, Tomé LMR, Nunes DT, Góes-Neto A (2018). ITS and secondary biomarkers in fungi: review on the evolution of their use based on scientific publications. Brazilian Journal of Botany 41(2):471-479.

Buyck B, Zoller S, Hofstetter V (2018). Walking the thin line… ten years later: the dilemma of above-versus below-ground features to support phylogenies in the Russulaceae (Basidiomycota). Fungal Diversity 89(1):267-292.

Caboň M, Li GJ, Saba M, Kolařík M, Jančovičová S, Khalid AN, ... Adamčík S (2019). Phylogenetic study documents different speciation mechanisms within the Russula globispora lineage in boreal and arctic environments of the Northern Hemisphere. IMA Fungus 10(1):1-16.

Caiafa MV, Gómez-Hernández M, Williams-Linera G, Ramírez-Cruz V (2017). Functional diversity of macromycete communities along an environmental gradient in a Mexican seasonally dry tropical forest. Fungal Ecology 28:66-75.

Chen B, Song J, Chen Y, Zhang J, Liang J (2021). Morphological and phylogenetic evidence for two new species of Russula subg. Heterophyllidia from Guangdong Province of China. MycoKeys 82:139-157.

Chen B, Liang J, Jiang X, Song J (2022). Morphological characters and molecular phylogeny reveal three new species of subgenus Russula from China. Life 12(4):480.

Dizkirici A, Kansu C, Onde S (2016). Molecular phylogeny of Triticum and Aegilops genera based on ITS and MatK sequence data. Pakistan Journal of Botany 48(1):143-153.

Drehmel D, Moncalvo JM, Vilgalys R (1999). Molecular phylogeny of Amanita based on large-subunit ribosomal DNA sequences: implications for taxonomy and character evolution. Mycologia 91(4):610-618.

Feitosa YB, Cruz-Magalhães V, Argolo-Filho RC, de Souza JT, Loguercio LL (2019). Characterization of genetic diversity on tropical Trichoderma germplasm by sequencing of rRNA internal transcribed spacers. BMC Research Notes 12(1):1-6.

Felsenstein J (1985). Confidence limits on the phylogenies: an approach using the bootstrap. Evolution 39:783-791.

Gómez-Hernández M, Ramírez-Antonio KG, Gándara E (2019). Ectomycorrhizal and wood-decay macromycete communities along development stages of managed Pinus patula stands in Southwest Mexico. Fungal Ecolology 39:109-116.

Gómez-Hernández M, Avendaño-Villegas E, Toledo-Garibaldi M, Gándara E (2021). Impact of urbanization on functional diversity in macromycete communities along an urban ecosystem in Southwest Mexico. PeerJ 9:e12191.

Guo J, Karunarathna SC, Mortimer PE, Xu JC, Hyde KD (2014). Phylogenetic diversity of Russula from Xiaozhongdian, Yunnan, China, inferred from internal transcribed spacer sequence data. Chiang Mai Journal of Science 41(4):811-821.

Hall TA (1999). Bioedit: A user-friendly biological sequence alignment editor and analyses program for windows 95/98/ NT. Nucleic Acids Symposium Series 41:95-98.

Kalmer A, A İsmail,Tekpinar AD (2018). Phylogeny of some Melanoleuca species (Fungi: Basidiomycota) in Turkey and identification of Melanoleuca angelesiana AH Sm. as a first record. Kastamonu University Journal of Forestry Faculty 18(3):314-326.

Kautmanová I, Brachtýr O, Gbúrová Štubňová E, Szabóová D, Šottník P, Lalinská-Voleková B (2021). Potentially toxic elements in macromycetes and plants from areas affected by antimony mining. Biologia 76(7):2133-2159.

Kiliçoğlu M, Özkoç İ (2008). Fungal sistematikteki moleküler gelişmeler. Anadolu Tarım Bilimleri Dergisi 23(1):65-72.

Ko KS, Hong SG, Jung HS (1997). Phylogenetic analysis of Trichaptum based on nuclear 18S, 5.8 S and ITS ribosomal DNA sequences. Mycologia 89(5):727-734.

Lagiotis G, Topalidou E, Bosmali I, Osathanunkul M, Madesis P (2021). DNA-based species identification of Greek micromycetes. Current Research in Environmental & Applied Mycology 11(1):373-390.

Loizides M, Bellanger JM, Yiangou Y, Moreau PA (2018). Preliminary phylogenetic investigations into the genus Amanita (Agaricales) in Cyprus, with a review of previous records and poisoning incidents. Documents Mycologiques 37:201-218.

Martínez-Escobedo NA, Vázquez-González F J, Valero-Galván J, Álvarez-Parrilla E, Garza-Ocañas F, Najera-Medellin JA, Quiñónez-Martínez M (2021) Antimicrobial activity, phenolic compounds content, and antioxidant capacity of four edible macromycete fungi from Chihuahua, Mexico. TIP. Revista Especializada en Ciencias Químico-Biológicas 24.

Mitchell AD, Bresinsky A (1999) Phylogenetic relationships of Agaricus species based on ITS-2 and 28S ribosomal DNA sequences. Mycologia 91(5):811-819.

Newbound M, Mccarthy MA, Lebel T (2010) Fungi and the urban environment: A review. Landscape and Urban Planning 96(3):138-145.

Panda MK, Das SK, Mohapatra S, Debata PR, Tayung K, Thatoi H (2021) Mycochemical composition, bioactivities, and phylogenetic placement of three wild edible Russula species from Northern Odisha, India. Plant Biosystems 155(5):1041-1055.

Rusevska K, Calonge FDD, Karadelev M, Martín MP (2019). Fungal DNA barcode (ITS nrDNA) reveals more diversity than expected in Tulostoma from Macedonia. Turkish Journal of Botany 43(1):102-115.

Spanbayev A, Tulegenova Z, Abiev S, Eken C (2009) Rust fungi on plants in gardens and Parks of Astana and Karaganda provinces, Kazakhstan. Atatürk Üniversitesi Ziraat Fakültesi Dergisi 40(2):11-13.

Shiryaev AG, Zmitrovich IV, Ezhov ON (2018) Taxonomic and ecological structure of basidial macromycetes biota in polar deserts of the Northern Hemisphere. Contemporary Problems of Ecology 11(5):458-471.

Stachowiak B, Reguła J (2012) Health-promoting potential of edible macromycetes under special consideration of polysaccharides: a review. European Food Research and Technology 234(3):369-380.

Sun YL, Choi IL, Lee YB, Choi KY, Hong SK, Kang HM (2014). Molecular diversity and phylogentic analysis of Capsicum annuum varieties using the nrDNA ITS region. Scientia Horticulturae 165:336-343.

Tajima F (1989). Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics 123:585-595.

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.

Vellinga EC, Sysouphanthong P, Hyde KD (2011) The family Agaricaceae: phylogenies and two new white-spored genera. Mycologia 103(3):494-509.

White TJ, Bruns T, Lee S, Taylor J(1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (Eds). PCR Protocols. A Guide to Methods and Applications. San Diego, CA: Academic Press; pp 315-322.

Zagryadskaya YA (2017). Comparative characteristics of the bacterial complex in the hyphosphere of basidial macromycetes. Biology Bulletin 44(3):251-260.

Zamora JC, de Diego Calonge F, Martín MP (2014). Combining morphological and phylogenetic analyses to unravel systematics in Geastrum sect. Schmidelia. Mycologia 106(6):1199-1211.

Zhang LF, Yang JB, Yang ZL (2004). Molecular phylogeny of eastern Asian species of Amanita (Agaricales, Basidiomycota): taxonomic and biogeographic implications. Fungal Diversity 17:219-238.



How to Cite

SEVİNDİK, E., SARSENOVA, A. N., ABIEVICH, A. S., SOFYALIOĞLU, E., ESENOMANOVNA, D. T., & EKEN, C. (2022). Phylogenetic analysis of some fungi species in West Kazakhstan based on nuclear ribosomal DNA ITS sequences. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 50(3), 12783.



Research Articles
DOI: 10.15835/nbha50312783