Comparison of rDNA regions (ITS, LSU, and SSU) of someAspergillus, Penicillium, and Talaromyces spp.

Aspergillus, Penicillium, and Talaromyces spp. are commonly found worldwide and include industrially and medicinally important members. These genera are deeply related with life from soil to health hazards via their industrial products, surface proteins, biodiversity, food spoilage, mycotoxins, etc. These three genera progressively encounter important taxonomic revisions, such as the one fungus-one name concept, and various methods are available to establish their evolutionary and phylogenetic relationships. Besides morphological, microscopic, and extrolite analyses, nucleotide sequence analysis is the most preferred method. In particular, rDNA regions, such as the internal transcribed spacer (ITS), large subunit (LSU), and small subunit (SSU), are commonly used for taxonomic and phylogenetic studies. Although the ITS locus is accepted as the barcode gene for fungal identification, it has some limitations. Therefore, the aim of the present study was to compare ITS, LSU, and SSU loci in terms of ease of application, discrimination of species, and phylogeny by using 43 strains belonging to the above-mentioned three genera of fungi. The results indicated that the ITS and LSU loci were the most effective, exhibiting identical topology and species discrimination, while the SSU locus was the least effective, demonstrating lower species discrimination and the worst topology. Furthermore, the long and high-quality ITS, LSU, and SSU sequences obtained in the present study, which belong to the above-mentioned three genera of fungi, have been deposited in the NCBI database.

PDF

___

Asan A (2004). Aspergillus, Penicillium, and related species reported from Turkey. Mycotaxon 89: 155-157.
Das S, Deb B (2015). DNA barcoding of fungi using Ribosomal ITS Marker for genetic diversity analysis: a review. International Journal of Pure and Applied Bioscience 3: 160-167.
Demirel R, Sariozlu NY (2014). Mycotoxigenic moulds and mycotoxins in flours consumed in Turkey. J Sci Food Agr 94: 1577-1584.
Demirel R, Sariozlu NY, İlhan S (2013). Polymerase chain reaction (PCR) identification of terverticillate Penicillium species isolated from agricultural soils in Eskişehir province. Braz Arch Biol Techn 56: 980-984.
Frisvad JC, Larsen TO, de Vries R, Meijer M, Houbraken J, Cabañes FJ, Ehrlich K, Samson RA (2007). Secondary metabolite profiling, growth profiles and other tools for species recognition and important Aspergillus mycotoxins. Stud Mycol 59: 31-37.
Hibbett DS, Binder M, Bischoff JF., Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lücking R et al. (2007). A higher-level phylogenetic classification of the Fungi. Mycol Res 111: 509-547.
Houbraken J, Samson RA (2011). Phylogeny of Penicillium and the segregation of Trichocomaceae in to three families. Stud Mycol 70: 1-51.
Houbraken J, Visagie CM, Meijer M, Frisvad JC, Busby PE, Pitt JI, Seifert KA, Louis-Seize G, Demirel R, Yilmaz N et al. (2014). A taxonomic and phylogenetic revision of Penicillium section Aspergilloides. Stud Mycol 78: 373-451.
Klich MA (2002). Identification of Common Aspergillus Species. 1st ed. Utrecht, the Netherlands: Centraalbureau voor Schimmelcultures.
Krijgsheld P, Bleichrodt R, van Veluw GJ, Wang F, Müller WH, Dijksterhuis J, Wösten HAB (2013). Development in Aspergillus. Stud Mycol 74: 1-29.
Liu K, Porras-Alfaro A, Kuske CR, Eichorst SA, Xiea G (2011). Accurate, rapid taxonomic classification of fungal large-subunit rRNA genes. Appl Environ Microb 78: 1523-1533.
Peterson SW (2012). Aspergillus and Penicillium identification using DNA sequences: barcode or MLST? Appl Microbiol Biot 95: 339-344.
Pitt JI (2000). A Laboratory Guide to Common Penicillium Species. 3rd ed. North Ryde, Australia: Food Science Australia.
Samson RA, Houbraken J, Thrane U, Frisvad JC, Andersen B (2010). Food and Indoor Fungi. Utrecht, the Netherlands: CBS KNAW Fungal Diversity Centre.Samson RA, Visagie CM, Houbraken J, Hong SB, Hubka V, Klaassen CHW, Perrone G, Seifert KA, Susca A, Tanney JB et al. (2014). Phylogeny, identification and nomenclature of the genus Aspergillus. Stud Mycol 78: 141-173.
Samson RA, Yilmaz N, Houbraken J, Spierenburg H, Seifert KA, Peterson SW, Varga J, Frisvad JC (2011). Phylogeny and nomenclature of the genus Talaromyces and taxa accommodated in Penicillium subgenus Biverticillium. Stud Mycol 70: 159-183.
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, André Levesque C, Chen W (2012). Fungal Barcoding Consortiuma, Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. P Natl Acad Sci USA 109: 6241-6246.
Seifert KA (2009). Progress towards DNA barcoding of fungi. Mol Ecol Resour 9: 83-89.
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.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30: 2725-2729.
Visagie CM, Houbraken J, Frisvad JC, Hong SB, Klaassen CHW, Perrone G, Seifert KA, Varga J, Yaguchi T, Samson RA (2014). Identification and nomenclature of the genus Penicillium. Stud Mycol 78: 343-371.
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, editors. PCR Protocols: A Guide to Methods and Applications. New York, NY, USA: Academic Press, pp. 315-322.
Yilmaz N, Visagie CM, Houbraken J, Frisvad JC, Samson RA (2014). Polyphasic taxonomy of the genus Talaromyces. Stud Mycol 78: 175341.