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Pyrosequencing analysis of fungal assemblages and the effect of ITS rDNA intragenomic variation on diversity estimates
Zelenka, Tomáš ; Kolařík, Miroslav (advisor) ; Větrovský, Tomáš (referee)
The ITS region of nuclear ribosomal DNA has recently become a frequently studied region for its use as a barcode marker. It is employed in environmental metagenomic analyses, the determination of fungi and in studies of fungal phylogenetics. In genomes, rDNA occurs in the form of large multicopy tandem arrays. Thus common Sanger sequencing leads to a consensus of many copies which in fact conceals most of the potential intragenomic variation. However 454 pyrosequencing reveals the sequence of single copies. Although it is believed that most of the variation among copies is reduced during a process called concerted evolution, some variation might still be conserved, including variation of non-functional pseudogenes. As a consequence, when using 454 pyrosequencing, we are not able to discriminate between this variation and real diversity. This could have a huge impact on the estimation of real diversity as well as on the correct assessment of pyrosequence studies. This thesis reviews current knowledge of intragenomic variation among fungi and summarizes some papers applying pyrosequencing in the research of fungal diversity. At the same time it indicates intragenomic variation as a potential cause of untrue diversity in diversity studies. Up until now there hasn't existed any experimental survey covering...
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Pyrosequencing analysis of fungal assemblages and the effect of ITS rDNA intragenomic variation on diversity estimates
Zelenka, Tomáš ; Kolařík, Miroslav (advisor) ; Větrovský, Tomáš (referee)
The ITS region of nuclear ribosomal DNA has recently become a frequently studied region for its use as a barcode marker. It is employed in environmental metagenomic analyses, the determination of fungi and in studies of fungal phylogenetics. In genomes, rDNA occurs in the form of large multicopy tandem arrays. Thus common Sanger sequencing leads to a consensus of many copies which in fact conceals most of the potential intragenomic variation. However 454 pyrosequencing reveals the sequence of single copies. Although it is believed that most of the variation among copies is reduced during a process called concerted evolution, some variation might still be conserved, including variation of non-functional pseudogenes. As a consequence, when using 454 pyrosequencing, we are not able to discriminate between this variation and real diversity. This could have a huge impact on the estimation of real diversity as well as on the correct assessment of pyrosequence studies. This thesis reviews current knowledge of intragenomic variation among fungi and summarizes some papers applying pyrosequencing in the research of fungal diversity. At the same time it indicates intragenomic variation as a potential cause of untrue diversity in diversity studies. Up until now there hasn't existed any experimental survey covering...
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Utilization of PCR-RFLP approach for evaluation of ITS polymorphism in selected \kur{Beauveria bassiana} strains/isolates
KOCKOVÁ, Lucie
The aim of this study was the evaluation of the suitability PCR-RFLP technique and ITS region analysis for determination the genetic variability of the entomopathogenic fungi - Beauveria bassiana, Beauveria brongniartii and Isaria fumosorosea. By the means of ITS-RFLP technique, it was possible to identify the uniformity of the B. bassiana isolates from NP Šumava, the higher level of polymorphism of B.bassiana isolates from different geographical areas was detected and it was possible to distinguish different entomopathogenic fungi used in this study.
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