Defense Date

12-4-2023

Document Type

Capstone

Degree Type

Master of Science

Degree Name

Biological Sciences

First Advisor

Dr. Navdeep Gill

Second Advisor

Dr. Matthew Johnston

Third Advisor

Dr. Christopher Blanar

Keywords

fungal diversity, metagenomics, internal transcribed sequences: ITS1, ITS2, fungal barcoding, phylogenetics, evolution, fungal pathogens, long read sequencing, primers, fungal genomics, variations

Abstract

Universal phylogenetic markers such as the nuclear ribosomal internal transcribed sequences (ITS), specifically ITS1 and ITS2, are routinely used to estimate fungal diversity in environmental samples. However, numerous studies report differences in the performance and efficacy of ITS1 and ITS2 in documenting fungal diversity. To better understand the implications of using ITS1 versus ITS2, a comprehensive representation of the diverse fungal taxa was necessary to conduct a meta-analysis of their use across multiple fungal taxa. In order to address this, a thorough literature review was conducted to compare and contrast the use of ITS1 and ITS2 as effective DNA barcodes. Publicly available datasets were used to synthesize a simulated fungal community representing diverse fungal taxonomic groups and the efficacy of the two amplicons was tested and compared to the complete ITS. This study hypothesized that ITS1 and ITS2 are not equally effective for the resolution of fungal taxa. Specifically, when comparing ITS1 and ITS2 for phylogenetic resolution, an overlapping set of taxa were identified by both approaches, whereas certain taxa were preferentially resolved by individual ITS amplicons. The evaluation presented here should allow readers to develop a better understanding of the uses and limitations of ITS1 versus ITS2 in studying fungal diversity and ecology and enable them to develop improved approaches for better taxonomic resolution as well as aid in identification of potentially novel species.

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