Comparative genomics of pathogenic fungi through sequence homology and phylogenetic similarities / Kenneth Tan Lee Shean

Kenneth Tan , Lee Shean (2023) Comparative genomics of pathogenic fungi through sequence homology and phylogenetic similarities / Kenneth Tan Lee Shean. PhD thesis, Universiti Malaya.

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Abstract

Fungal pathogenicity is one of the most vigorously tackled ecological and medicinal issues facing many scientists. The emergence of DNA sequencing had allowed massive genome sequencing projects of many important and most fatal pathogenic fungi in the world, coupling with upstream bioinformatics analysis which includes genome assembly and genome annotation had resulted in publicly available datasets that can be utilized for applied bioinformatics research. This study involves building of an aggregate Fungal Pathogenicity-related gene database with 5,183 protein sequences from PHI-base, 921,174 protein sequences from Carbohydrate-Active enZYme Database, and 2,058 protein sequences from Database of Virulence Factors in Fungal Pathogens. Local database was created using makeblastdb within NCBI-BLAST+ application and homology search of protein sequences of 86 fungal species was carried out with BLASTP resulting in identification of potential common pathogenic genes between fungus in study, also to identify potential biomarkers and understanding phylogenetic relationships of pathogenic fungi. The database can be utilized as an aggregated application for fungal pathogenic genes annotation that contributes to a wider research community.

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