Document Details
|
Document Type |
: |
Thesis |
|
Document Title |
: |
Whole genome & Genetic Adaptation of Pseudomonas sp. Toward Crude Oil الجينوم الكلى والتكيف الوراثى للنوع سيدوموناس اتجاه النفط الخام |
|
Subject |
: |
Faculty of Science |
|
Document Language |
: |
Arabic |
|
Abstract |
: |
Bacterial species due to their capability to diverse biotransformation of aromatic and aliphatic compounds, the genus Pseudomonas has a high potential for crude oil degradation and other pollutants. The goal of this research is to sequence, analyze, and investigate the adaptation of the Pseudomonas sp. S5 genome to crude oil. PacBio Denovo assembly techniques and FastQC software for quality genome checking were used for this genome sequencing. For genome annotation, the Patrice server and Prokka software were used, as well as the CGView server for genome visualization and the KEGG automatic annotation server for functional analysis and mining genes for degrading crude oil. The microscope server performed pan-genome analysis. The Type (Strain) Genome Server (TYGS) platform was used for taxonomic analysis of the entire genome and the identification of closely related type strains. Using the Genome-to-Genome Distance Calculator, digital DNA-DNA hybridization was used to identify Pseudomonas sp. S5 species in silico (dDDH) (GGDC 2.1). The Microbial Genomes Atlas (MIGA) server reveals average nucleotide identity (ANI) and average amino identity (AAI). The S5 strain was assembled, annotated, and analyzed, yielding 3 contigs with a total genome of 4,365,230 bp, 4,023 CDS, 63 tRNAs, and 12 rRNAs. Phylogenomic analysis supports the S5 strain's relationship to Pseudomonas balearica. Functional analysis suggests that the following genes are involved in crude oil degradation: alkane 1-monooxygenease (AlkB1, AlkB2), halobenzoate 1,2-dioxygenase large subunit, cytochrome P450, toluene 1.2-dioxygenase alpha subunit, toluene 1.2-dioxygenase beta subunit, halobenzoate 1,2-dioxygenase small subunit, benzoate/toluate 1,2-dioxygenate reductase component, dihydroxycyclohexadiene carboxylate dehydrogenase component, xylene monooxygenase electron transfer subunit, xylene monooxygenase hydrolase subunit, octaprenylphenol hydroxylase and Nitrite reductase [NADPH], but no hit for toluene dioxygenase. Therefore, it is concluded that Pseudomonas sp. S5 has the potential to degrade crude oil, and its genome helps to understand the adaptation mechanisms of bacteria for survival in crude oil, which allows the use of bacteria as a technique for bioremediation. |
|
Supervisor |
: |
Dr. Yasir Anwar Ul haq |
|
Thesis Type |
: |
Master Thesis |
|
Publishing Year |
: |
1444 AH
2023 AD |
|
Added Date |
: |
Tuesday, July 18, 2023 |
|
Researchers
| حمدى نصر عيسى | Issa, Hamdy Nasr | Researcher | Master | |
|
Back To Researches Page
|