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Functional pan-genome analyses of hydrocarbon biodegradation by diverse Pseudomonas aeruginosa(PDF)

Chinese Journal of Applied & Environmental Biology[ISSN:1006-687X/CN:51-1482/Q]

2021 05
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Functional pan-genome analyses of hydrocarbon biodegradation by diverse Pseudomonas aeruginosa
PAN Jincheng1 LI Yanbing1 LI Jing2? & MA Yanling1?
1College of Life Science, Northwest University, Xi’an 710069, China 2Xi’an Rege Biotechnology Co. Ltd., Xi’an 710065, China
Pseudomonas aeruginosa pan-genome core genome unique genome biodegradation

As a versatile degrader, Pseudomonas aeruginosa has promising applications in removing both saturated aliphatic and aromatic hydrocarbons. To present bacterial genomic characteristics, functional genomic analysis of 10 P. aeruginosa strains was employed to interpret the core genome and pan-genome, the potential of hydrocarbon biodegradation, and the central pathway of aromatic compound degradation. Most of the homologous genes constituted the core genome that contained 4 923 genes accounting for 56.2% of the pan-genome, with a tiny portion of unique types of genomic evidence in these strains. The open pan-genome was about to close momentarily with its growing number of genomes, implying that the ability to exchange genetic information with the external condition by HGT was feeble among the selected strains of P. aeruginosa. The most abundant genes within the core genome were those that encode nutrient transporters and a two-component system. Genes that encode amino acid metabolism (synthesis and degradation), biofilm formation, and flagella assembly?were all part of the core genome. Moreover, the KEGG annotation of the core genes demonstrated that β-ketoadipate, homoprotocatechuate, homogentisate, and gentisate pathways were the main catabolic processes of aromatic compounds in the P. aeruginosa strains, which concurrently possessed a relatively complete alkane hydroxylase system. Based on the GC content, flanked transposase, and integrase coding genes, it could be concluded that the aromatic compound degradation gene clusters in P. aeruginosa could be obtained through horizontal gene transfer. Functional pan-genome analysis of these 10 strains showed that the frequency of HGT in P. aeruginosa to obtain new genes from the outside world was relatively weak and had a complete system to degrade hydrocarbons. The results would be beneficial for better understanding the genomic composition and characteristics and providing useful information on the potential and mechanism of degradation of P. aeruginosa.


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