Genome dynamics, codon usage patterns and influencing factors in Aeromonas hydrophila phages

Virus Res. 2022 Aug 24:198900. doi: 10.1016/j.virusres.2022.198900. Online ahead of print.ABSTRACTIn the present study, genome characteristics and codon usage patterns of 44 Aeromonas hydrophila phages were studied. Phage genomes varied from 30.8 to 262.0 kb with mean±SD and median values of 111.3±81.4 kb and 79.4 kb, respectively. Though the great variation in phage GC contents (35.1% - 62.2%) was observed, GC contents of all phages (except two phages) were significantly less than the GC content (62.4±5.6%) of the host. The effective number of codons (ENC) values of phage genes ranged from 27.7 to 61 with a mean±SD value of 47.4±6.8. Out of a total 5,773 phage genes, 207 (3.6%), 3,528 (61.1%) and 2,012 (34.9%) genes had strong (ENC<35), moderate (35<ENC<50) and low (ENC≥50) codon usage bias, respectively. During relative synonymous codon usage (RSCU) analysis, shared usage of preferred codons was also observed between the phages and host. During codon adaptation index (CAI) analysis, 1,028 (17.8%) phage genes showed significant adaptation towards the host. Among these genes, 797 (78.0%) genes encoded hypothetical proteins or proteins of unknown function; whereas 118 (12%) genes encoded the phage structural and packaging proteins. Segregation of ENC, RSCU and CAI analysis results based on genome size also indicated that codon usage bias was more prominent in phages with small genomes. Correlation, neutrality and GC3 versus ENC analyses indicated a more dominan...

Source: Virus Research - August 27, 2022 Category: Virology Authors: Anuj Tyagi Vandan Nagar Source Type: research