Tyagi Anuj, Nagar Vandan
Department of Aquatic Environment, College of Fisheries, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab 141004, India.
Food Microbiology Group, Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400085, India.
Virus Res. 2022 Oct 15;320:198900. doi: 10.1016/j.virusres.2022.198900. Epub 2022 Aug 24.
In 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 5773 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, 1028 (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 analyzes indicated a more dominant role of natural selection in shaping the codon usage patterns of A. hydrophila phages. The findings of the current study could be useful from evolutionary and host-pathogen interaction perspectives leading to efficient utilization of phages for therapeutic and other applications.
在本研究中，对44株嗜水气单胞菌噬菌体的基因组特征和密码子使用模式进行了研究。噬菌体基因组大小在30.8至262.0 kb之间，平均值±标准差和中位数分别为111.3 ± 81.4 kb和79.4 kb。虽然观察到噬菌体GC含量存在很大差异（35.1 - 62.2%），但所有噬菌体（除两个噬菌体外）的GC含量均显著低于宿主的GC含量（62.4 ± 5.6%）。噬菌体基因的有效密码子数（ENC）值在27.7至61之间，平均值±标准差为47.4 ± 6.8。在总共5773个噬菌体基因中，分别有207个（3.6%）、3528个（61.1%）和2012个（34.9%）基因具有强（ENC < 35）、中度（35 < ENC < 50）和低（ENC ≥ 50）密码子使用偏好。在相对同义密码子使用（RSCU）分析中，还观察到噬菌体和宿主之间存在偏好密码子的共同使用情况。在密码子适应指数（CAI）分析中，1028个（17.8%）噬菌体基因显示出对宿主的显著适应性。在这些基因中，797个（78.0%）基因编码假设蛋白或功能未知的蛋白；而118个（12%）基因编码噬菌体结构和包装蛋白。基于基因组大小对ENC、RSCU和CAI分析结果的分类也表明，密码子使用偏好在小基因组噬菌体中更为突出。相关性、中性以及GC3与ENC分析表明，自然选择在塑造嗜水气单胞菌噬菌体的密码子使用模式中起更主导的作用。本研究结果从进化和宿主 - 病原体相互作用的角度来看可能是有用的，这有助于高效利用噬菌体进行治疗和其他应用。
