Complete genome analysis of PaGz-1 and PaZq-1, two novel phages belonging to the genus Pakpunavirus
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Complete genome analysis of PaGz‑1 and PaZq‑1, two novel phages belonging to the genus Pakpunavirus Lingling Wen1,2 · Ling Chen1 · Shengjian Yuan1,2 · Linyu Tian3 · Tingwei Yan3 · Haoran Zhang1 · Yang Tan1 · Yue Yu1 · Hui Wen1 · Yingfei Ma1 · Ting Wei1 · Shuqiang Huang1 Received: 14 February 2020 / Accepted: 22 June 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract Pseudomonas phages PaGz-1 and PaZq-1, two new phages infecting Pseudomonas aeruginosa, were isolated from fresh water in Guangdong province, China. The genomes of these two phages consist of 93,975 bp and 94,315 bp and contain 175 and 172 open reading frames (ORFs), respectively. The genome sequences of PaGz-1 and PaZq-1 share 95.8% identity with a query coverage of 94%, suggesting that these two phages belong to two different species. Based on results of nucleotide sequence alignment, gene annotation, and phylogenetic analysis, we propose PaGz-1 and PaZq-1 as representative isolates of two species in the genus Pakpunavirus within the family Myoviridae. Pseudomonas aeruginosa, a major pathogen causing respiratory infections in immunodeficient individuals, has been listed as an increasingly antibiotic-resistant priority pathogen [1]. Phage therapy has been considered as a potential alternative to prevent or treat relevant infections. Screening and analysis of phages able to infect P. aeruginosa are of importance to provide sufficient candidates for the development of such phage therapy.
Handling Editor: Johannes Wittmann. Lingling Wen and Ling Chen contributed equally to this study. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00705-020-04745-w) contains supplementary material, which is available to authorized users. * Ting Wei [email protected] * Shuqiang Huang [email protected] 1
CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
2
University of Chinese Academy of Sciences, Beijing 100049, China
3
College of Life Science and Technology, Jinan University, Guangzhou 510632, China
In this study, P. aeruginosa PAO1 was used as a host bacterium to isolate phages from freshwater samples using methods described previously [2]. Two phages that could lyse PAO1 were isolated and named “PaGz-1” and “PaZq1”. Total DNA was extracted from the purified phage particles, randomly sheared by sonication to construct a library, and subjected to sequencing using an Illumina HiSeq1500 sequencer (Illumina Inc., USA). The filtered reads with high quality were assembled de novo using SOAPdenove [3] and CLC Bio Genomics Workbench v10.1 (QIAGEN, Denmark). The genome ends were identified based on their significantly higher sequencing coverage compared with the average coverage values obtained from mapping the filtered reads on the assembled whole genom
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