Characterization and Genome Analysis of a Novel Mu-like Phage VW-6B Isolated from the Napahai Plateau Wetland of China
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Characterization and Genome Analysis of a Novel Mu‑like Phage VW‑6B Isolated from the Napahai Plateau Wetland of China Zihong Cui1 · Zhiwei Xu1 · Yunlin Wei1 · Qi Zhang1 · Kunhao Qin1 · Xiuling Ji1 Received: 3 March 2020 / Accepted: 27 October 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Although bacteriophages are more numerous and have smaller genomes than their bacterial hosts, relatively few have their genomes sequenced. Here, we isolated the Pseudomonas fluorescens bacteriophage from Napahai plateau wetland and performed de novo genome sequencing. Based on the previous biological characteristics and bioinformatics analysis, it was determined that VW-6B was a linear double-stranded DNA (dsDNA) phage with 35,306 bp, with 56.76% G+C content and 197 bp tandem repeats. The VW-6B genome contained 46 open-reading frames (ORFs), and no tRNA genes were found. Based on phage genome structure, sequence comparison, and collinear analysis, VW-6B should be classified into the family Siphoviridae and be considered as a member of a new species in the Mu-like phage. The newly isolated bacteriophage can specifically infect P. fluorescens, which further enriches the diversity of known bacteriophages and provides a basis for the subsequent research and application of bacteriophages.
Introduction Viruses are considered to be the most abundant biological substance on earth, with estimated 1031 species in the biosphere for now [1]. Bacteriophages (phages) are viruses that infect and replicate in bacterial cells [2]. The number of sequenced virus genomes is approximately 8,000 and increases rapidly [3]. However, the number of bacteriophages genomes lags far behind their host bacteria [4–6]. With the continuous development of sequencing technology, more and more phages have completed genome-wide sequencing. Phage Φ X174 is the first bacteriophage having completed the whole genome sequencing with singlestranded DNA. In recent years, with the abuse of antibiotics and the research on the interaction mechanism between phage and host [6–8], the number of phages that have completed genome-wide sequencing is exploding.
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00284-020-02277-9) contains supplementary material, which is available to authorized users. * Xiuling Ji [email protected] 1
Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
In the 1970s, the tailed phage was first classified based on morphology and nucleic acid composition [9–11]. In the following years, new methods of phage classification emerged, including genome-wide and proteome comparisons, and then new phage taxonomic groups were established, including 19 subfamilies and more than 250 genera in Myoviridae, Siphoviridae, and Podoviridae [12]. Currently, 85 phages of Pseudomonas fluorescens have been sequenced, but only two P. fluorescens Siphoviridae family phages VW-6S and VW-6B have been sequenced and sub
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