Abstract
Tailed phages with genomes larger than 200 kbp are classified as jumbo phage and exhibit extremely high diversity. In this study, a novel jumbo phage, vB_BpuM_BpSp, infecting pathogenic Bacillus pumilus, the cause of ginger rhizome rot disease, was isolated. Notable features of phage vB_BpuM_BpSp are the large phage capsid of 137 nm and baseplate-attached curly tail fibers. The genome of the phage is 255,569 bp in size with G+C content of 25.9 %, and it shows low similarity to known biological entities. The phage genome contains 318 predicted coding sequences. Among these predicted coding sequences, 26 genes responsible for nucleotide metabolism were found, and seven structural genes could be identified. The findings of this study provide new understanding of the genetic diversity of phages.
Similar content being viewed by others
References
Abbasifar R, Griffiths MW, Sabour PM, Ackermann HW, Vandersteegen K, Lavigne R, Noben JP, Villa AA, Abbasifar A, Nash JHE, Kropinski AM (2014) Supersize me: Cronobacter sakazakii phage GAP32. Virology 460:138–146
Ackermann HW, Yoshino S, Ogata S (1995) A Bacillus phage that is a living fossil. Can J Microbiol 41:294–297
Ackermann HW, Prangishvili D (2012) Prokaryote viruses studied by electron microscopy. Arch Virol 157:1843–1849
Belyaeva NN, Azizbeky RR (1968) Fine structure of new Bacillus subtilis phage Ar9 with complex morphology. Virology 34:176
Chang HC, Chen CR, Lin JW, Shen GH, Chang KM, Tseng YH, Weng SF (2005) Isolation and characterization of novel giant Stenotrophomonas maltophilia phage phi SMA5. Appl Environ Microb 71:1387–1393
Cole JR, Wang Q, Fish JA, Chai BL, McGarrell DM, Sun YN, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM (2014) Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42:D633–D642
Drulis-Kawa Z, Olszak T, Danis K, Majkowska-Skrobek G, Ackermann HW (2014) A giant Pseudomonas phage from Poland. Arch Virol 159:567–572
Eiserlin FA (1967) Structure of Bacillus subtilis bacteriophage Pbs 1. J Ultra Mol Struct R 17:342–347
Hendrix RW (2009) Jumbo bacteriophages. Curr Top Microbiol 328:229–240
Hertveldt K, Lavigne R, Pleteneva E, Sernova N, Kurochkina L, Korchevskii R, Robben J, Mesyanzhinov V, Krylov VN, Volckaert G (2005) Genome comparison of Pseudomonas aeruginosa large phages. J Mol Biol 354:536–545
Hu B, Margolin W, Molineux IJ, Liu J (2015) Structural remodeling of bacteriophage T4 and host membranes during infection initiation. Proc Natl Acad Sci USA 112:E4919–E4928
Jin T, Zhang X, Zhang Y, Hu Z, Fu Z, Fan J, Wu M, Wang Y, Shen P, Chen X (2014) Biological and genomic analysis of a PBSX-like defective phage induced from Bacillus pumilus AB94180. Arch Virol 159:739–752
Kiljunen S, Hakala K, Pinta E, Huttunen S, Pluta P, Gador A, Lonnberg H, Skurnik M (2005) Yersiniophage phi R1-37 is a tailed bacteriophage having a 270 kb DNA genome with thymidine replaced by deoxyuridine. Microbiol-Sgm 151:4093–4102
Lecoutere E, Ceyssens PJ, Miroshnikov KA, Mesyanzhinov VV, Krylov VN, Noben JP, Robben J, Hertveldt K, Volckaert G, Lavigne R (2009) Identification and comparative analysis of the structural proteomes of phi KZ and EL, two giant Pseudomonas aeruginosa bacteriophages. Proteomics 9:3215–3219
Mizuno CM, Rodriguez-Valera F, Kimes NE, Ghai R (2013) Expanding the marine virosphere using metagenomics. PLoS Genet 9:e1003987
Murphy JS, Philipson L (1962) Purification of B. megatherium phage G and evidence for a muralytic enzyme as an integral part of the phage. J Gen Physiol 45:155–168
Peng Q, Yuan YH, Gao MY (2013) Bacillus pumilus, a novel ginger rhizome rot pathogen in China. Plant Dis 97:1308–1315
Rohwer F (2003) Global phage diversity. Cell 113:141
Schade SZ, Adler J, Ris H (1967) How bacteriophage chi attacks motile bacteria. J Virol 1:599–609
Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:W686–W689
Serwer P, Hayes SJ, Thomas JA, Hardies SC (2007) Propagating the missing bacteriophages: a large bacteriophage in a new class. Virol J 4:21
Skurnik M, Hyytiainen HJ, Happonen LJ, Kiljunen S, Datta N, Mattinen L, Williamson K, Kristo P, Szeliga M, Kalin-Manttari L, Ahola-Iivarinen E, Kalkkinen N, Butcher SJ (2012) Characterization of the genome, proteome, and structure of yersiniophage phi R1-37. J Virol 86:12625–12642
Thomas JA, Hardies SC, Rolando M, Hayes SJ, Lieman K, Carroll CA, Weintraub ST, Serwer P (2007) Complete genomic sequence and mass spectrometric analysis of highly diverse, atypical Bacillus thuringiensis phage 0305 phi 8-36. Virology 368:405–421
Yamada T, Satoh S, Ishikawa H, Fujiwara A, Kawasaki T, Fujie M, Ogata H (2010) A jumbo phage infecting the phytopathogen Ralstonia solanacearum defines a new lineage of the Myoviridae family. Virology 398:135–147
Yuan YH, Gao MY, Wu DD, Liu PM, Wu Y (2012) Genome Characteristics of a Novel Phage from Bacillus thuringiensis Showing High Similarity with Phage from Bacillus cereus. Plos One 7:e37557
Yuan YH, Gao MY (2015) Genomic analysis of a ginger pathogen Bacillus pumilus providing the understanding to the pathogenesis and the novel control strategy. Sci Rep-UK 5:10259
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829
Acknowledgments
This study was supported by the National Natural Science Foundation of China (No. 31500155, 31170123).
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Yuan, Y., Gao, M. Characteristics and complete genome analysis of a novel jumbo phage infecting pathogenic Bacillus pumilus causing ginger rhizome rot disease. Arch Virol 161, 3597–3600 (2016). https://doi.org/10.1007/s00705-016-3053-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-016-3053-y