Paenibacillus larvae Phage Tripp Genome Has 378-Base-Pair Terminal Repeats

Abstract

Paenibacillus larvae bacteriophage Tripp was isolated from an American foulbrood diseased honey bee hive in North Carolina, USA. The 54,439-bp genome is 48.3% G+C, encodes 92 proteins, no tRNAs, and has 378-bp direct terminal repeats. It is currently unique in Genbank.

Genomic Analysis of 48 Paenibacillus larvae Bacteriophages

“…For the UNLV phages Diane, Fern, Harrison, Hayley, Paisley, Vadim, Vegas, Willow and Xenia, the number of genes differs from previous work [ 18 , 27 ] because the genome annotation of these phages was revised with the updated protocol used to annotate the more recently published phages. This also applies to phages phiIBB_Pl23, HB10c2, Diva, Rani, Redbud, Shelly, Sitara, Lily and Tripp [ 14 , 15 , 16 , 17 ], which were annotated and published by their respective groups, but were re-annotated by our group using our annotation protocol for the purposes of this paper for consistency.…”

“…In phages Dragolir, Wanderer and LincolnB, this 3′ overhang sequence was not found, but when these genomes were rearranged as described above, the genome ends were found to contain the sequence “CGACGGCCC”, indicating a point mutation in the 3’ overhang sequence. Phages Ash, Ley, C7Cdelta, Halcyone, Heath, Scottie, and Unity have sequence similarity to phage Tripp [ 17 ], which uses the Direct Terminal Repeats (DTR) packaging strategy, and we thus searched these phages for a DTR sequence. The DTR sequence was identified using Pile-up Analysis Using Starts & Ends (PAUSE) (cpt.tamu.edu/computer-resources/pause) and Geneious, looking for a sharply delimited region with double coverage depth, as detailed in [ 29 ] and shown in Figure 1 .…”

“… 1 Number of genes differs from [ 18 , 27 ] because phages were re-annotated using new criteria for gene calling. 2 Number of genes differs from [ 14 , 15 , 16 , 17 ] because phages were re-annotated by our group for consistency. …”

“…However, in the last five years, the number of sequenced P. larvae phages has increased significantly, standing at 48 as of this writing. P. larvae phages have been isolated and sequenced in Portugal [ 14 ], Germany [ 15 ], and the United States [ 16 , 17 , 18 , 19 , 20 , 21 ], with the latter accounting for the vast majority of published genomes. In addition, six studies have been published within the last two years on treating AFB with P. larvae phages or P. larvae phage endolysins [ 15 , 22 , 23 , 24 , 25 , 26 ].…”

“…The first P. larvae phage to have its genome sequenced was phiIBB_Pl23, isolated in Portugal, in 2013 [ 14 ], followed by phage HB10c2 in Germany [ 15 ], and phages Diva, Lily, Rani, Redbud, Shelly, Sitara and Tripp, isolated in North Carolina [ 16 , 17 ]. In 2015, the genomes of 9 P. larvae phages from the University of Nevada, Las Vegas (UNLV) were published [ 18 ], followed by the first comparative genomics analysis of P. larvae phages [ 27 ].…”