Genome Sequences of Six Paenibacillus larvae Siphoviridae Phages

Abstract

Six sequenced and annotated genomes of Paenibacillus larvae phages isolated from the combs of American foulbrood-diseased beehives are 37 to 45 kbp and have approximately 42% G+C content and 60 to 74 protein-coding genes. Phage Lily is most divergent from Diva, Rani, Redbud, Shelly, and Sitara.

Comparative genomics of 9 novelPaenibacillus larvaebacteriophages

“…Comparative analysis shows our phages use the cohesive ends with 3′ overhangs DNA packaging strategy. Diva, Rani, Redbud, Shelly and Sitara (whose large terminases are either 98% or 100% identical with those of our phages) are known to possess 9-bp 3′ overhangs with the sequence “CGACTGCCC.” 25 We found the same 9-bp sequence in Diane/Vadim/Vegas, Hayley, Fern/Willow and Xenia, and rearranged their genomes so that base 1 is the first base immediately after the last overhang base. When the genomes are rearranged this way, the first gene in the genome is the small terminase, which begins 50 bp downstream of base 1, exactly like in Diva, Rani, Redbud, Shelly and Sitara.…”

“…Since 2013, several bacteriophages that infect P. larvae were purified, sequenced, and characterized. 23-26 Phage phiIBB_Pl23, isolated in Portugal in 2013, was the first to be sequenced and characterized, 24 followed in 2015 by phages Diva, Lily, Rani, Redbud, Shelly and Sitara, isolated in North Carolina, 25 and phage HB10c2 in Germany. 23 Our group recently sequenced and published the genomes of 9 P. larvae phages.…”

Complete Genome Sequences of Nine Phages Capable of Infecting Paenibacillus larvae, the Causative Agent of American Foulbrood Disease in Honeybees

“…Phages that infect and lyse P. larvae are a potentially promising treatment, but they have only recently begun to be characterized. There are currently seven complete P. larvae phage genome sequences in the literature (4, 5). Here, we have isolated and sequenced the genomes of nine P. larvae phages obtained from samples across the United States.…”

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

“…The genome of P. larvae phage Tripp differs considerably from the genomes of other Siphoviridae P. larvae -infecting bacteriophages isolated in North Carolina ( 2 ) and from elsewhere in the world ( 6 – 8 ). While all other P. larvae phages to date are cos type with 5′ or 3′ overhanging ends, Tripp has terminal repeats of 378 bp.…”

“…A phage Tripp plaque was purified three times and then amplified using the whole plate lysis method. DNA was extracted from the high titer lysate, and a sequencing library was prepared and analyzed using Illumina MiSeq procedures as described previously ( 2 ). FastQ files were assembled using CLC genomics workbench software (release 2014) with 10,071-fold coverage, and annotation was performed using DNA Master ( http://cobamide2.bio.pitt.edu ), GeneMark ( 3 ), NCBI BLASTp ( 4 ), ShineFind in the Galaxy bioinformatics suite ( https://galaxyproject.org/ ), and HHPred ( 5 ).…”