Key Points Aberrations in genome maintenance and DNA repair genes including POT1 occur at a high frequency in Sézary syndrome. Candidate driver genes and affected pathways in Sézary syndrome show extensive heterogeneity but overlap with other mature T-cell lymphomas.

BackgroundPhylogenetic comparison of bacteriophages requires whole genome approaches such as dotplot analysis, genome pairwise maps, and gene content analysis. Currently mycobacteriophages, a highly studied phage group, are categorized into related clusters based on the comparative analysis of whole genome sequences. With the recent explosion of phage isolation, a simple method for phage cluster prediction would facilitate analysis of crude or complex samples without whole genome isolation and sequencing. The hypothesis of this study was that mycobacteriophage-cluster prediction is possible using comparison of a single, ubiquitous, semi-conserved gene. Tape Measure Protein (TMP) was selected to test the hypothesis because it is typically the longest gene in mycobacteriophage genomes and because regions within the TMP gene are conserved.ResultsA single gene, TMP, identified the known Mycobacteriophage clusters and subclusters using a Gepard dotplot comparison or a phylogenetic tree constructed from global alignment and maximum likelihood comparisons. Gepard analysis of 247 mycobacteriophage TMP sequences appropriately recovered 98.8% of the subcluster assignments that were made by whole-genome comparison. Subcluster-specific primers within TMP allow for PCR determination of the mycobacteriophage subcluster from DNA samples. Using the single-gene comparison approach for siphovirus coliphages, phage groupings by TMP comparison reflected relationships observed in a whole genome dotplot comparison and confirm the potential utility of this approach to another widely studied group of phages.ConclusionsTMP sequence comparison and PCR results support the hypothesis that a single gene can be used for distinguishing phage cluster and subcluster assignments. TMP single-gene analysis can quickly and accurately aid in mycobacteriophage classification.

Paenibacillus larvae is a pathogen of honeybees that causes American foulbrood (AFB). We isolated bacteriophages from soil containing bee debris collected near beehives in Utah. We announce five high-quality complete genome sequences, which represent the first completed genome sequences submitted to GenBank for any P. larvae bacteriophage.

The Bacillus cereus group is an assemblage of highly related firmicute bacteria that cause a variety of diseases in animals, including insects and humans. We announce three high-quality, complete genome sequences of bacteriophages we isolated from soil samples taken at the bases of fruit trees in Utah County, Utah. While two of the phages (Shanette and JL) are highly related myoviruses, the bacteriophage Basilisk is a siphovirus.

The species infected by the five bacteriophages was misidentified as Paenibacillus larvae. The article title should read as given above, and the organism identified as Paenibacillus larvae should be identified as Brevibacillus laterosporus throughout. Page 1: The abstract should read as follows. "Brevibacillus laterosporus is a secondary invader following European foulbrood (EFB) infection of honeybees. We isolated bacteriophages from soil containing bee debris collected near beehives in Utah. We announce five high-quality complete genome sequences, which represent the first completed genome sequences submitted to GenBank for any B. laterosporus bacteriophage." Page 1: The first paragraph of the text should read as follows. "Brevibacillus laterosporus is an anaerobic, spore-forming bacterium that invades beehives following European foulbrood (EFB) infection (1). Honeybee bacterial diseases, including EFB and American foulbrood (AFB), kill honeybee larvae, contribute to colony collapse disorder (2), and limit agricultural yields (3). Phage therapy is a potential treatment for bee foulbroods, yet few P. larvae-specific phages have been described (5-8), and prior to this work there was no research investigating B. laterosporus phages." Page 1, column 1: Lines 12 and 13 should read as follows. "The 16S rRNA sequencing showed similarity to two Paenibacillus larvae subsp. pulvifaciens (9) isolates, but further tests indicated that these samples were B. laterosporus." Page 1, column 2: Lines 16-18 should read as follows. "A coding potential map was generated using GeneMark 2.5p (14) for each phage based on Bacillus cereus ATCC 14579, the closest available relative to B. laterosporus."