ABSTRACT

GENOME ANNOUNCEMENT

The increasing numbers of bacteriophages that infect Streptomyces hosts and have sequenced genomes available show them to have considerable genetic diversity (1), similar to that reported for phages of Mycobacterium (2) and Gordonia (3) hosts. Here, we report eight newly isolated Streptomyces bacteriophages recovered using either direct plating or enrichment on three Streptomyces hosts, Streptomyces griseus ATCC 10137 (phages NootNoot, Paradiddles, Samisti12, Sushi23, and Warpy), Streptomyces lividans JI 1326 (phages Jay2Jay and Peebs), and Streptomyces viridochromogenes DSM40736 (phage Mildred21). Isolates were obtained from soil samples collected in Missouri, Pennsylvania, and Texas (Table 1).

Phage genomes were sequenced using the Illumina MiSeq platform (except for Samisti12, which was sequenced using Ion Torrent), and genomes were assembled using Newbler. The resulting assemblies each contained a single major contig with at least 185× coverage, long terminal repeats, and defined ends (Table 1). The physical ends of each genome were identified by a substantial increase in the number of reads beginning at a single base position and an approximately 2-fold increase in coverage between these ends defined the terminal repeats. Their genomes range in size from 131,086 bp to 133,917 bp, with a mean genome size of 132,969 bp (Table 1). All phages have G+C contents of 50% ± 0.5%, approximately 20% lower than those of their hosts. The eight phages are closely related, with pairwise average nucleotide identities from 0.79 to 0.98, and they are grouped together in subcluster BE1; Mildred21 is the least similar to other BE1 phages. Electron microscopy shows these phages to have a siphoviral morphology and isometric capsids.

All genomes were annotated using Glimmer and GeneMarkS and refined using BLAST alignments to previous manually annotated genes; start codon choice was evaluated using multiple sequence alignments of closely related genes. Putative functions were assigned using BLASTP (4) and HHpred (5) or by protein-threading assessments using Phyre2 (6); potential functions were assigned to approximately 20% of the protein-coding genes. Annotated gene functions include virion structure and assembly, DNA/RNA metabolism, lysis, and DNA packaging.

The direct terminal repeats of approximately 11 kbp are the longest found in any of the actinobacteriophages to date, and they are similar in size to previously reported long repeats in phages, such as T5 and SPO1, which have terminal repeats of 10,139 and 13,185 bp, respectively (7, 8). The direct repeats are predicted to include 20 to 25 open reading frames, including an lsr2-like gene; the other genes are of unknown function. These subcluster BE1 phages each carry a single transfer-messenger RNA (tmRNA) gene and the largest numbers of tRNA genes (43 to 48) among any phages of actinobacterial hosts, including at least one tRNA gene for each of the 20 amino acids. This large tRNA gene repertoire could act to counter tRNA-based degradation defense systems or to optimize gene expression in hosts that have widely different G+C contents and differing codon usage preferences (9).

ACKNOWLEDGMENTS

Footnotes

REFERENCES