Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data

Abstract

BackgroundMost tailed bacteriophages (phages) feature linear dsDNA genomes. Characterizing novel phages requires an understanding of complete genome sequences, including the definition of genome physical ends.ResultWe sequenced 48 Bacillus cereus phage isolates and analyzed Next-generation sequencing (NGS) data to resolve the genome configuration of these novel phages. Most assembled contigs featured reads that mapped to both contig ends and formed circularized contigs. Independent assemblies of 31 nearly identical I48-like Bacillus phage isolates allowed us to observe that the assembly programs tended to produce random cleavage on circularized contigs. However, currently available assemblers were not capable of reporting the underlying phage genome configuration from sequence data. To identify the genome configuration of sequenced phage in silico, a terminus prediction method was developed by means of ‘neighboring coverage ratios’ and ‘read edge frequencies’ from read alignment files. Termini were confirmed by primer walking and supported by phylogenetic inference of large DNA terminase protein sequences.ConclusionsThe Terminus package using phage NGS data along with the contig circularity could efficiently identify the proximal positions of phage genome terminus. Complete phage genome sequences allow a proposed characterization of the potential packaging mechanisms and more precise genome annotation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3744-0) contains supplementary material, which is available to authorized users.

Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut

“…Our data indicated that linear phage genomes with TDRs were erroneously assembled as CCs. The TDRs are the source of this mis-assembly, which could be corrected by mapping the reads to CCs as described previously [34].…”

Genomic Analysis of the Recent Viral Isolate vB_BthP-Goe4 Reveals Increased Diversity of φ29-Like Phages

“…A global blastn analysis using the Goe4 genome as query against the non-redundant nucleotide data base of NCBI resulted in the identification of nine closely related virus strains (Juan (MF156577), RadRaab (MF156580.1), Stich (KX349901.1), KonjoTrouble (MF156578.1), Aurora (KX349899.1), QCM11 (KX961631.1) [ 42 ], SerPounce (KY947509.1) [ 43 ], Claudi (KX349900.1) and MG-B1 (KC685370.1) [ 44 ]). Many of those employ B. thuringiesnis as host, but also other members of the B. cereus clade [ 45 ] like B. weihenstephanensis [ 44 ], phage QCM11 in B. anthracis [ 42 ]. Members of this bacterial clade are genomically conserved and mainly differ in number and content of plasmids, which define their lifestyle [ 45 ].…”

PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data

“…This procedure can be very time-consuming and contains numerous steps requiring bioinformatic skills, including the installation of the Phamerator program 29 and the management of the related SQL databases. Finally, a concomitant study 30 predicted genome terminus by calculating two criteria, read edge frequencies and neighboring coverage ratio. Finding these procedures heavy and unwieldy for most phage scientists was that motivated us to develop PhageTerm as an easy-to-use program that consolidates into a single straightforward analysis numerous highly-valuable pieces of information about phage termini and packaging mode.…”