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

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Tailed bacteriophages (phages) possess linear double-stranded DNA (dsDNA) genomes.
• Complete characterization of novel phages necessitates defining the physical ends of their genomes.

Purpose of the Study:

• To develop and validate an in silico method for identifying phage genome termini from next-generation sequencing (NGS) data.
• To overcome limitations of current assembly programs in determining phage genome configuration.

Main Methods:

• Sequencing of 48 Bacillus cereus phage isolates.
• Analysis of NGS data, including read alignment files.
• Development of a terminus prediction method utilizing 'neighboring coverage ratios' and 'read edge frequencies'.
• Validation through primer walking and phylogenetic inference of terminase protein sequences.

Main Results:

• A novel in silico method was successfully developed to predict phage genome termini.
• The method effectively identified proximal terminus positions using phage NGS data and contig circularity.
• Primer walking and phylogenetic analysis confirmed the predicted termini.

Conclusions:

• The Terminus package efficiently identifies phage genome termini from NGS data.
• Complete phage genome sequences enable better characterization of packaging mechanisms.
• Precise genome annotation is facilitated by accurate determination of genome ends.