Comparative analysis of prophage regions

The chromosome sequence of strain TW14359 was reannotated by dfast [46 (link)], and its PP regions were predicted by phaster [47, 48 (link)], followed by manual curation to precisely identify each PP region, including attL and attR sequences. IEs not detected by phaster were identified by searching genes annotated as ‘integrase genes’, followed by manual inspection. For the other closed genomes, PP/IE integration sites (attB sites) identified in strain TW14359 were analysed for the presence of PPs/IEs and their sequences, if present. PPs/IEs not found in strain TW14359 were identified by integrase gene search, as described above. The PPs/IEs found in all closed genomes (Table S3) were annotated by dfast, followed by manual curation. Insertion sequences (ISs) in the PP/IE sequences were detected and typed by ISfinder [49 (link)]. Genetic organizations of PPs/IEs were visualized by GenomeMatcher v3.0.2. Sequence similarity of PPs/IEs located at the same loci was analysed by dot-plot analyses using GenomeMatcher v3.0.2 and by calculating pairwise Mash distances [50 (link)] with default parameters (k-mer size of 21, and sketch size of 1000). The results of pairwise Mash distance analysis are presented as violin plots using RAWGraphs 2.0 beta (https://dl.acm.org/doi/10.1145/3125571.3125585).

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Miyata T., Taniguchi I., Nakamura K., Gotoh Y., Yoshimura D., Itoh T., Hirai S., Yokoyama E., Ohnishi M., Iyoda S., Ogura Y, & Hayashi T. (2023). Alteration of a Shiga toxin-encoding phage associated with a change in toxin production level and disease severity in Escherichia coli. Microbial Genomics, 9(2), mgen000935.

Publication 2023

Attr Chromosome Gene Genomes Integrase Organizations Sequences insertion Strain

Corresponding Organization :

Other organizations : Kyushu University, Tokyo Institute of Technology, National Institute of Infectious Diseases, Chiba Prefectural Institute of Public Health, Kurume University

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Variable analysis

independent variables

Chromosome sequence of strain TW14359 was reannotated by dfast
PP regions were predicted by phaster, followed by manual curation
IEs not detected by phaster were identified by searching genes annotated as 'integrase genes', followed by manual inspection
PP/IE integration sites (attB sites) identified in strain TW14359 were analysed for the presence of PPs/IEs and their sequences
PPs/IEs not found in strain TW14359 were identified by integrase gene search
PPs/IEs found in all closed genomes were annotated by dfast, followed by manual curation
Insertion sequences (ISs) in the PP/IE sequences were detected and typed by ISfinder
Sequence similarity of PPs/IEs located at the same loci was analysed by dot-plot analyses using GenomeMatcher v3.0.2 and by calculating pairwise Mash distances

dependent variables

Identification of PP regions and their precise boundaries, including attL and attR sequences
Identification of IEs not detected by phaster
Presence and sequences of PPs/IEs at the PP/IE integration sites (attB sites) identified in strain TW14359
Identification of PPs/IEs not found in strain TW14359
Annotation of PPs/IEs found in all closed genomes
Identification and typing of insertion sequences (ISs) in the PP/IE sequences
Sequence similarity of PPs/IEs located at the same loci

control variables

Strain TW14359 was used as a reference for identifying PP/IE integration sites and their presence in other closed genomes

Annotations

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