Supplementary File 1: Annotations of complete integrons, CALINs, and In0 elements from 22 phage genomes predicted by IntegronFinder 2.0 in GenBank format. We screened 10,705 bacteriophage genomes from the NCBI Genome database for integrons and attC recombination sites using previously described IntegronFinder and HattCI + INFERNAL bioinformatic pipelines. We detected 3 complete integrons and an integron-integrase without gene cassettes (ln0 element) residing in temperate phage genomes (Table 1), and 18 CALINs obtained from virulent, temperate, and uncharacterised phages (Table 2 and Supplementary Table S1). Usage Notes - The file "22_Bacteriophage_Genomes.fasta" contains the genomes of the abovementioned 22 bacteriophage genomes which were downloaded from the NCBI Nucleotide database. - IntegronFinder 2.0 (Néron et al, 2022) should be installed on MacOS Terminal or Linux according to the authors' instructions. - Search for integrons, CALINs and ln0 elements with IntegronFinder 2.0 using the command "for i in *fasta; do integron_finder --local-max --func-annot --gbk $i; done". - The output files are GBK files containing annotations for the predicted integrons or integron components and can be viewed using a bioinformatic software such as Geneious or SnapGene. - All the attC recombination sites predicted by IntegronFinder 2.0 should then be compiled into a single FASTA file. - An in-house script attC-taxa.sh (Ghaly et al, 2022) can be downloaded from https://github.com/timghaly/attC-taxa. Using the compiled FASTA file of attC sites from the previous step as input, the attC sites can be classified according to sequence and structural homologies of chromosomal attC sequences in eleven bacterial taxa. References: - Néron B, Littner E, Haudiquet M, Perrin A, Cury J, Rocha EPC. IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella. Microorganisms. 2022 Mar 24;10(4):700. doi: 10.3390/microorganisms10040700. PMID: 35456751; PMCID: PMC9024848. - Ghaly TM, Penesyan A, Pritchard A, Qi Q, Rajabal V, Tetu SG, Gillings MR. Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities. Microb Genom. 2022 Mar;8(3):000788. doi: 10.1099/mgen.0.000788. PMID: 35298369; PMCID: PMC9176274.