## 4 Materials and Methods
### Genome Sequencing, Assembly and Annotation  
The DNA of phages (3 ug of each one) was sequenced using TruSeq DNA Nano protocol on an Illumina HiSeq platform, using 150 bp pair-end sequencing reads, performed at Laboratory of Genomic Services (LABSERGEN) in LANGEBIO-CINVESTAV (Irapuato, Mexico). Raw sequence reads were checked for quality using FastQC in the Galaxy platform ([[https://usegalaxy.org/](https://usegalaxy.org/)]([https://usegalaxy.org/](https://usegalaxy.org/)), accessed on 30 January 2021) and trimmed with Cutadapt 1.16 (Parameters: Minimum length 20; Quality cutoff 30, 30; Trimm N's on end of reads). Quality trimmed reads were de novo assembled into a linear contig using SPAdes 3.12.0 [61] with careful correction using different K-mer values (22, 33, 55, 77). The quality of assembly was evaluated using QUAST v5.0.2. and quality trimmed reads were mapped into the assembled genome using Bowtie2. Termini were determined with PhageTerm v1.0.12 [36]implemented in Galaxy from Pasteur Institute Platform ([[https://galaxy.pasteur.fr/](https://galaxy.pasteur.fr/)]([https://galaxy.pasteur.fr/](https://galaxy.pasteur.fr/)), accessed on 23 February 2021) and genomes were reoriented placing DTRs only at the start of genome. Potential ORFs were predicted using GeneMarkS [62]. Functional annotation was done using BLASTP and PSI-BLAST algorithms at NCBI (minimum E-value: 1 \(\times\) 10\({}^{-5}\)). Potential genes encoding tRNAs were predicted using tRNAsan-SE (\(\Delta\)G-10 kcal/mol) [63] and ARAGORN [64]. Codon usage (r\({}_{i}\)) was calculated as previously reported by [21], using the _Xanthomonas vesicatoria_ ATCC 35937 reference genome (Accession no. CP018725) as a representative genome of the host. Codon counts were calculated on the Codon Usage Calculator website ([[https://jamiemcgowan.ie/bioinf/codon_usage.html](https://jamiemcgowan.ie/bioinf/codon_usage.html)]([https://jamiemcgowan.ie/bioinf/codon_usage.html](https://jamiemcgowan.ie/bioinf/codon_usage.html)), accessed on 10 December 2023). Predicted proteins were also analyzed to identify possible virulence factors using the Virulence Factors Database (VFDB, [[http://www.mgc.ac.cn/VFs/](http://www.mgc.ac.cn/VFs/)]([http://www.mgc.ac.cn/VFs/](http://www.mgc.ac.cn/VFs/)), accessed on 30 April 2021) using a E-value cutoff of 1 \(\times\) 10\({}^{-5}\); and VirulenceFinder 2.0 ([[https://cge.cbs.dtu.dk/services/VirulenceFinder/](https://cge.cbs.dtu.dk/services/VirulenceFinder/)]([https://cge.cbs.dtu.dk/services/VirulenceFinder/](https://cge.cbs.dtu.dk/services/VirulenceFinder/)), accessed on 24 March 2021); for antimicrobial resistance genes, we used ResFinder 4.1 ([[https://cge.cbs.dtu.dk/services/ResFinder/](https://cge.cbs.dtu.dk/services/ResFinder/)]([https://cge.cbs.dtu.dk/services/ResFinder/](https://cge.cbs.dtu.dk/services/ResFinder/)), accessed on 24 March 2021). The phage lifestyle was predicted with PHACTS ([[https://edwards.sdsu.edu/PHACTS](https://edwards.sdsu.edu/PHACTS)]([https://edwards.sdsu.edu/PHACTS](https://edwards.sdsu.edu/PHACTS)), accessed on 3 March 2021) [65]. The genomes of phages NaCl and XbC2 were deposited in GenBank under the accession numbers OR258281 and OP292654, respectively.