## 2 Results
### General Genome Features  
Raw reads were filtered and assembled with SPAdes, resulting in a single contig for each phage, and showing higher percentages of mapping (about 98%) with Bowtie2 using the assembled genome as a reference (Table S1). Regarding termini, the NaCl and XbC2 phages were analyzed with PhageTerm, revealing that both phages have redundant and non-permuted direct terminal repeats (DTR) and long ends type T5; the DTR were 32,031 bp and 17,581 bp in length in NaCl and XbC2, respectively (Supplemental Materials S1 and S2). The assembled genomes of the two Xanthomonas phages showed genome sizes larger than 200 kb, indicating they represent jumbo phages (Table 2). A survey in the GenBank database revealed that XbC2 and XaC1 are the largest Xanthomonas phages reported, with 367,901 bp and 348,967 bp, respectively, even though the phage XacN1 has been reported with a genome size of 384,670 bp (revised October 2023) [21]. The XacN1 genome length includes 65,875 bp DTRs at the start and at the end of the reported genome; meanwhile, the XaC1 and XbC2 genome length was calculated considering only one DTR at the start of genome, as we mentioned in the Section 4. The G+C content of XaC1 and XbC2 was 35.1 y 37.5%, respectively, a lower value in comparison to that of representative Xanthomonas species, which is about 65% [22]. Phage XaC1 encodes 550 ORFs, of which 426 were annotated as hypothetical proteins. Meanwhile, XbC2 encodes 557 ORFs, and 416 were predicted as hypothetical proteins (Tables S2 and S3). The DTR regions were found to encode 70 ORFs for XaC1 and 35 ORFs for XbC2, all encoding hypothetical proteins. Interestingly, Xanthomonas phages contained several genes encoding for tRNAs. The XaC1 phage was found to contain eight genes encoding for tRNAs, whereas XbC2 contained 34 genes encoding for tRNAs, indicating that Xanthomonas phages encode their own tRNAs independently from the host (Table 1, Tables S4 and S5). Codon usage analysis revealed that XaC1 and XbC2 exhibited a higher usage of 25 and 28 tRNAs than the host, respectively; meanwhile, only six tRNAs showed a similar usage, and 33 and 30 tRNAs were more frequently used by the representative host (Figure 3). Moreover, five tRNAs encoded by XaC1 were classified within the higher codon usage phage group, while two tRNAs showed a similar codon usage and only one tRNA was found with a higher usage by the host. In the case of XbC2, 16 tRNAs were located in the higher codon usage phage group, six tRNAs showed a similar codon usage and 12 tRNAs encoded by XbC2 showed a higher codon usage by the host (Tables S6-S8). The prediction of lifestyle with PHACTS suggested that XaC1 and XbC2 are lytic phages, consistent with the presence of clear plaques observed in double agar plates (Figure 1). Moreover, analyses in VFBD, ResFinder and Virulence Finder revealed that the XaC1 and XbC2 phages did not contain genes encoding potential virulence factors or antibiotic resistance genes. In silico restriction analysis of the phage genomes revealed that XaC1 and XbC2 have several restriction sites with the three enzymes used in this study (Supplemental Materials S3 and S4), which is inconsistent with the inability of EcoRV and \begin{table}
\begin{tabular}{c c c} \hline \hline
**Feature** & **XaC1** & **XbC2** \\ \hline Genome size & 348,967 bp & 367,901 bp \\ \% GC & 35.1 & 37.5 \\ ORFs & 550 & 557 \\ ORFs with homology & 124 & 141 \\ Hypothetical proteins & 426 & 416 \\ tRNAs 1 & 8 & 34 \\ Lifestyle 2 & Lytic & Lytic \\ Virulence factor 3 & No & No \\ Antibiotic resistance genes 4 & No & No \\ \hline \hline \end{tabular} \({}^{\dagger}\) Determined with Aragorn V.1.2.41 and tRNA-SCAN-SE v.2.0. \({}^{\ddagger}\) Determined with PHACTS. \({}^{\ddagger}\) Determined with VFDB and Virulence Finder. \({}^{\ddagger}\) Determined with ResFinder.  
\end{table} 
Table 2: Genomic features of _Xanthomonas_ jumbo phages. Ndel to cut XaC1 and XbC2 genomes (Figure 2).