3.1 | Occurrence and diversity of CRISPR/Cas systems inK. variicola
The 487 genomes of K. variicola strains from the NCBI database were analyzed the occurrence and diversity of CRISPR/Cas system. Based on CRISPRCasFinder search results, 21.56% of K. variicolastrains (105/487) harbored CRISPR/Cas systems, which was lower than the estimated occurrence rate of other bacteria (45%) [34]. Based on signature Cas proteins and repeat sequence, three different types of CRISPR/Cas systems (i.e., type I-E, I-E* and IV-A) were identified, which were located on the chromosome or the plasmids. The type I system was the most prevalent CRISPR/Cas system in K. variicola . Specifically, 72 type I-E, 10 type I-E* and 29 IV-A systems were identified among 105 strains (Figure 1A). As shown in Table S2, most strains (94.29%, 99/105) only had one type of CRISPR/Cas system, but 6 strains were found to contain two different types of systems. Type I-E and IV-A systems coexisted in five strains (strain HUMB 14438, K5-12018, 7041, CRE843, and TUM14103), and type I-E* and IV-A system coexisted in strain AS012291. Furthermore, most of CRISPR/Cas systems (91.89%, 102/111) harbored a series of intact cas gene clusters, but the partial absence of cas genes were observed in 9 type I-E CRISPR/Cas systems. As described in Figure S1, 6 strains were absent ofcas2 , 2 strains were absent of cas3 , and 1 strain was absent of both cas2 and cas3 . Interestingly, we observed that the order of type I-E cas genes was slightly different from that of type I-E* cas genes. Regarding the type IV-A, csf1, cas6, csf4, csf3 and csf2 genes were encoded by the strains (Figure 1B).