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).